The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the t...The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.展开更多
Complete mitochondrial genomes(mitogenomes) can provide useful information for phylogenetic relationships,gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoid...Complete mitochondrial genomes(mitogenomes) can provide useful information for phylogenetic relationships,gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoidea(Cleistostoma dilatatum and Euplax sp.) were reported for the first time, which are 15 444 bp and16 129 bp in length, respectively. Cleistostoma dilatatum is the first species in the family Camptandriidae whose complete mitogenome was sequenced. Each mitogenome contains an entire set of 37 genes and a putative control region, but their gene arrangements are largely different. Tandem duplication and random loss model is proposed to account for their gene arrangements. Comparative genomic analyses of 19 mitogenomes clustering in one branch reveal that 18 of them shared the same gene rearrangement, while that of C. dilatatum mitogenome was consistent with the ancestral gene arrangement of Brachyura. The dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. Phylogenetic analyses show that all Macrophalmidae species cluster together as a group, and then form a sister clade with Camptandriidae. Moreover, the polyphyly of three superfamilies(Ocypodoidea, Eriphioidea, and Grapsoidea) is reconfirmed. These findings help to confirm the phylogenetic position of Camptandriidae, as well as provide new insights into the phylogeny of Brachyura.展开更多
The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scie...The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scientific interest.Despite this interest,the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus.Herein,we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes(mitogenomes)from 13 morphological species to reconstruct the phylogenetic relationships,biogeographic history,and species diversity of Silurus.Our phylogenetic reconstructions identified eight clades,supported by both maximum-likelihood and Bayesian inference.Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units(MOTUs)in several taxa,including the Silurus asotus complex(four MOTUs)and Silurus microdorsalis(two MOTUs),suggesting that species diversity is underestimated in the genus.A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago(Ma),with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma,and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma.Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula,with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma.Key factors such as the Eocene-Oligocene extinction event,onset and intensification of the monsoon system,and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.展开更多
The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-c...The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-coding genes,22 transfer RNAs,two ribosomal RNAs,and one control region.The genome composition was A+T biased(58.64%)and exhibited a positive AT-skew(0.095)and a negative GC-skew(-0.283).Compared with other Sisoridae fishes,the characteristics of nucleotide skews,codon usage,and amino acid usage of the P.hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes.Furthermore,the phylogenetic trees show that Sisoridae fishes fall into four major clades and P.hodgarti(CladeⅠ)is basal to the Sisoridae family,forming a sister clade to the Glyptosternoids(CladeⅣ).The topological structures constructed in this study raised doubts over the traditional classification system.These results will help better understand the feature s of the P.hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.展开更多
Solemyidae is an ancient group of protobranch bivalves,and most solemyids are symbiotic with chemoautotrophic and gill-hosted bacteria,enabling them to survive in unusual habitats such as deepsea chemosynthetic enviro...Solemyidae is an ancient group of protobranch bivalves,and most solemyids are symbiotic with chemoautotrophic and gill-hosted bacteria,enabling them to survive in unusual habitats such as deepsea chemosynthetic environments.However,evolution of the mitogenomes in this family and their phylogenetic relationships remain poorly understood.The complete mitogenome of Acharax sp.was determined and compared with other available mitogenomes of solemyids.The mitogenome of Acharax sp.is 18970 bp in length and consists of 13 protein-coding genes,2 ribosomal RNA genes,and 22 transfer RNA genes.The gene arrangement was identical to those of other sequenced solemyids.For the present five mitogenomes of Solemyidae species,all protein-coding genes were initiated with the typical ATD(ATA,ATG,and ATT)codon and terminated with the TAA/TAG codon.Furthermore,the incomplete termination codon was detected.The Ka/Ks ratio analyses indicated that 13 protein-coding genes of five Solemyidae mitogenomes suffered strong purifying selection.Compared to 45 existing shallow water equivalents,the 18 available mitogenomes from the deep-sea,including the Acharax sp.in this study,show significantly more nonpolar amino acids in the 13 protein-coding genes,which indicates the adaptation to the deep-sea environment.The phylogenetic tree based on 48 Bivalvia complete mitogenomes provided further information to support the scientific classification of protobranchs.The relationships among Solemyidae were assessed based on 2 mitochondrial(16S rRNA and COX1)and 3 nuclear(18S rRNA,28S rRNA,and histone H3)gene sequences from 17 in-group species.The two genera Acharax and Solemya formed a monophyletic clade each,and Acharax sp.clustered with previously reported Acharax bivalves with high support values.展开更多
Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitocho...Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae species.So far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy.Here,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were compared.The length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity.Like most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the L-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in C.puncticpes mitogenome.The typical IQM order(tRNA-Ile-Gln-Met)changed to QIM order.Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C.puncticpes mitogenome.Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future.展开更多
