Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting,resolve blood stasis and relieve pain.However,the intrageneric classification and phylogenetic relationships withi...Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting,resolve blood stasis and relieve pain.However,the intrageneric classification and phylogenetic relationships within Veratrum have long been controversial due to the complexity of morphological variations and lack of high-resolution molecular markers.In this study,we reevaluated the infrageneric relationships with the genus Veratrum using complete chloroplast genome sequence data.Herein,the complete cp genomes of ten species of Veratrum were newly sequenced and characterized.The complete cp genomes of ten species of Veratrum had the typical quadripartite structure,ranging from 151,597 bp to 153,711 bp in size and comprising a total of 135 genes.The structure of Veratrum cp genomes(i.e.,gene order,content,and genome components)was highly similar across species.The number of simple sequence repeats(SSRs)ranged from 63 to 7&and of long repeats ranged from 31 to 35.Eight highly divergent regions(ndhF,psbC-psbZ,psbK-psbl,rpoB-tmCjGCA,tmK_UUU-tmQ_UUG,tmS_GCU-tmG_UCC,tmT_UGU-tmL_UAA and ycfl)were identified and are potentially useful for the DNA barcoding of Veratrum.Phylogenetic analysis among 29 taxa based on cp genomes,total genes,protein-coding genes and intergenic regions strongly supported the monophyly of Veratrum.The circumscription and relationships of the infrageneric taxa of Veratrum were well-presented with great resolution.These results will facilitate the identification,taxonomy,and utilization of Veratrum plants as well as the evolutionary studies of Melanthiaceae.展开更多
Ginkgo biloba is a famous living“fossil”and has played an important role in the evolution of the Plant Kingdom.Here,the complete chloroplast genome of G.biloba was sequenced and analysed.The chloroplast genome was 1...Ginkgo biloba is a famous living“fossil”and has played an important role in the evolution of the Plant Kingdom.Here,the complete chloroplast genome of G.biloba was sequenced and analysed.The chloroplast genome was 156,990 bp long and predicted to encode 134 genes including 85 protein-coding genes,41 tRNA genes and 8 rRNA genes.The chloroplast genome has a typical quadripartite structure with a pair of inverted repeat regions(IRa and IRb,17,732 bp),a large(LSC,99,259 bp)and small single(SSC,22,267 bp)copy region.After an extensive comparison to previously published gymnosperm plastomes,the gene content and organisation of G.biloba showed high divergence,although part was relatively conserved.The two typical IR regions in the G.biloba chloroplast genome were relatively shorter because it the ycf2 gene.In addition,it was obvious that the IR regions and gene loss were responsible for changes in chloroplast genome size and structure stability,which influenced plastome evolution in different gymnosperms.Phylogenetic analysis revealed that G.biloba is sister to cycads rather than to gnetophytes,cupressophytes,and Pinaceae.Overall,the study showed that the genomic characteristics of G.biloba would be of great help in the further research on the taxonomy,species identification and evolutionary history of gymnosperms,especially for their position in plant systematics and evolution.展开更多
The genus Hippophae includes deciduous shrubs or small trees,which provide many ecological,economic,and social benefi ts.We assembled and annotated the chloroplast genomes of sympatric Hippophae gyantsensis(Rousi)Lian...The genus Hippophae includes deciduous shrubs or small trees,which provide many ecological,economic,and social benefi ts.We assembled and annotated the chloroplast genomes of sympatric Hippophae gyantsensis(Rousi)Lian and Hippophae rhamnoides Linn subsp.yunnanensis Rousi and comparatively analyzed their sequences.The fulllength chloroplast genomes of H.gyantsensis and H.rhamnoides subsp.yunnanensis were 155,260 and 156,415 bp,respectively;both featured a quadripartite structure with two copies of a large inverted repeat(IR)separated by small(SSC)and large(LSC)single-copy regions.Each Hippophae chloroplast genome contained 131 genes,comprising 85 protein-coding,8 ribosomal RNA,and 38 transfer RNA genes.Of 1302 nucleotide substitutions found between these twogenomes,824(63.29%)occurred in the intergenic region or intron sequences,and 478(36.71%)were located in the coding sequences.The SSC region had the highest mutation rate,followed by the LSC region and IR regions.Among the protein-coding genes,three had a ratio of nonsynonymous to synonymous substitutions(Ka/Ks)>1 yet none were signifi-cant,and 66 had Ka/Ks<1,of which 46 were signifi cant.We found 20 and 16 optimal codons,most of which ended with A or U,for chloroplast protein-coding genes of H.gyantsensis and H.rhamnoides subsp.yunnanensis,respectively.Phylogenetic analysis of fi ve available whole chloroplast genome sequences in the family Elaeagnaceae—using one Ziziphus jujube sequence as the outgroup—revealed that all fi ve plant species formed a monophyletic clade with two subclades:one subclade consisted of three Hippophae species,while the other was formed by two Elaeagnus species,supported by 100%bootstrap values.Together,these results suggest the chloroplast genomes among Hippophae species are conserved,both in structure and gene composition,due to general purifying selection;like many other plants,a signifi cant AT preference was discerned for most proteincoding genes in the Hippophae chloroplast genome.This study provides a valuable reference tool for future research on the general characteristics and evolution of chloroplast genomes in the genus Hippophae.展开更多
<i><span style="font-family:"">Poa</span></i><span style="font-family:""> <i>pratensis</i> </span><span style="font-family:"&q...<i><span style="font-family:"">Poa</span></i><span style="font-family:""> <i>pratensis</i> </span><span style="font-family:"">L. (Poaceae) is a hardy, persistent, attractive forage and turf grass adapted to a wide range of soils and climate. In this study, we release and detail the complete chloroplast genome sequences of <i>P</i>. <i>pratensis</i>. The whole chloroplast genome was 135,649 bp in length and comprised 131 genes, including 85 protein-coding genes, 38 tRNA genes, 8 rRNA genes. The <i>P</i>. <i>pratensis</i> chloroplast genome had a GC content of 38.3%. The result of phylogenetic analysis showed that <i>P</i>. <i>pratensis</i> was closely related to <i>P</i>. <i>pratensis</i> cv. <i>Qinghai</i> and <i>P</i>. <i>poophagorum</i>. This study would provide useful genetic information for the protection of <i>P</i>. <i>pratensis</i> and other related species.展开更多
Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespre...Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.展开更多
