Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta ...Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.展开更多
Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we...Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74%increase of the earlier largest sampling)representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylogenetic context.Our major results include:(1)the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades;(2)the Sinensis group is resolved as sister to S.subg.Pulviniella with strong support in two of the three analyses;(3)most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family;and(4)an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l.is split into seven subfamilies(corresponding to the current six subgenera t the Sinensis group)and 19 genera(the major diagnosable clades)with nine new species-poor genera.We support the conservation of Selaginella with a new type,S.flabellata,to minimize nomenclatural instability.We provide a key to subfamilies and genera,images illustrating their morphology,their morphological and geographical synopses,a list of constituent species,and necessary new combinations.This new classification will hopefully facilitate communication,promote further studies,and help conservation.展开更多
The timing of mammalian diversification in relation to the Cretaceous-Paleogene(KPg)mass extinction continues to be a subject of substantial debate.Previous studies have either focused on limited taxonomic samples wit...The timing of mammalian diversification in relation to the Cretaceous-Paleogene(KPg)mass extinction continues to be a subject of substantial debate.Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples.In the present study,we improved an existing dataset from the landmark study of Meredith et al.(2011)by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers.Using these two datasets,we then constructed phylogenies for extant mammalian families,providing improved resolution of many conflicting relationships.Moreover,the timetrees generated,which were calibrated using appropriate molecular clock models and multiple fossil records,indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period.Additionally,intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary,supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification.Thus,our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.展开更多
The marine and freshwater Hildenbrandia samples were collected from diverse locations of China and Japan,and mor-phological characterization and molecular phylogenetic analysis were conducted on these samples.Morpholo...The marine and freshwater Hildenbrandia samples were collected from diverse locations of China and Japan,and mor-phological characterization and molecular phylogenetic analysis were conducted on these samples.Morphological measurements of freshwater specimens were consistent with the results of H.jigongshanensis,whereas cell dimensions of marine specimens were slightly larger than those of widely distributed H.rubra and H.crouanii.Phylogenetic trees based on rbcL,psbA and UPA sequences were consistent.Freshwater specimens collected in this study formed an independent clade with H.jigongshanensis supported by high values.Species attribution was confirmed further by the similar ITS2 secondary structures among the samples of H.jigongshan-ensis.It was found that the intraspecific divergence of rbcL gene in H.jigongshanensis was smaller than other two freshwater species H.rivularis and H.angolensis.Phylogenetic trees showed that marine specimens in this study grouped together with H.rubra samples of North America,and were different with the H.rubra samples of Europe.Combining the comparison results of CBC numbers in ITS2 secondary structure,we propose the marine samples collected in this study to be a new species Hildenbrandia qingdaoensis sp.nov.The separation of the marine and freshwater specimens was supported by the rbcL,UPA and psbA phylogeny as well as ITS2 se-condary structure inference.Biogeographical reconstruction showed the ancestor of freshwater Hildenbrandia might derive from South America and dispersed from North America to Europe and then to Asian countries,which needs to be verified further with more sam-ples and molecular evidences from South America.展开更多
Cholera is a significant public health threat across the globe, especially in coastal regions with poor water supply. This study was carried out to determine the antibiogram, genomic, and phylogeny of stool and seafoo...Cholera is a significant public health threat across the globe, especially in coastal regions with poor water supply. This study was carried out to determine the antibiogram, genomic, and phylogeny of stool and seafood isolates from some cholera-prone coastal communities in Rivers State, Nigeria. A total of 400 stool samples and 42 different seafood were aseptically collected and examined using standard microbiology and molecular techniques. An antibiogram of isolates from seafood and stool samples was assayed. Genes for virulence, resistance, and relatedness of bacteria identified were also determined. The isolates from the stool and seafood were examined for susceptibility to some selected antibiotics. The findings showed the prevalence rate of cholera in the communities as follows: 16% in Kaa, 30% in Andoni, 4% in Ogu/Bolo, and 10% in Abua/Odual. The isolates from stool were susceptible to Ciprofloxacin and Gentamycin with a susceptibility rate of 94.12% each while 100% resistance was recorded against Amoxicillin-clavulanic acid, 94.12% against Amikacin and 88.24% against Colistin. For the sea foods, the isolates were susceptible to gentamycin and ciprofloxacin with a susceptibility rate of 91.43% and 82.86% respectively. Resistance was also recorded against Colistin (88.57%) and Azithromycin (82.86%). Testing the isolates for the presence of 16SrRNA genes showed that all were positive with 1500 bp 16SrRNA gene band size. TEM, OXA, SHV, and CTX-M resistant genes were detected whereas the virulence genes were TDH and AcrB. The phylogenetic analysis revealed isolates from seafood to be Aeromonas dhakensis, Vibrio parahaemolyticus, Vibrio azureus, and Providencia rettgeri, while in stool samples they were Enterobacter sichuanensis, Enterobacter hormaechei, Providencia sneebia, and Proteus vulgaris. Providencia stuartii, Proteus mirabilis, Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae were common isolates from both seafood and stool samples. This study has shown that not all reported cases of cholera are caused by Vibrio cholerae. Therefore, attention should be paid to other water-borne bacteria in every outbreak, especially in coastal communities.展开更多