The species within Xenarthra(sloths,anteaters,and armadillos)are quintessential South American mammals.Of the three groups,Vermilingua(anteaters)contains the fewest extant and paleontological species.Here,we sampled a...The species within Xenarthra(sloths,anteaters,and armadillos)are quintessential South American mammals.Of the three groups,Vermilingua(anteaters)contains the fewest extant and paleontological species.Here,we sampled and sequenced the entire mitochondrial genomes(mitogenomes)of two Tamandua species(Tamandua tetradactyla and T.mexicana)(n=74)from Central and South America,as well as Myrmecophaga tridactyla(n=41)from South America.Within Tamandua,we detected three different haplogroups.The oldest(THI)contained many specimens with the T.tetradactyla morphotype(but also several with the T.mexicana morphotype)and originated in southeastern South America(currently Uruguay)before moving towards northern South America,where the THII haplogroup originated.THII primarily contained specimens with the T.mexicana morphotype(but also several with the T.tetradactyla morphotype)and was distributed in Central America,Colombia,and Ecuador.THI and THII yielded a genetic distance of 4%.THII originated in either northern South America or“in situ”in Central America with haplogroup THIII,which consisted of~50%T.mexicana and 50%T.tetradactyla phenotypes.THIII was mostly located in the same areas as THII,i.e.,Central America,Ecuador,and Colombia,though mainly in the latter.The three haplogroups overlapped in Colombia and Ecuador.Thus,T.tetradactyla and T.mexicana were not reciprocally monophyletic.For this reason,we considered that a unique species of Tamandua likely exists,i.e.,T.tetradactyla.In contrast to Tamandua,M.tridactyla did not show different morphotypes throughout its geographical range in the Neotropics.However,two very divergent genetic haplogroups(MHI and MHII),with a genetic distance of~10%,were detected.The basal haplogroup,MHI,originated in northwestern South America,whereas the more geographically derived haplogroup,MHII,overlapped with MHI,but also expanded into central and southern South America.Thus,Tamandua migrated from south to north whereas Myrmecophaga migrated from north to south.Our results also showed that temporal mitochondrial diversification for Tamandua began during the Late Pliocene and Upper Pleistocene,but for Myrmecophaga began during the Late Miocene.Furthermore,both taxa showed elevated levels of mitochondrial genetic diversity.Tamandua showed more evidence of female population expansion than Myrmecophaga.Tamandua experienced population expansion~0.6–0.17 million years ago(Mya),whereas Myrmecophaga showed possible population expansion~0.3–0.2 Mya.However,both taxa experienced a conspicuous female decline in the last 10000–20000 years.Our results also showed little spatial genetic structure for both taxa.However,several analyses revealed higher spatial structure in Tamandua than in Myrmecophaga.Therefore,Tamandua and Myrmecophaga were not subjected to the same biogeographical,geological,or climatological events in shaping their genetic structures.展开更多
The complete mitochondrial genome （mitogenome） of Gampsocleis gratiosa was determined. The 15,929 bp in the size of G. gratiosa mitogenome contains a typical gene content, base composition, and codon usage found in ...The complete mitochondrial genome （mitogenome） of Gampsocleis gratiosa was determined. The 15,929 bp in the size of G. gratiosa mitogenome contains a typical gene content, base composition, and codon usage found in metazoan. All 13 protein coding genes （PCGs） of the G gratiosa mitogenome start with a typical ATN codon. The usual termination codons （TAA and TAG） were found from 10 PCGs. However, the atp6, had4, and had5 had incomplete termination codon （T）. The anticodons of all tRNAs are identical to those observed in Drosophila yakuba and Locusta migratoria, and can be folded in the form of a typical clover leaf structure except for trnS （AGN）. The secondary structure of trnS （AGN） was drawn according with the Steinberg-Cedergren tertiary structure. The A＋T content （67.4%） of the A＋T-rich region is relatively lower among the mitogenome regions, in contrast, it usually contains the highest A＋T content for most insects. Two isolated sequence repeat regions （202 bp） were found in the A＋T-rich region with mapping and secondary structure information.展开更多
Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiati...Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist （mostly in southwestern China and adjacent areas）. Only three forms of Blarinella have been recognized as either species or subspecies However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages, one a close relative to B. quadraticauda, whereas the other--comprised of topotype specimens from southern Gansu-iverged from other Blarinella in the middle Miocene （ca. 18.2 million years ago （Ma）, 95% confidence interval=13.4-23.6 Ma）. Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper p4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly, some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella.Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.展开更多
The yellow meal worm （Tenebrio molitor L.） is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. rnolit...The yellow meal worm （Tenebrio molitor L.） is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. rnolitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A＋T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons （CTA in ND2 and AAT in COX1）, and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNASer （AGN）, which lacked a dihydrouridine （DHU） arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm.展开更多
The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little gene...The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses （ML and BI） among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.展开更多
Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular evolution.Currently,the phylogenetic location of the gen...Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular evolution.Currently,the phylogenetic location of the genus Varuna(Brachyura:Varunidae)has not been well resolved mainly because of limited representatives(only two extant species).Here,we determined a new mitogenome of this genus(Varuna litterata)and added the published mitogenomes to reconstruct the phylogeny of Varunidae.The 16368-bp mitogenome contains the entire set of 37 genes and a putative control region.The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes.All 16 analyzed mitogenomes have identical gene order and similar molecular features.The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity,with comparatively low variability of COI and COII,and high variability of ND6.The nonsynonymous/synonymous substitution rates(dN/dS ratio)analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure.Twelve tRNA genes,two rRNAs,one PCG,and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order.Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes.Phylogenetic analyses show that all Varunidae species are placed into one group,and form a sister clade with Macrophthalmidae.Nevertheless,the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study.These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes,as well as provide insights into the phylogenetic studies of Brachyura.展开更多