The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,...The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.展开更多
Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop improvement.We produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines repres...Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop improvement.We produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 B.oleracea breeding lines.We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major repeats.Nuclear genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 accessions.Interestingly,some SNPs showed subspecies enrichment at certain chromosomal regions.The assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and indels.The 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 lines.The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another group.The morphotypes diverged during the last 0.17 million years.The Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead.The polymorphic Cp markers provide a classification system for the cytoplasm types in B.oleracea.Furthermore,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active recently.Overall,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B.oleracea morphotypes.展开更多
Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the f...Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.展开更多
Cryptomeria fortunei(Chinese cedar)is a highly adaptable woody species and one of the main forest plantation trees in subtropical high-altitude areas in China.However,there are few studies on its chloroplast(cp)genome...Cryptomeria fortunei(Chinese cedar)is a highly adaptable woody species and one of the main forest plantation trees in subtropical high-altitude areas in China.However,there are few studies on its chloroplast(cp)genome.In this study,the complete cp genome of C.fortunei was sequenced and evaluated via comparative analyses with those of related species(formerly the Taxodiaceae)in Cupressaceae.The C.fortunei cp genome was 131,580 bp in length,and the GC content of the whole genome was 35.38%.It lost one relevant large inverted repeat and contained 114 unique genes,including 82 protein-coding genes,28 tRNAs and 4 rRNAs.The relative synonymous codon usage(RSCU)of codons ending with A/U was more than twice that of codons ending with G/C.Thirty long repeat structures(LRSs)and 213 simple sequence repeat(SSR)loci were detected in the C.fortunei cp genome.Comparative analyses of 10 cp genomes revealed that substantial rearrangements occurred in the gene organization.Additionally,6 cp hotspot regions(trnS-GGA,ycf1,trnP-GGG,trnC-GCA,psbZ and accD)were identified,and 4 genes(petL,psbM,rpl22 and psaM)had likely underwent positive selection.Phylogenetic analysis showed that Cupressaceae,Taxaceae and Cephalotaxaceae clustered to form a clade and that C.fortunei was most closely related to C.japonica(Japanese cedar),C.japonica cv.Wogon Hort and Taxodium distichum(baldcypress).These results provide references for future studies of population genetics,phylogenetic status and molecular markers among Cupressaceae species and for the cultivation of improved varieties.展开更多
Cerasus Campanulata is one of several species belonging to the Prunoideae focke,a subfamily of the flowering plant Rosaceae.We investigated the details of its chloroplast genome which may reveal its genus independent ...Cerasus Campanulata is one of several species belonging to the Prunoideae focke,a subfamily of the flowering plant Rosaceae.We investigated the details of its chloroplast genome which may reveal its genus independent of morphological determination.Here,we determined the complete chloroplast(cp)genome sequence of C.campanulata and performed sequence analysis to reveal the presence of 18 forward repeats,20 palindrome repeats,2 complement repeats,4 reverse repeats and 93 simple sequence repeats(SSRs).We additionally performed a comparative study of C.campanulata and seven other Prunoideae focke species.Then,maximum parsimony(MP)and maximum likelihood(ML)phylogenetic analyses were carried out in the little part of Rosaceae,respectively.The results strongly support a position of C.campanulata as a member of the Cerasus in the Rosaceae family.Moreover,the complete cp genome can be used for plant phylogenetic and evolutionary studies that will provide insight into the degree of gene conservation.展开更多
Lilium nepalense D. Don is an ornamental plant and exhibits high morphological variation across its distribution range in China. There is incongruence between different data sets for the status of it in Lilium. In thi...Lilium nepalense D. Don is an ornamental plant and exhibits high morphological variation across its distribution range in China. There is incongruence between different data sets for the status of it in Lilium. In this study, we reported a complete chloroplast genome of L. nepalense sampled in Hengduan Mountains, China. The whole chloroplast genome possessed a total length of 152,206 bp with typical circular structure, and contained a large single copy (LSC) of 81,854 bp and a small single copy (SSC) of 17,563 bp, which were separated by a pair of inverted repeats (IRa/IRb) of 26,399 bp. The average GC content among the whole chloroplast genome sequence was 37%, and the GC content in LSC, SSC, IRs regions were 34.8%, 30.6%, and 42.5%, respectively. There were 135 genes detected from the whole chloroplast genome sequence, including 89 protein-coding genes, 38 tRNAs, and 8 rRNAs. Phylogenetic results using maximum likelihood and Bayesian methods showed congruent results that L. nepalense together with the other two L. nepalense samples collected from different habitats formed a single branch, indicating a close relationship of L. nepalense with L. taliense belonging to the section Sinomartagon. This newly characterized chloroplast genome will provide essential data for the further population genetics research of L. nepalense.展开更多
Objective In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage,codon usage patt...Objective In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage,codon usage patterns of chloroplast genome,we determine the complete chloroplast(cp)genome of B.falcatum and clarify the main factors that influence codon usage patterns of 78 genes in B.falcatum chloroplast genome.Methods The total genomic DNA of fresh leaves from a single individual of B.falcatum was extracted with EASYspin plus Total DNA Isolation Kit and 2μg genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform.The cp genome of B.falcatum was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters.Python script and Codon W were used to calculate the codon usage bias parameters.Results The full length of B.falcatum cp genome was 155851 bp,132 different genes were annotated in this cp genome containing 80 protein-coding genes,30 tRNA genes,and four rRNA genes.The codon usage models tended to use A/T-ending codons.The neutrality plot,ENC plot,PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in B.falcatum cp genome.Furthermore,three optimal codons were identified and most of these three optimal codons ended with G/U.Conclusion The cp genome of B.falcatum has been characterized and the codon usage bias in B.falcatum cp genome is influenced by natural selection,mutation pressure and nucleotide composition.The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes,genetic engineering and molecular evolution in B.falcatum.展开更多