Indigenous pigs in South China are valuable genetic resources with many specific and unique characters, which have played an important role in the establishment of some western modern pig breeds. However, the origin a...Indigenous pigs in South China are valuable genetic resources with many specific and unique characters, which have played an important role in the establishment of some western modern pig breeds. However, the origin and genetic diversity of indigenous pigs in South China have not been fully understood. In the present study, we sequenced 534 novel mitochondrial DNA (mtDNA) D-loop and assembled 54 complete mitogenome sequences for all 17 indigenous pig breeds from Fujian, Guangdong, Guangxi and Hainan in South China. These data were analyzed together with previously published homologous sequences relevant to this study. We found that all 13 coding genes of the mitogenomes were under purifying selection, but ND1 had the most variable sites and CYTB contained the most non-synonymous SNPs. Phylogenetic analysis showed that all indigenous pigs in South China were clustered into the D haplogroup with D1a1, D1b, D1c and D1e sub-haplogroups found to be dominant. Haplotype and nucleotide diversities of D-loop sequences ranged from 0.427 to 0.899 and from 0.00342 to 0.00695, respectively, among which all pigs in Guangdong had the lowest diversity. The estimates of pairwise FST, gene flow (Nm) and genetic distance (Da) indicated that most of these indigenous pig breeds differentiated from each other significantly (P<0.05). Among the western modern breeds, Berkshire and Yorkshire had significant Asian matrilineal footprints from indigenous pigs in South China, especially the Spotted pigs distributed in Guangdong and Guangxi. The neutrality test (Fu’s FS) indicated that indigenous pigs from Fujian and Guangxi had gone through recent population expansion events (P<0.05). It is concluded that indigenous pigs in South China were most likely derived from the Mekong region and the middle and downstream regions of Yangtze River through Guangxi and Fujian. Our findings provide a complete and in-depth insight on the origin and distribution pattern of maternal genetic diversity of indigenous pigs in South China.展开更多
Knowledge of complete mitochondrial genomes(mitogenomes)can help understand the molecular evolution and phylogenetic relationships of various species.To date,the phylogenetic status of Leucosiidae within Brachyura rem...Knowledge of complete mitochondrial genomes(mitogenomes)can help understand the molecular evolution and phylogenetic relationships of various species.To date,the phylogenetic status of Leucosiidae within Brachyura remains unresolved because of the limited number of mitogenomes available.In the present study,the complete mitogenome of Myra affinis was sequenced using next-generation sequencing to supplement the limited mitogenome information of Leucosiidae.The 15349 bp-long mitogenome includes 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),2 ribosomal RNAs(rRNAs),and a putative control region.The overall base composition is 34.5%A,36.1%T,11.5%G,and 17.9%C,with a high AT bias(70.6%).All 13 PCGs start with the standard ATN codon and stop with the TAN codon or incomplete T.Except for tRNA-Ser,all other tRNAs have a typical cloverleaf-like secondary structure.Phylogenetic analyses based on the maximum likelihood and Bayesian inference methods are employed to generate identical phylogenetic topologies,thereby supporting the sister relationship between Leucosiidae and Matutidae for the first time.The monophyly of Eubrachyura is well established,and its sister relationship with Raninoida is strongly supported.The results of this work will not only help achieve a better understanding of the characteristics of the M.affinis mitogenome and the phylogenetic position of Leucosiidae,but also provide relevant information for further studies on the phylogeny of Brachyura.展开更多
Sequencing technology has developed rapidly in recent years. Complete or nearly complete mitochondrial genomes(mitogenomes) of 155 species from 47 families in Heteroptera have been sequenced. However, the amounts of m...Sequencing technology has developed rapidly in recent years. Complete or nearly complete mitochondrial genomes(mitogenomes) of 155 species from 47 families in Heteroptera have been sequenced. However, the amounts of mitogenomes between those families are unbalanced, which makes it difficult to correctly discern the patterns of mitogenome rearrangement in Heteroptera. Among 21 species from ten families, ten variations in mitogenome rearrangement had been previously reported, among which the translocation between tRNA-Thr and tRNA-Pro was considered as a synapomorphy of Pyrrhocoroidea based on two mitogenomes. As only one mitogenome in each of Largidae and Pyrrhocoridae had been sequenced to conclude the synapomorphy, more mitogenomes of Pyrrhocoroidea need to be explored. In this study, additional two mitogenomes of Pyrrhocoroidea(Macrocheraia grandis grandis(Gray, 1832) and Myrmoplasta mira Gerst-cker, 1892) were sequenced. Both of them also possess the same translocation between tRNA-Thr and tRNA-Pro, which reaffirms that this kind of rearrangement is a molecular synapomorphy of Pyrrhocoroidea. Moreover, we discovered a more complex rearrangement in Myrmoplasta mira, in which six nearly identical duplications of tRNA-Thr were found located downstream of tRNA-Pro. Considering the high biodiversity of Heteroptera, more mitogenomic studies are needed to improve our knowledge about mitogenome rearrangements and the potential synapomorphies.展开更多
Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first time.The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmi...Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first time.The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae species.The 15646-bp mitogenome contains 13 protein-coding genes(PCGs),two ribosomal RNA genes(r RNAs),22 transfer RNA genes(t RNAs),and an A-T rich region.All of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete T.The pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection,whereas the ATP8 gene is an outlier,with pairwise comparison values ranging from neutral selection(0.000)to positive selection(1.039).The gene arrangement of P.eumolpe compared with ancestral Decapoda shows the translocation of two t RNAs(t RNA-His and t RNA-Gln),which is identical to other Sesarmidae species.Phylogenetic analyses show that all Sesarmidae species are placed into one group,and the polyphyly of Eriphioidea,Ocypodoidea,and Grapsoidea is well supported.The relationship between gaps in the QIM region and the phylogeny of Sesarmidae is analyzed.It is obvious that both the G5(the gap between Q and I)and G6(the gap between I and M)decrease progressively with the evolution process.These results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura.展开更多