Pyrrosia petiolosa,Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium(PF)and commonly used as Chinese herbal medicines.Due to the similar morphological features of PF and its adu...Pyrrosia petiolosa,Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium(PF)and commonly used as Chinese herbal medicines.Due to the similar morphological features of PF and its adulterants,common DNA barcodes cannot accurately distinguish PF species.Knowledge of the chloroplast(cp)genome is widely used in species identification,molecular marker and phylogenetic analyses.Herein,we determined the complete cp genomes of three original species of PF via highthroughput sequencing technologies.The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158165 to 163026 bp.The cp genomes of P.petiolosa and P.lingua encoded 130 genes,whilst that of P.sheareri encoded 131 genes.The complete cp genomes were compared,and five highly divergent regions of pet A-psb J,mat K-rps16,ndh C-trn M,psb M-pet N and psa Cndh E were screened as potential DNA barcodes for identification of Pyrrosia genus species.The phylogenetic tree we obtained indicated that P.petiolosa and P.lingua are clustered in a single clade and,thus,share a close relationship.This study provides invaluable information for further studies on the species identification,taxonomy and phylogeny of Pyrrosia genus species.展开更多
Objective:Amomum villosum(AV)is an herb whose dried fruit has been extensively used in modern medicine to treat digestive system diseases such as dysentery,vomiting and abdominal pain.This paper aims to supplement chl...Objective:Amomum villosum(AV)is an herb whose dried fruit has been extensively used in modern medicine to treat digestive system diseases such as dysentery,vomiting and abdominal pain.This paper aims to supplement chloroplast(cp)genomic resources and to be used in phylogenetic studies and identification of AV related plants.Methods:High-throughput sequencing technology was used to determine the complete sequence of the AV cp genome,and the sequence was then compared with three related species.Results:The genome size of AV we obtained was 163,968 bp with an obvious tetrad structure.The AV cp genome was observed to contain 125 unique genes and 81 simple sequence repeat(SSRs)had been determined and the majority of which were adenine–thymine(AT)-rich.Comparative analysis of genome sequence of four ginger plants showed that the atpF,clpP and rpl32 genes are potential markers for identifying Amomum species.Phylogenetic analysis suggested that AV was closely related to A.kravanh and A.compactum.Conclusion:These results have brought useful genetic resources for further identification researches,DNA barcoding,resolving taxonomy and understanding the evolutionary mode of Zingiberaceae cp genome.展开更多
Objective:Schisandra sphenanthera and S.chinensis are the two important medicinal plants that have long been used under the names of"Nan-Wuweizi"and"Wuweizi",respectively.The misuse of"NanWuwe...Objective:Schisandra sphenanthera and S.chinensis are the two important medicinal plants that have long been used under the names of"Nan-Wuweizi"and"Wuweizi",respectively.The misuse of"NanWuweizi"and"Wuweizi"in herbal medical products calls for an accurate method to distinguish these herbs.Chloroplast(cp)genomes have been widely used in species delimitation and phylogeny due to their uniparental inheritance and lower substitution rates than that of the nuclear genomes.To develop more efficient DNA markers for distinguishing S.sphenanthera,S.chinensis,and the related species,we sequenced the cp genome ofS.sphenanthera and compared it to that of S.chinensis.Methods:The cp genome of S.sphenanthera was sequenced at the lllumina HiSeq platform,and the reference-guided mapping of contigs was obtained with a de novo assembly procedure.Then,comparative analyses of the cp genomes of S.sphenanthera and S.chinensis were carried out.Results:The cp genome of S.sphenanthera was 146853 bp in length and consisted of a large single copy(LSC)region of 95627 bp,a small single copy(SSC)region of 18292 bp,and a pair of inverted repeats(IR)of 16467 bp.GC content was 39.6%.A total of 126 functional genes were predicted,of which 113 genes were unique,including 79 protein-coding genes,30 transfer RNA(tRNA)genes,and four ribosomal RNA(rRNA)genes.Five tRNA,four protein-coding genes,and all rRNA were duplicated in the IR regions.There were 18 intron-containing genes,including six tRNA genes and 12 protein-coding genes.In addition,45 SSRs were detected.The whole cp genome of S.sphenanthera was 123 bp longer than that of S.chinensis.A total of 474 SNPs and 97 InDels were identified.Five genetic regions with high levels of variation(Pi>0.015),trnS-trnG,ccsA-ndhD,psbI-trnS,trnT-psbD and ndhF-rpl32 were revealed.Conclusion:We reported the cp genome ofS.sphenanthera and revealed the SNPs and InDels between the cp genomes of S.sphenanthera and S.chinensis.This study shed light on the species identification and further phylogenetic study within the genus of Schisandra.展开更多
Sargassum vachellianum is an ecologically important brown alga.It is China-specific and mainly inhabits in rocky intertidal zones in southeast coastal waters of China.In this study,we sequenced its circular complete c...Sargassum vachellianum is an ecologically important brown alga.It is China-specific and mainly inhabits in rocky intertidal zones in southeast coastal waters of China.In this study,we sequenced its circular complete chloroplast genome(cpDNA)and compared it with cpDNAs from S.vachellianum,S.horneri and S.thunbergii.The complete S.vachellianum cpDNA was 124,582 bp in length and consisted of a pair of inverted repeats(IRs)of 5435 bp,a large single copy(LSC)region of 73,721 bp and a small single copy(SSC)region of 39,991 bp.Totally 160 genes were predicted,including 132 protein-coding genes,four ribosomal RNA genes and 24 tRNA genes,and the coding sequences contributed 77.48%of the whole genome.In addition,25 SSR loci and 28 highly variable regions were identified from the S.vachellianum cpDNA,which might be used as candidates for developing DNA barcode markers of Sargassum species.The phylogenetic tree based on datasets of all the plastid-encoded proteins demonstrated that species of S.subgenus Bactrophycus were firstly combined and then clustered with S.vachellianum,which belongs to S.subgen.Sargassum.The results indicate that the chloroplast genomes are good resources for developing new DNA markers for taxonomy,and also as tools for evolutionary research of closely related species in future studies.展开更多