We describe the complete mitochondrial genome of a small-scaled forest agamid （Pseudocalotes microlepis）, which is 17 873 bp in size, containing 13 PCGs, 2 rRNAs, 22 tRNAs and non-coding regions. The mitogenome has ...We describe the complete mitochondrial genome of a small-scaled forest agamid （Pseudocalotes microlepis）, which is 17 873 bp in size, containing 13 PCGs, 2 rRNAs, 22 tRNAs and non-coding regions. The mitogenome has a typical gene order among squamates. 13 PCGs include 2 start codons （ATG and ATA）, 3 stop codons （TAG, TAA and AGG）, and an incomplete stop codon （T-）. Codon usage analyses showed that CUA-Leul and CGG-Arg are the most frequently and rarely used codon, respectively. All 22 tRNAs were predicted to form canonical cloverleaf secondary structures, except for two tRNAs （tRNAcys and tRNASer （AGY）） lacking the dihydorouridine （DHU） arm. The large non- coding region （control region） is 2 687 bp long （28.3% T, 18.2% C, 42.3% A, and 11.2% G）, with four different types of repeating sequences. The phylogenetic tree resulting from BEAST analyses based on concatenated 2 rRNAs and 13 PCGs in sequence revealed that the newly sequenced P. microlepis, where the genus Acanthosaura were aggregated. Together with Calotes versicolor, they constitute the subfamily Draconinae.展开更多
The first complete mitogenome of Cyclommatus stag beetles, Cyclommatus vitalisi（Coleoptera： Lucanidae） is sequenced using the next generation sequening. The genomic structure is a closed circular molecule with 17,8...The first complete mitogenome of Cyclommatus stag beetles, Cyclommatus vitalisi（Coleoptera： Lucanidae） is sequenced using the next generation sequening. The genomic structure is a closed circular molecule with 17,853 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes（t RNAs）, 2 ribosomal RNAs（r RNAs） and a control region. The sequence has neither a gene rearrangement nor a non-coding region. The nucleotide composition is A（36. 31%）, C（21. 48%）, T（31. 20%） and G（11. 01%）, with overall AT content of 73. 61%. The phylogenetic analysis of 13 stag beetles and another three scarab beetles show that Cyclommatus vitalisi shares a close ancestry with Lucanus mazama and Lucanus fortunei.展开更多
The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the c...The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the complete mitochondrial genome （mitogenome） of T. daii, which includes thirteen protein-coding genes （PCGs）, twenty-two transfer RNA genes, two ribosomal RNA genes and an A＋T-rich region, and we find the mitogenome is 15,482 bp in length （GenBank no. KY091643）. The genes order and orientation in the T. daii mitogenome are similar to other sequenced lepidopteran species. Except for cox1, all of the PCGs started with ATN. Twelve PCGs stopped at TAA except for cox1 which stops at a single T. Thirteen PCGs of available species are used to demonstrate the inner phylogenetic relationships of Bombycoidea. The bombycid species form a monophyletic clade with a bootstrap value of 100% and a posterior probability of 1.00.展开更多
Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt lakes.D.tibetana can adapt to saline wat...Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt lakes.D.tibetana can adapt to saline waters,whereas the other species of the superorder Cladocera can only inhabit in freshwater.However,the phylogenetic status of D.tibetana in Branchiopoda remains unclear primarily because of limited mitogenome.In this study,complete mitochondrial genome sequences of D.tibetana were sequenced and annotated for the first time to obtain a comprehensive understanding of its phylogenetic status.The complete mitogenome of D.tibetana is 16196 bp in length.It contains 37 genes,including two ribosomal RNAs(12S and 16S rRNAs)genes,22 transfer RNA(tRNA)genes,13 protein-coding genes,and one non-coding region.The overall base composition is 29.6%A,33.2%T,19.0%G,and 18.2%C with a high AT bias(62.8%).Except for trnS1(GCT),most tRNAs have a typical cloverleaf secondary structure.Phylogenetic analysis based on maximum likelihood and Bayesian inference generates identical phylogenetic topology and shows the phylogenetic status of D.tibetana,which reconfirm the distinction between the genera Daphniopsis and Daphnia.Meanwhile,the class Branchiopoda is clustered into three clades(Anostraca,Notostraca,and Diplostraca)with high support values.These results provide not only a comprehensive understanding of the characteristics of D.tibetana mitogenome and its phylogenetic position in Diplostraca,but also information for future research on the phylogeny of Branchiopoda.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)Science and Technology Basic Resources Investigation Program of China(2021FY100200)+1 种基金Yunnan Revitalization Talent Support Program“Young Talent”and"Innovation Team"Projectsthe 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Science(XTBG-1450101)。
文摘The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.
文摘Complete mitochondrial genomes(mitogenomes) can provide useful information for phylogenetic relationships,gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoidea(Cleistostoma dilatatum and Euplax sp.) were reported for the first time, which are 15 444 bp and16 129 bp in length, respectively. Cleistostoma dilatatum is the first species in the family Camptandriidae whose complete mitogenome was sequenced. Each mitogenome contains an entire set of 37 genes and a putative control region, but their gene arrangements are largely different. Tandem duplication and random loss model is proposed to account for their gene arrangements. Comparative genomic analyses of 19 mitogenomes clustering in one branch reveal that 18 of them shared the same gene rearrangement, while that of C. dilatatum mitogenome was consistent with the ancestral gene arrangement of Brachyura. The dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. Phylogenetic analyses show that all Macrophalmidae species cluster together as a group, and then form a sister clade with Camptandriidae. Moreover, the polyphyly of three superfamilies(Ocypodoidea, Eriphioidea, and Grapsoidea) is reconfirmed. These findings help to confirm the phylogenetic position of Camptandriidae, as well as provide new insights into the phylogeny of Brachyura.
基金National Natural Science Foundation of China(32000306)Project of Innovation Team of Survey and Assessment of the Pearl River Fishery Resources(2023TD-10)Natural Science Foundation of Shaanxi Province(2023-JC-YB-325)。
文摘The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scientific interest.Despite this interest,the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus.Herein,we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes(mitogenomes)from 13 morphological species to reconstruct the phylogenetic relationships,biogeographic history,and species diversity of Silurus.Our phylogenetic reconstructions identified eight clades,supported by both maximum-likelihood and Bayesian inference.Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units(MOTUs)in several taxa,including the Silurus asotus complex(four MOTUs)and Silurus microdorsalis(two MOTUs),suggesting that species diversity is underestimated in the genus.A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago(Ma),with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma,and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma.Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula,with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma.Key factors such as the Eocene-Oligocene extinction event,onset and intensification of the monsoon system,and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.
基金Supported by the National Natural Science Foundation of China(Nos.41806156,31702321)the Zhejiang Provincial Natural Science Foundation of China(Nos.LY22D060001,LY20C190008)+4 种基金the Fund of Guangdong Provincial Key Laboratory of Fishery Ecology and Environment(No.FEEL-2021-8)the Open Foundation from Key Laboratory of Tropical Marine Bio-resources and Ecology,Chinese Academy of Sciences(No.LMB20201005)the Science and Technology Project of Zhoushan(No.2020C21016)the Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes(No.2021J008)the Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang(Nos.20200201,20200202)。
文摘The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-coding genes,22 transfer RNAs,two ribosomal RNAs,and one control region.The genome composition was A+T biased(58.64%)and exhibited a positive AT-skew(0.095)and a negative GC-skew(-0.283).Compared with other Sisoridae fishes,the characteristics of nucleotide skews,codon usage,and amino acid usage of the P.hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes.Furthermore,the phylogenetic trees show that Sisoridae fishes fall into four major clades and P.hodgarti(CladeⅠ)is basal to the Sisoridae family,forming a sister clade to the Glyptosternoids(CladeⅣ).The topological structures constructed in this study raised doubts over the traditional classification system.These results will help better understand the feature s of the P.hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.
基金Supported by the Senior User Project of R/V Kexue(No.KEXUE2020GZ01)the National Natural Science Foundation of China(No.42176114)。
文摘Solemyidae is an ancient group of protobranch bivalves,and most solemyids are symbiotic with chemoautotrophic and gill-hosted bacteria,enabling them to survive in unusual habitats such as deepsea chemosynthetic environments.However,evolution of the mitogenomes in this family and their phylogenetic relationships remain poorly understood.The complete mitogenome of Acharax sp.was determined and compared with other available mitogenomes of solemyids.The mitogenome of Acharax sp.is 18970 bp in length and consists of 13 protein-coding genes,2 ribosomal RNA genes,and 22 transfer RNA genes.The gene arrangement was identical to those of other sequenced solemyids.For the present five mitogenomes of Solemyidae species,all protein-coding genes were initiated with the typical ATD(ATA,ATG,and ATT)codon and terminated with the TAA/TAG codon.Furthermore,the incomplete termination codon was detected.The Ka/Ks ratio analyses indicated that 13 protein-coding genes of five Solemyidae mitogenomes suffered strong purifying selection.Compared to 45 existing shallow water equivalents,the 18 available mitogenomes from the deep-sea,including the Acharax sp.in this study,show significantly more nonpolar amino acids in the 13 protein-coding genes,which indicates the adaptation to the deep-sea environment.The phylogenetic tree based on 48 Bivalvia complete mitogenomes provided further information to support the scientific classification of protobranchs.The relationships among Solemyidae were assessed based on 2 mitochondrial(16S rRNA and COX1)and 3 nuclear(18S rRNA,28S rRNA,and histone H3)gene sequences from 17 in-group species.The two genera Acharax and Solemya formed a monophyletic clade each,and Acharax sp.clustered with previously reported Acharax bivalves with high support values.
基金The Natural Science Foundation of Zhejiang Province under contract No.LY21C190007the Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities under contract No.2021JZ003the Zhoushan Science and Technology Bureau under contract No.2021C21007。
文摘Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae species.So far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy.Here,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were compared.The length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity.Like most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the L-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in C.puncticpes mitogenome.The typical IQM order(tRNA-Ile-Gln-Met)changed to QIM order.Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C.puncticpes mitogenome.Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future.