Background:Anisodus acutangulus(Solanaceae),an important folk medicinal herb in China,produces up to 1.2%alkaloids more than that in other Solanaceae plants such as Hyoscyamus niger,while its evolutionary position in ...Background:Anisodus acutangulus(Solanaceae),an important folk medicinal herb in China,produces up to 1.2%alkaloids more than that in other Solanaceae plants such as Hyoscyamus niger,while its evolutionary position in Hyoscyameae is not very clear.Objective:To explain the evolutionary position of A.acutangulus in the Solanaceae via complete chloroplast genome(cp)sequence.Methods:Complete chloroplast genome of A.acutangulus was obtained and characterized using the Illumina PE150 pair-end sequencing data.Structure of the genome,codon usage,nucleotide variability(Pi)value,distribution of repeats and SSRs between A.acutangulus and other seven Solanaceae species were analyzed.Previously published 22 Solanaceae cp genomes were used to construct phylogenetic tree.Results:The complete cp genome of A.acutangulus is 156082 bp in length,showed the typical quadripartite structure.The complete cp genome of A.acutangulus was highly conserved.A total of 112 unique genes were found in cp genome of A.acutangulus,among which 17 were duplicated.Further,we found eight hotspot regions for genome divergence could be explored as new DNA barcodes for the identification of the Solanaceae species.Phylogenetic analysis showed that A.acutangulus formed a clade with H.niger.Conclusion:A.acutangulus belongs to Hyoscyameae subfamily and the complete cp genome provides valuable information for phylogenetic reconstruction or comparative genomics of A.acutangulus.展开更多
Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuc...Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.展开更多
Bulbophyllum is the largest genus in Orchidaceae with a pan tropical distribution.Due to highly significant diversifications,it is considered to be one of the most taxonomically and phylogenetically complex taxa.The d...Bulbophyllum is the largest genus in Orchidaceae with a pan tropical distribution.Due to highly significant diversifications,it is considered to be one of the most taxonomically and phylogenetically complex taxa.The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus,and suitable molecular markers are necessary for species determination and phylogenetic analysis.A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study.Here,we sequenced the complete chloroplast genome of four Bulbophyllum species,including three species from section Macrocaulia.The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp.The chloroplast genomes included 113 unique genes encoding 79 proteins,30 tRNAs and 4 rRNAs.Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents,and shared a number of indels,which mainly contribute to its monophyly.In addition,interspecific divergence level was also great.Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms.A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum.All of chloroplast genes in four Bulbophyllum species were under purifying selection,while 13 sites within six genes exhibited sitespecific selection.A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood,Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum.Our findings provide valuable molecular markers to use in accurately identifying species,clarifying taxonomy,and resolving the phylogeny and evolution of the genus Bulbophyllum.The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.展开更多
Populus alba is a foundation species in evolutionary and ecological studies in the northern hemisphere.In this study,the chloroplast genome and gene map of P.alba were constructed.The P.alba chloroplast genome is 156,...Populus alba is a foundation species in evolutionary and ecological studies in the northern hemisphere.In this study,the chloroplast genome and gene map of P.alba were constructed.The P.alba chloroplast genome is 156,505 bp in length comprising a large single-copy region,two inverted repeat regions and a small single-copy region.The genome contains 131 genes,including 86 protein-coding genes(77 PCG species),eight ribosomal RNA genes(four rRNA species)and 37 transfer RNA genes(30 tRNA species).Phylogenetic analysis indicates that all Populus chloroplast genome sequences are clustered together and divided into three large branches.Among reported Populus chloroplast genomes,the leuce section formed monophyletic,indicating that all Populus spp.have a common maternal ancestor.P.rotundifolia and P.tremula are closely related and are sisters to P.davidiana.P.alba is closely related to P.adenopoda.Population genetic research in ecology and evolution may be easily developed through chloroplast genomes as they are conserved.This research will benefit future studies related to Populus,one of the world’s most ecologically and economically important genera.展开更多
文摘Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting,resolve blood stasis and relieve pain.However,the intrageneric classification and phylogenetic relationships within Veratrum have long been controversial due to the complexity of morphological variations and lack of high-resolution molecular markers.In this study,we reevaluated the infrageneric relationships with the genus Veratrum using complete chloroplast genome sequence data.Herein,the complete cp genomes of ten species of Veratrum were newly sequenced and characterized.The complete cp genomes of ten species of Veratrum had the typical quadripartite structure,ranging from 151,597 bp to 153,711 bp in size and comprising a total of 135 genes.The structure of Veratrum cp genomes(i.e.,gene order,content,and genome components)was highly similar across species.The number of simple sequence repeats(SSRs)ranged from 63 to 7&and of long repeats ranged from 31 to 35.Eight highly divergent regions(ndhF,psbC-psbZ,psbK-psbl,rpoB-tmCjGCA,tmK_UUU-tmQ_UUG,tmS_GCU-tmG_UCC,tmT_UGU-tmL_UAA and ycfl)were identified and are potentially useful for the DNA barcoding of Veratrum.Phylogenetic analysis among 29 taxa based on cp genomes,total genes,protein-coding genes and intergenic regions strongly supported the monophyly of Veratrum.The circumscription and relationships of the infrageneric taxa of Veratrum were well-presented with great resolution.These results will facilitate the identification,taxonomy,and utilization of Veratrum plants as well as the evolutionary studies of Melanthiaceae.
基金supported by the Key Forestry Public Welfare Project of China(201504105)the National Key Research and Development Program of China(2017YFD0600700)the Agricultural Science and Technology Independent Innovation Funds of Jiangsu Province[CX(16)1005].
文摘Ginkgo biloba is a famous living“fossil”and has played an important role in the evolution of the Plant Kingdom.Here,the complete chloroplast genome of G.biloba was sequenced and analysed.The chloroplast genome was 156,990 bp long and predicted to encode 134 genes including 85 protein-coding genes,41 tRNA genes and 8 rRNA genes.The chloroplast genome has a typical quadripartite structure with a pair of inverted repeat regions(IRa and IRb,17,732 bp),a large(LSC,99,259 bp)and small single(SSC,22,267 bp)copy region.After an extensive comparison to previously published gymnosperm plastomes,the gene content and organisation of G.biloba showed high divergence,although part was relatively conserved.The two typical IR regions in the G.biloba chloroplast genome were relatively shorter because it the ycf2 gene.In addition,it was obvious that the IR regions and gene loss were responsible for changes in chloroplast genome size and structure stability,which influenced plastome evolution in different gymnosperms.Phylogenetic analysis revealed that G.biloba is sister to cycads rather than to gnetophytes,cupressophytes,and Pinaceae.Overall,the study showed that the genomic characteristics of G.biloba would be of great help in the further research on the taxonomy,species identification and evolutionary history of gymnosperms,especially for their position in plant systematics and evolution.
基金the National Natural Science Foundation of China(31670666)the Fundamental Research Funds for the Central Non-profit Research Institution of Chinese Academy of Forestry(ZDRIF201706).
文摘The genus Hippophae includes deciduous shrubs or small trees,which provide many ecological,economic,and social benefi ts.We assembled and annotated the chloroplast genomes of sympatric Hippophae gyantsensis(Rousi)Lian and Hippophae rhamnoides Linn subsp.yunnanensis Rousi and comparatively analyzed their sequences.The fulllength chloroplast genomes of H.gyantsensis and H.rhamnoides subsp.yunnanensis were 155,260 and 156,415 bp,respectively;both featured a quadripartite structure with two copies of a large inverted repeat(IR)separated by small(SSC)and large(LSC)single-copy regions.Each Hippophae chloroplast genome contained 131 genes,comprising 85 protein-coding,8 ribosomal RNA,and 38 transfer RNA genes.Of 1302 nucleotide substitutions found between these twogenomes,824(63.29%)occurred in the intergenic region or intron sequences,and 478(36.71%)were located in the coding sequences.The SSC region had the highest mutation rate,followed by the LSC region and IR regions.Among the protein-coding genes,three had a ratio of nonsynonymous to synonymous substitutions(Ka/Ks)>1 yet none were signifi-cant,and 66 had Ka/Ks<1,of which 46 were signifi cant.We found 20 and 16 optimal codons,most of which ended with A or U,for chloroplast protein-coding genes of H.gyantsensis and H.rhamnoides subsp.yunnanensis,respectively.Phylogenetic analysis of fi ve available whole chloroplast genome sequences in the family Elaeagnaceae—using one Ziziphus jujube sequence as the outgroup—revealed that all fi ve plant species formed a monophyletic clade with two subclades:one subclade consisted of three Hippophae species,while the other was formed by two Elaeagnus species,supported by 100%bootstrap values.Together,these results suggest the chloroplast genomes among Hippophae species are conserved,both in structure and gene composition,due to general purifying selection;like many other plants,a signifi cant AT preference was discerned for most proteincoding genes in the Hippophae chloroplast genome.This study provides a valuable reference tool for future research on the general characteristics and evolution of chloroplast genomes in the genus Hippophae.
文摘<i><span style="font-family:"">Poa</span></i><span style="font-family:""> <i>pratensis</i> </span><span style="font-family:"">L. (Poaceae) is a hardy, persistent, attractive forage and turf grass adapted to a wide range of soils and climate. In this study, we release and detail the complete chloroplast genome sequences of <i>P</i>. <i>pratensis</i>. The whole chloroplast genome was 135,649 bp in length and comprised 131 genes, including 85 protein-coding genes, 38 tRNA genes, 8 rRNA genes. The <i>P</i>. <i>pratensis</i> chloroplast genome had a GC content of 38.3%. The result of phylogenetic analysis showed that <i>P</i>. <i>pratensis</i> was closely related to <i>P</i>. <i>pratensis</i> cv. <i>Qinghai</i> and <i>P</i>. <i>poophagorum</i>. This study would provide useful genetic information for the protection of <i>P</i>. <i>pratensis</i> and other related species.
基金funded by Kunyu Mountain National Nature Reserve Administration。
文摘Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.