文摘The species within Xenarthra(sloths,anteaters,and armadillos)are quintessential South American mammals.Of the three groups,Vermilingua(anteaters)contains the fewest extant and paleontological species.Here,we sampled and sequenced the entire mitochondrial genomes(mitogenomes)of two Tamandua species(Tamandua tetradactyla and T.mexicana)(n=74)from Central and South America,as well as Myrmecophaga tridactyla(n=41)from South America.Within Tamandua,we detected three different haplogroups.The oldest(THI)contained many specimens with the T.tetradactyla morphotype(but also several with the T.mexicana morphotype)and originated in southeastern South America(currently Uruguay)before moving towards northern South America,where the THII haplogroup originated.THII primarily contained specimens with the T.mexicana morphotype(but also several with the T.tetradactyla morphotype)and was distributed in Central America,Colombia,and Ecuador.THI and THII yielded a genetic distance of 4%.THII originated in either northern South America or“in situ”in Central America with haplogroup THIII,which consisted of~50%T.mexicana and 50%T.tetradactyla phenotypes.THIII was mostly located in the same areas as THII,i.e.,Central America,Ecuador,and Colombia,though mainly in the latter.The three haplogroups overlapped in Colombia and Ecuador.Thus,T.tetradactyla and T.mexicana were not reciprocally monophyletic.For this reason,we considered that a unique species of Tamandua likely exists,i.e.,T.tetradactyla.In contrast to Tamandua,M.tridactyla did not show different morphotypes throughout its geographical range in the Neotropics.However,two very divergent genetic haplogroups(MHI and MHII),with a genetic distance of~10%,were detected.The basal haplogroup,MHI,originated in northwestern South America,whereas the more geographically derived haplogroup,MHII,overlapped with MHI,but also expanded into central and southern South America.Thus,Tamandua migrated from south to north whereas Myrmecophaga migrated from north to south.Our results also showed that temporal mitochondrial diversification for Tamandua began during the Late Pliocene and Upper Pleistocene,but for Myrmecophaga began during the Late Miocene.Furthermore,both taxa showed elevated levels of mitochondrial genetic diversity.Tamandua showed more evidence of female population expansion than Myrmecophaga.Tamandua experienced population expansion~0.6–0.17 million years ago(Mya),whereas Myrmecophaga showed possible population expansion~0.3–0.2 Mya.However,both taxa experienced a conspicuous female decline in the last 10000–20000 years.Our results also showed little spatial genetic structure for both taxa.However,several analyses revealed higher spatial structure in Tamandua than in Myrmecophaga.Therefore,Tamandua and Myrmecophaga were not subjected to the same biogeographical,geological,or climatological events in shaping their genetic structures.
基金supported by the National Natural Science Foundation of China(No.30470238 and 30670279)Innovation Foundation of the Graduate Student Cultivation of the Shaanxi Normal University(No.2006CXB003).
文摘The complete mitochondrial genome （mitogenome） of Gampsocleis gratiosa was determined. The 15,929 bp in the size of G. gratiosa mitogenome contains a typical gene content, base composition, and codon usage found in metazoan. All 13 protein coding genes （PCGs） of the G gratiosa mitogenome start with a typical ATN codon. The usual termination codons （TAA and TAG） were found from 10 PCGs. However, the atp6, had4, and had5 had incomplete termination codon （T）. The anticodons of all tRNAs are identical to those observed in Drosophila yakuba and Locusta migratoria, and can be folded in the form of a typical clover leaf structure except for trnS （AGN）. The secondary structure of trnS （AGN） was drawn according with the Steinberg-Cedergren tertiary structure. The A＋T content （67.4%） of the A＋T-rich region is relatively lower among the mitogenome regions, in contrast, it usually contains the highest A＋T content for most insects. Two isolated sequence repeat regions （202 bp） were found in the A＋T-rich region with mapping and secondary structure information.
基金supported by a Natural Sciences and Engineering Research Council(NSERC)of Canada Discovery Grant(RGPIN/238838-2011)NSERC Discovery Accelerator Supplement(RGPAS/412336-2011)+2 种基金University of Manitoba Research Grants Program Award(#41342)to K.L.C.K.H. was supported by the Youth Innovation Promotion AssociationChinese Academy of Sciencesa JSPS Postdoctoral Fellowship for Overseas Researchers(P16092)
文摘Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist （mostly in southwestern China and adjacent areas）. Only three forms of Blarinella have been recognized as either species or subspecies However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages, one a close relative to B. quadraticauda, whereas the other--comprised of topotype specimens from southern Gansu-iverged from other Blarinella in the middle Miocene （ca. 18.2 million years ago （Ma）, 95% confidence interval=13.4-23.6 Ma）. Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper p4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly, some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella.Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.
基金This work was supported by grant from the Science and Technology Committee of Yunnan Province （2011 FB141 ） We thank Dr. Zhong-Bao ZHAO for helpful suggestions during manuscript preparation.
文摘The yellow meal worm （Tenebrio molitor L.） is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. rnolitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A＋T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons （CTA in ND2 and AAT in COX1）, and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNASer （AGN）, which lacked a dihydrouridine （DHU） arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm.
基金supported by a grant from the Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01)
文摘The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses （ML and BI） among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.
基金The Natural Science Foundation of Zhejiang Province under contract No.LY21C190007。
文摘Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular evolution.Currently,the phylogenetic location of the genus Varuna(Brachyura:Varunidae)has not been well resolved mainly because of limited representatives(only two extant species).Here,we determined a new mitogenome of this genus(Varuna litterata)and added the published mitogenomes to reconstruct the phylogeny of Varunidae.The 16368-bp mitogenome contains the entire set of 37 genes and a putative control region.The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes.All 16 analyzed mitogenomes have identical gene order and similar molecular features.The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity,with comparatively low variability of COI and COII,and high variability of ND6.The nonsynonymous/synonymous substitution rates(dN/dS ratio)analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure.Twelve tRNA genes,two rRNAs,one PCG,and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order.Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes.Phylogenetic analyses show that all Varunidae species are placed into one group,and form a sister clade with Macrophthalmidae.Nevertheless,the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study.These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes,as well as provide insights into the phylogenetic studies of Brachyura.