基金Supported by the Science&Technology Basic Resources Investigation Program of China(No.2018FY100205)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050302)+2 种基金the National Key R&D Program of China(No.2018YFD0901500)the National Natural Science Foundation of China(No.41776153)the Key R&D Program of Shandong Province(No.2019GSF107012)。
文摘The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.
基金Golden Seed Project(Center for Horticultural Seed Development,Grant No.213003-04-1-SB430)Ministry of Agriculture,Food and Rural Affairs(MAFRA)+1 种基金Ministry of Oceans and Fisheries(MOF)“Cooperative Research Program for Agriculture Science&Technology Development(Grant No.PJ013238)”Rural Development Administration,Republic of Korea。
文摘Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop improvement.We produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 B.oleracea breeding lines.We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major repeats.Nuclear genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 accessions.Interestingly,some SNPs showed subspecies enrichment at certain chromosomal regions.The assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and indels.The 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 lines.The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another group.The morphotypes diverged during the last 0.17 million years.The Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead.The polymorphic Cp markers provide a classification system for the cytoplasm types in B.oleracea.Furthermore,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active recently.Overall,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B.oleracea morphotypes.
基金the Science and Technology Project of Changsha City(No.kq2004038)Program for Innovative Leading Talents for Science and Technology of Xianyang City。
文摘Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.
基金This research was funded by the National Forestry and Grassland Administration of China,National Forestry Public Welfare Industry Research Project(Grant No.201304104)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Cryptomeria fortunei(Chinese cedar)is a highly adaptable woody species and one of the main forest plantation trees in subtropical high-altitude areas in China.However,there are few studies on its chloroplast(cp)genome.In this study,the complete cp genome of C.fortunei was sequenced and evaluated via comparative analyses with those of related species(formerly the Taxodiaceae)in Cupressaceae.The C.fortunei cp genome was 131,580 bp in length,and the GC content of the whole genome was 35.38%.It lost one relevant large inverted repeat and contained 114 unique genes,including 82 protein-coding genes,28 tRNAs and 4 rRNAs.The relative synonymous codon usage(RSCU)of codons ending with A/U was more than twice that of codons ending with G/C.Thirty long repeat structures(LRSs)and 213 simple sequence repeat(SSR)loci were detected in the C.fortunei cp genome.Comparative analyses of 10 cp genomes revealed that substantial rearrangements occurred in the gene organization.Additionally,6 cp hotspot regions(trnS-GGA,ycf1,trnP-GGG,trnC-GCA,psbZ and accD)were identified,and 4 genes(petL,psbM,rpl22 and psaM)had likely underwent positive selection.Phylogenetic analysis showed that Cupressaceae,Taxaceae and Cephalotaxaceae clustered to form a clade and that C.fortunei was most closely related to C.japonica(Japanese cedar),C.japonica cv.Wogon Hort and Taxodium distichum(baldcypress).These results provide references for future studies of population genetics,phylogenetic status and molecular markers among Cupressaceae species and for the cultivation of improved varieties.
基金This work was supported by key research and development plan of Foundation of Jiangsu Forestry Bureau(LYKJ[2017]42),Jiangsu Province(BE2017376)the Nature Science Foundation of China(31770715)the Qinglan project of Jiangsu Province,and Priority Academic Program Development of Jiangsu Higher Education Institutions.
文摘Cerasus Campanulata is one of several species belonging to the Prunoideae focke,a subfamily of the flowering plant Rosaceae.We investigated the details of its chloroplast genome which may reveal its genus independent of morphological determination.Here,we determined the complete chloroplast(cp)genome sequence of C.campanulata and performed sequence analysis to reveal the presence of 18 forward repeats,20 palindrome repeats,2 complement repeats,4 reverse repeats and 93 simple sequence repeats(SSRs).We additionally performed a comparative study of C.campanulata and seven other Prunoideae focke species.Then,maximum parsimony(MP)and maximum likelihood(ML)phylogenetic analyses were carried out in the little part of Rosaceae,respectively.The results strongly support a position of C.campanulata as a member of the Cerasus in the Rosaceae family.Moreover,the complete cp genome can be used for plant phylogenetic and evolutionary studies that will provide insight into the degree of gene conservation.
文摘Lilium nepalense D. Don is an ornamental plant and exhibits high morphological variation across its distribution range in China. There is incongruence between different data sets for the status of it in Lilium. In this study, we reported a complete chloroplast genome of L. nepalense sampled in Hengduan Mountains, China. The whole chloroplast genome possessed a total length of 152,206 bp with typical circular structure, and contained a large single copy (LSC) of 81,854 bp and a small single copy (SSC) of 17,563 bp, which were separated by a pair of inverted repeats (IRa/IRb) of 26,399 bp. The average GC content among the whole chloroplast genome sequence was 37%, and the GC content in LSC, SSC, IRs regions were 34.8%, 30.6%, and 42.5%, respectively. There were 135 genes detected from the whole chloroplast genome sequence, including 89 protein-coding genes, 38 tRNAs, and 8 rRNAs. Phylogenetic results using maximum likelihood and Bayesian methods showed congruent results that L. nepalense together with the other two L. nepalense samples collected from different habitats formed a single branch, indicating a close relationship of L. nepalense with L. taliense belonging to the section Sinomartagon. This newly characterized chloroplast genome will provide essential data for the further population genetics research of L. nepalense.
基金supported by the National Natural Science Foundation of China(82204567,81973430)Natural Science Foundation of Hebei Province(H2020201006)+3 种基金Medical Science Foundation of Hebei University(2021B10)China University Student Innovation and Entrepreneurship Training Program Project(2022333)Advanced Talents Incubation Program of the Hebei University(521000981177,521000981170)Resources Development of“Qin Drug”of Shaanxi University of Chinese Medicine Innovation Team Project(2019-QN01).
文摘Objective In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage,codon usage patterns of chloroplast genome,we determine the complete chloroplast(cp)genome of B.falcatum and clarify the main factors that influence codon usage patterns of 78 genes in B.falcatum chloroplast genome.Methods The total genomic DNA of fresh leaves from a single individual of B.falcatum was extracted with EASYspin plus Total DNA Isolation Kit and 2μg genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform.The cp genome of B.falcatum was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters.Python script and Codon W were used to calculate the codon usage bias parameters.Results The full length of B.falcatum cp genome was 155851 bp,132 different genes were annotated in this cp genome containing 80 protein-coding genes,30 tRNA genes,and four rRNA genes.The codon usage models tended to use A/T-ending codons.The neutrality plot,ENC plot,PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in B.falcatum cp genome.Furthermore,three optimal codons were identified and most of these three optimal codons ended with G/U.Conclusion The cp genome of B.falcatum has been characterized and the codon usage bias in B.falcatum cp genome is influenced by natural selection,mutation pressure and nucleotide composition.The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes,genetic engineering and molecular evolution in B.falcatum.
基金supported by the Major Scientific and Technological Special Project for“Significant New Drugs Creation”(No.2018ZX09711001-008-007)the Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences(CIFMS,No.2016-I2M-3-016)。
文摘Pyrrosia petiolosa,Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium(PF)and commonly used as Chinese herbal medicines.Due to the similar morphological features of PF and its adulterants,common DNA barcodes cannot accurately distinguish PF species.Knowledge of the chloroplast(cp)genome is widely used in species identification,molecular marker and phylogenetic analyses.Herein,we determined the complete cp genomes of three original species of PF via highthroughput sequencing technologies.The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158165 to 163026 bp.The cp genomes of P.petiolosa and P.lingua encoded 130 genes,whilst that of P.sheareri encoded 131 genes.The complete cp genomes were compared,and five highly divergent regions of pet A-psb J,mat K-rps16,ndh C-trn M,psb M-pet N and psa Cndh E were screened as potential DNA barcodes for identification of Pyrrosia genus species.The phylogenetic tree we obtained indicated that P.petiolosa and P.lingua are clustered in a single clade and,thus,share a close relationship.This study provides invaluable information for further studies on the species identification,taxonomy and phylogeny of Pyrrosia genus species.
基金supported by the National Key R&D Program of China(2017YFC1701104)Guangdong Province Applied Science and Technology R&D Special Fund Project(2015B020234002)。
文摘Objective:Amomum villosum(AV)is an herb whose dried fruit has been extensively used in modern medicine to treat digestive system diseases such as dysentery,vomiting and abdominal pain.This paper aims to supplement chloroplast(cp)genomic resources and to be used in phylogenetic studies and identification of AV related plants.Methods:High-throughput sequencing technology was used to determine the complete sequence of the AV cp genome,and the sequence was then compared with three related species.Results:The genome size of AV we obtained was 163,968 bp with an obvious tetrad structure.The AV cp genome was observed to contain 125 unique genes and 81 simple sequence repeat(SSRs)had been determined and the majority of which were adenine–thymine(AT)-rich.Comparative analysis of genome sequence of four ginger plants showed that the atpF,clpP and rpl32 genes are potential markers for identifying Amomum species.Phylogenetic analysis suggested that AV was closely related to A.kravanh and A.compactum.Conclusion:These results have brought useful genetic resources for further identification researches,DNA barcoding,resolving taxonomy and understanding the evolutionary mode of Zingiberaceae cp genome.
基金This study was financially supported by the National Natural Science Foundation of China(Grant No.81703650)the CAMS Initiative for Innovative Medicine(CAMS-I2M)(Grant No.2016-I2M-2-003).The funders had no role in study design,data collection and analysis,decision to publish,or preparation of the manuscript.
文摘Objective:Schisandra sphenanthera and S.chinensis are the two important medicinal plants that have long been used under the names of"Nan-Wuweizi"and"Wuweizi",respectively.The misuse of"NanWuweizi"and"Wuweizi"in herbal medical products calls for an accurate method to distinguish these herbs.Chloroplast(cp)genomes have been widely used in species delimitation and phylogeny due to their uniparental inheritance and lower substitution rates than that of the nuclear genomes.To develop more efficient DNA markers for distinguishing S.sphenanthera,S.chinensis,and the related species,we sequenced the cp genome ofS.sphenanthera and compared it to that of S.chinensis.Methods:The cp genome of S.sphenanthera was sequenced at the lllumina HiSeq platform,and the reference-guided mapping of contigs was obtained with a de novo assembly procedure.Then,comparative analyses of the cp genomes of S.sphenanthera and S.chinensis were carried out.Results:The cp genome of S.sphenanthera was 146853 bp in length and consisted of a large single copy(LSC)region of 95627 bp,a small single copy(SSC)region of 18292 bp,and a pair of inverted repeats(IR)of 16467 bp.GC content was 39.6%.A total of 126 functional genes were predicted,of which 113 genes were unique,including 79 protein-coding genes,30 transfer RNA(tRNA)genes,and four ribosomal RNA(rRNA)genes.Five tRNA,four protein-coding genes,and all rRNA were duplicated in the IR regions.There were 18 intron-containing genes,including six tRNA genes and 12 protein-coding genes.In addition,45 SSRs were detected.The whole cp genome of S.sphenanthera was 123 bp longer than that of S.chinensis.A total of 474 SNPs and 97 InDels were identified.Five genetic regions with high levels of variation(Pi>0.015),trnS-trnG,ccsA-ndhD,psbI-trnS,trnT-psbD and ndhF-rpl32 were revealed.Conclusion:We reported the cp genome ofS.sphenanthera and revealed the SNPs and InDels between the cp genomes of S.sphenanthera and S.chinensis.This study shed light on the species identification and further phylogenetic study within the genus of Schisandra.