基金supported by the Basic Work of Science and Technology Project, China (2014FY120800)the Science and Technology Project of Guangdong Province, China (2014YT02H042, 2014B020202001)
文摘Indigenous pigs in South China are valuable genetic resources with many specific and unique characters, which have played an important role in the establishment of some western modern pig breeds. However, the origin and genetic diversity of indigenous pigs in South China have not been fully understood. In the present study, we sequenced 534 novel mitochondrial DNA (mtDNA) D-loop and assembled 54 complete mitogenome sequences for all 17 indigenous pig breeds from Fujian, Guangdong, Guangxi and Hainan in South China. These data were analyzed together with previously published homologous sequences relevant to this study. We found that all 13 coding genes of the mitogenomes were under purifying selection, but ND1 had the most variable sites and CYTB contained the most non-synonymous SNPs. Phylogenetic analysis showed that all indigenous pigs in South China were clustered into the D haplogroup with D1a1, D1b, D1c and D1e sub-haplogroups found to be dominant. Haplotype and nucleotide diversities of D-loop sequences ranged from 0.427 to 0.899 and from 0.00342 to 0.00695, respectively, among which all pigs in Guangdong had the lowest diversity. The estimates of pairwise FST, gene flow (Nm) and genetic distance (Da) indicated that most of these indigenous pig breeds differentiated from each other significantly (P<0.05). Among the western modern breeds, Berkshire and Yorkshire had significant Asian matrilineal footprints from indigenous pigs in South China, especially the Spotted pigs distributed in Guangdong and Guangxi. The neutrality test (Fu’s FS) indicated that indigenous pigs from Fujian and Guangxi had gone through recent population expansion events (P<0.05). It is concluded that indigenous pigs in South China were most likely derived from the Mekong region and the middle and downstream regions of Yangtze River through Guangxi and Fujian. Our findings provide a complete and in-depth insight on the origin and distribution pattern of maternal genetic diversity of indigenous pigs in South China.
基金supported by the Natural Science Foundation of Zhejiang Province (No. LY21C190007)the Zhoushan Science and Technology Bureau (No. 2021C21 007)
文摘Knowledge of complete mitochondrial genomes(mitogenomes)can help understand the molecular evolution and phylogenetic relationships of various species.To date,the phylogenetic status of Leucosiidae within Brachyura remains unresolved because of the limited number of mitogenomes available.In the present study,the complete mitogenome of Myra affinis was sequenced using next-generation sequencing to supplement the limited mitogenome information of Leucosiidae.The 15349 bp-long mitogenome includes 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),2 ribosomal RNAs(rRNAs),and a putative control region.The overall base composition is 34.5%A,36.1%T,11.5%G,and 17.9%C,with a high AT bias(70.6%).All 13 PCGs start with the standard ATN codon and stop with the TAN codon or incomplete T.Except for tRNA-Ser,all other tRNAs have a typical cloverleaf-like secondary structure.Phylogenetic analyses based on the maximum likelihood and Bayesian inference methods are employed to generate identical phylogenetic topologies,thereby supporting the sister relationship between Leucosiidae and Matutidae for the first time.The monophyly of Eubrachyura is well established,and its sister relationship with Raninoida is strongly supported.The results of this work will not only help achieve a better understanding of the characteristics of the M.affinis mitogenome and the phylogenetic position of Leucosiidae,but also provide relevant information for further studies on the phylogeny of Brachyura.
基金financially supported by the Ministry of Culture of the Czech Republic(DKRVO 2019/5.I.a,National Museum,00023272)
文摘Sequencing technology has developed rapidly in recent years. Complete or nearly complete mitochondrial genomes(mitogenomes) of 155 species from 47 families in Heteroptera have been sequenced. However, the amounts of mitogenomes between those families are unbalanced, which makes it difficult to correctly discern the patterns of mitogenome rearrangement in Heteroptera. Among 21 species from ten families, ten variations in mitogenome rearrangement had been previously reported, among which the translocation between tRNA-Thr and tRNA-Pro was considered as a synapomorphy of Pyrrhocoroidea based on two mitogenomes. As only one mitogenome in each of Largidae and Pyrrhocoridae had been sequenced to conclude the synapomorphy, more mitogenomes of Pyrrhocoroidea need to be explored. In this study, additional two mitogenomes of Pyrrhocoroidea(Macrocheraia grandis grandis(Gray, 1832) and Myrmoplasta mira Gerst-cker, 1892) were sequenced. Both of them also possess the same translocation between tRNA-Thr and tRNA-Pro, which reaffirms that this kind of rearrangement is a molecular synapomorphy of Pyrrhocoroidea. Moreover, we discovered a more complex rearrangement in Myrmoplasta mira, in which six nearly identical duplications of tRNA-Thr were found located downstream of tRNA-Pro. Considering the high biodiversity of Heteroptera, more mitogenomic studies are needed to improve our knowledge about mitogenome rearrangements and the potential synapomorphies.