基金This research was supported by Ocean Public Welfare Scientific Research Project(No.201405040)Shanghai Universities Plateau Discipline Project of Marine Sciences.
文摘Sargassum vachellianum is an ecologically important brown alga.It is China-specific and mainly inhabits in rocky intertidal zones in southeast coastal waters of China.In this study,we sequenced its circular complete chloroplast genome(cpDNA)and compared it with cpDNAs from S.vachellianum,S.horneri and S.thunbergii.The complete S.vachellianum cpDNA was 124,582 bp in length and consisted of a pair of inverted repeats(IRs)of 5435 bp,a large single copy(LSC)region of 73,721 bp and a small single copy(SSC)region of 39,991 bp.Totally 160 genes were predicted,including 132 protein-coding genes,four ribosomal RNA genes and 24 tRNA genes,and the coding sequences contributed 77.48%of the whole genome.In addition,25 SSR loci and 28 highly variable regions were identified from the S.vachellianum cpDNA,which might be used as candidates for developing DNA barcode markers of Sargassum species.The phylogenetic tree based on datasets of all the plastid-encoded proteins demonstrated that species of S.subgenus Bactrophycus were firstly combined and then clustered with S.vachellianum,which belongs to S.subgen.Sargassum.The results indicate that the chloroplast genomes are good resources for developing new DNA markers for taxonomy,and also as tools for evolutionary research of closely related species in future studies.
基金This work was financially supported by the National Key R&D Program of China(2018YFC1706200)National Natural Science Fund of China(81522049,31571735,82003888)+1 种基金Zhejiang Provincial Ten Thousands Program for Leading Talents of Science and Technology In-novation(2018R520)Zhejiang Provincial Program for the Cultivation of High-level Innovative Health talents.
文摘Background:Anisodus acutangulus(Solanaceae),an important folk medicinal herb in China,produces up to 1.2%alkaloids more than that in other Solanaceae plants such as Hyoscyamus niger,while its evolutionary position in Hyoscyameae is not very clear.Objective:To explain the evolutionary position of A.acutangulus in the Solanaceae via complete chloroplast genome(cp)sequence.Methods:Complete chloroplast genome of A.acutangulus was obtained and characterized using the Illumina PE150 pair-end sequencing data.Structure of the genome,codon usage,nucleotide variability(Pi)value,distribution of repeats and SSRs between A.acutangulus and other seven Solanaceae species were analyzed.Previously published 22 Solanaceae cp genomes were used to construct phylogenetic tree.Results:The complete cp genome of A.acutangulus is 156082 bp in length,showed the typical quadripartite structure.The complete cp genome of A.acutangulus was highly conserved.A total of 112 unique genes were found in cp genome of A.acutangulus,among which 17 were duplicated.Further,we found eight hotspot regions for genome divergence could be explored as new DNA barcodes for the identification of the Solanaceae species.Phylogenetic analysis showed that A.acutangulus formed a clade with H.niger.Conclusion:A.acutangulus belongs to Hyoscyameae subfamily and the complete cp genome provides valuable information for phylogenetic reconstruction or comparative genomics of A.acutangulus.
基金This work was supported by grants from National Natural Science Foundation of China(No.32170381 and 31770200).
文摘Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.
基金supported by the National Natural Science Foundation of China(No.31870183,No.U1702235)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01)。
文摘Bulbophyllum is the largest genus in Orchidaceae with a pan tropical distribution.Due to highly significant diversifications,it is considered to be one of the most taxonomically and phylogenetically complex taxa.The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus,and suitable molecular markers are necessary for species determination and phylogenetic analysis.A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study.Here,we sequenced the complete chloroplast genome of four Bulbophyllum species,including three species from section Macrocaulia.The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp.The chloroplast genomes included 113 unique genes encoding 79 proteins,30 tRNAs and 4 rRNAs.Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents,and shared a number of indels,which mainly contribute to its monophyly.In addition,interspecific divergence level was also great.Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms.A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum.All of chloroplast genes in four Bulbophyllum species were under purifying selection,while 13 sites within six genes exhibited sitespecific selection.A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood,Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum.Our findings provide valuable molecular markers to use in accurately identifying species,clarifying taxonomy,and resolving the phylogeny and evolution of the genus Bulbophyllum.The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.
基金The work was supported by the Fundamental Research Funds of the Chinese Academy of Forestry(No.CAFYBB2017ZX001-1)the National Natural Science Foundation of China(No.31470665).
文摘Populus alba is a foundation species in evolutionary and ecological studies in the northern hemisphere.In this study,the chloroplast genome and gene map of P.alba were constructed.The P.alba chloroplast genome is 156,505 bp in length comprising a large single-copy region,two inverted repeat regions and a small single-copy region.The genome contains 131 genes,including 86 protein-coding genes(77 PCG species),eight ribosomal RNA genes(four rRNA species)and 37 transfer RNA genes(30 tRNA species).Phylogenetic analysis indicates that all Populus chloroplast genome sequences are clustered together and divided into three large branches.Among reported Populus chloroplast genomes,the leuce section formed monophyletic,indicating that all Populus spp.have a common maternal ancestor.P.rotundifolia and P.tremula are closely related and are sisters to P.davidiana.P.alba is closely related to P.adenopoda.Population genetic research in ecology and evolution may be easily developed through chloroplast genomes as they are conserved.This research will benefit future studies related to Populus,one of the world’s most ecologically and economically important genera.