基金The National Natural Science Foundation of China under contract No.41706176the Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities under contract No.2019J00022。
文摘Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first time.The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae species.The 15646-bp mitogenome contains 13 protein-coding genes(PCGs),two ribosomal RNA genes(r RNAs),22 transfer RNA genes(t RNAs),and an A-T rich region.All of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete T.The pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection,whereas the ATP8 gene is an outlier,with pairwise comparison values ranging from neutral selection(0.000)to positive selection(1.039).The gene arrangement of P.eumolpe compared with ancestral Decapoda shows the translocation of two t RNAs(t RNA-His and t RNA-Gln),which is identical to other Sesarmidae species.Phylogenetic analyses show that all Sesarmidae species are placed into one group,and the polyphyly of Eriphioidea,Ocypodoidea,and Grapsoidea is well supported.The relationship between gaps in the QIM region and the phylogeny of Sesarmidae is analyzed.It is obvious that both the G5(the gap between Q and I)and G6(the gap between I and M)decrease progressively with the evolution process.These results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura.
基金provided by grant from Zhejiang Provincial Natural Science Foundation to Longhui LIN (LY17C030003)grants from the National Natural Science Foundation of China (31270571 and 31670422)
文摘We describe the complete mitochondrial genome of a small-scaled forest agamid （Pseudocalotes microlepis）, which is 17 873 bp in size, containing 13 PCGs, 2 rRNAs, 22 tRNAs and non-coding regions. The mitogenome has a typical gene order among squamates. 13 PCGs include 2 start codons （ATG and ATA）, 3 stop codons （TAG, TAA and AGG）, and an incomplete stop codon （T-）. Codon usage analyses showed that CUA-Leul and CGG-Arg are the most frequently and rarely used codon, respectively. All 22 tRNAs were predicted to form canonical cloverleaf secondary structures, except for two tRNAs （tRNAcys and tRNASer （AGY）） lacking the dihydorouridine （DHU） arm. The large non- coding region （control region） is 2 687 bp long （28.3% T, 18.2% C, 42.3% A, and 11.2% G）, with four different types of repeating sequences. The phylogenetic tree resulting from BEAST analyses based on concatenated 2 rRNAs and 13 PCGs in sequence revealed that the newly sequenced P. microlepis, where the genus Acanthosaura were aggregated. Together with Calotes versicolor, they constitute the subfamily Draconinae.
基金supported by the National Natural Science Foundation of China(31201745,31071954 and 31572311)
文摘The first complete mitogenome of Cyclommatus stag beetles, Cyclommatus vitalisi（Coleoptera： Lucanidae） is sequenced using the next generation sequening. The genomic structure is a closed circular molecule with 17,853 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes（t RNAs）, 2 ribosomal RNAs（r RNAs） and a control region. The sequence has neither a gene rearrangement nor a non-coding region. The nucleotide composition is A（36. 31%）, C（21. 48%）, T（31. 20%） and G（11. 01%）, with overall AT content of 73. 61%. The phylogenetic analysis of 13 stag beetles and another three scarab beetles show that Cyclommatus vitalisi shares a close ancestry with Lucanus mazama and Lucanus fortunei.
基金supported by the National Natural Science Foundation of China(31100482,31411140034)the Scientific Research Fund of Hunan Provincial Education Department(16B119)
文摘The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the complete mitochondrial genome （mitogenome） of T. daii, which includes thirteen protein-coding genes （PCGs）, twenty-two transfer RNA genes, two ribosomal RNA genes and an A＋T-rich region, and we find the mitogenome is 15,482 bp in length （GenBank no. KY091643）. The genes order and orientation in the T. daii mitogenome are similar to other sequenced lepidopteran species. Except for cox1, all of the PCGs started with ATN. Twelve PCGs stopped at TAA except for cox1 which stops at a single T. Thirteen PCGs of available species are used to demonstrate the inner phylogenetic relationships of Bombycoidea. The bombycid species form a monophyletic clade with a bootstrap value of 100% and a posterior probability of 1.00.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(Nos.LY22D060001,LY20C190008)the National Natural Science Foundation of China(Nos.41806156,31702321)+3 种基金the Fund of Guangdong Provincial Key Laboratory of Fishery Ecology and Environment(FEEL-2021-8)the Open Foundation from Key Laboratory of Tropical Marine Bio-resources and Ecology,Chinese Academy of Sciences(No.LMB20201005)the Science and Technology Project of Zhoushan(No.2020 C21016),the Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang(Nos.20200201,20200202)the Starting Research Fund from the Zhejiang Ocean University.
文摘Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt lakes.D.tibetana can adapt to saline waters,whereas the other species of the superorder Cladocera can only inhabit in freshwater.However,the phylogenetic status of D.tibetana in Branchiopoda remains unclear primarily because of limited mitogenome.In this study,complete mitochondrial genome sequences of D.tibetana were sequenced and annotated for the first time to obtain a comprehensive understanding of its phylogenetic status.The complete mitogenome of D.tibetana is 16196 bp in length.It contains 37 genes,including two ribosomal RNAs(12S and 16S rRNAs)genes,22 transfer RNA(tRNA)genes,13 protein-coding genes,and one non-coding region.The overall base composition is 29.6%A,33.2%T,19.0%G,and 18.2%C with a high AT bias(62.8%).Except for trnS1(GCT),most tRNAs have a typical cloverleaf secondary structure.Phylogenetic analysis based on maximum likelihood and Bayesian inference generates identical phylogenetic topology and shows the phylogenetic status of D.tibetana,which reconfirm the distinction between the genera Daphniopsis and Daphnia.Meanwhile,the class Branchiopoda is clustered into three clades(Anostraca,Notostraca,and Diplostraca)with high support values.These results provide not only a comprehensive understanding of the characteristics of D.tibetana mitogenome and its phylogenetic position in Diplostraca,but also information for future research on the phylogeny of Branchiopoda.