The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 specie...The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.展开更多
The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as ...The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as sample taxa. The sequence constitutions and variations were analyzed and the molecular phylogenetic trees were reconstructed based on the combined sequence data （795bp length in total） of 12S rDNA and 16S rDNA, using the grasshopper Pyrgomorpha conica of Pyrgomorphidae as the outgroup. The results showed that the rates of the two kinds of transitions are obviously much higher than that of the four kinds of Wansversions in these combined 12S＋16S rDNA sequence data. The saturation ofnucleotide substitutions happened in 12S and 16S rDNA sequence data. The molecular phylogenetic trees indicated that Oedipodinae is a monophyletic group and this subfamily is a natural one, but Catantopinae and Acridinae are non-monophyletic. Oedipodnae is a relatively primitive group within the Acrididae, whereas the Oxyinae may have diverged later than Oedipodinae, but earlier than most other species of Acridide.展开更多
The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trn L-F region were sequenced for 41 species of the Aceraceae, representing both genera Acer and Dipteronia, to reconstruct phylogen...The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trn L-F region were sequenced for 41 species of the Aceraceae, representing both genera Acer and Dipteronia, to reconstruct phylogeny of this family, especially within Acer. The analyses were performed in separate and combined sequence data sets, with the Sapindaceae and Hippocastanaceae being selected as outgroups. It was indicated that the Aceraceae was monophyletic and D. sinensis was basal to the rest of the family but the two genera of it might be not monophyletic because Dipteronia dyerana was nested within Acer. The result inferred from the combined data showed greater resolution within Acer than that from the two separate data sets. The monophyly of most sections in Xu's system (1996) were supported with high bootstrap values, and some relationships between (or among) sections were also inferred, such as sect. Palmata and sect. Microcarpa; sect. Platanoidea, sect. Lithocarpa and sect. Macrophylla; sect. Integrifolia, sect. Trifoliata and sect. Pentaphylla; and sect. Acer, sect. Goniocarpa and sect. Saccharina (sensu Ogata). However, the sectional status and circumscriptions of some of the above-mentioned sections should be further adjusted. It seemed that the Xu's delimitations of sect. Rubra and sect. Saccharodendran should be revaluated.展开更多
The molecular phylogeny of the Lardizabalaceae is reconstructed based on chloroplast trn L_F sequences alone and combined trn L_F and rbc L sequences. The phylogenetic topologies agree well with Qin's and...The molecular phylogeny of the Lardizabalaceae is reconstructed based on chloroplast trn L_F sequences alone and combined trn L_F and rbc L sequences. The phylogenetic topologies agree well with Qin's and Takhtajan's tribal classification in both analyses. Decaisneae and Sinofranchetieae are basal clades in the phylogenetic trees and external to all other taxa in the family. Lardizabaleae consisting of Boquila and Lardizabala are well supported in both trn L_F (100%) analysis and trn L_F and rbc L combined analysis (99%). Tribe Akebieae are strongly supported by a bootstrap value of 100% in both trn L_F analysis and trn L_F and rbc L combined analysis. However, the new genus Archakebia is nested within the genus Akebia in the trn L_F trees. In the combined trees, Archakebia is sister to Akebia with high bootstrap support. The inter_relationships among three closely related genera Parvatia , Holboellia and Stauntonia are still problematic. P. brunoniana ssp. elliptica is sister to H. latifolia in both analyses with low bootstrap support. H. parviflora is nested within the Stauntonia and sister to S. cavalerieana . Therefore, these three genera of tribe Akebieae may not be monophylytic and their generic boundary and delimitation need to be further studied, by exploring more molecular data, together with more morphological characters.展开更多
[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homol...[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homologous sequences between them and 11 relative species of Artemia from GenBank were compared;the molecular phylogenetic tree was constructed by Mega Microsoft using Artemiopsis stefanssoni as outgroup.[Result] Artemia persimilis was the primal group in genus Artemia;Artemia franciscana and Artemia monica were the evolved groups;Artemia urmiana,Artemia sinica and other Artemia species from China shared a close genetic relationship.[Conclusion] Based on the 16S rDNA sequence of them,the phylogenetic relationships of these bisexual Artemia species were A.persimilis→A.urmiana,A.sinica and A.tibetiana→A.tunisiana→A.monica→A.Franciscan.展开更多
The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fi...The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fishes. Sister groups A (S. hollandi) and B-E (S. sinensis + S. denticulatus + S. yunnanensis + S. polylepis) represent the first phyletic branching within the genus Spinibarbus. The phyletic division of second sister groups B (S. sinensis) and C-E (S. denticulatus + S. yunnanensis + S. polylepis) is supposed to be resulted from the upheaval of Yunnan-Guizhou Plateau and the subsequent drainages' division. The phyletic division of third sister groups C (S. denticulatus) and D^E (S. yunnanensis + S. polylepis) is supposed to be resulted from the environmental differentiation between Yunnan-Guizhou Plateau and the lowlands of middle and lower Pearl and Yuanjiang Rivers.展开更多
The phylogenetic relationships among the Nepomorpha （Hemiptera： Heteroptera） were analyzed based on nuclear protein coding genes-partial sequences of four Hox genes： abd-A, Dfd, Ubx and pb. Fifteen taxa, of which ...The phylogenetic relationships among the Nepomorpha （Hemiptera： Heteroptera） were analyzed based on nuclear protein coding genes-partial sequences of four Hox genes： abd-A, Dfd, Ubx and pb. Fifteen taxa, of which eleven were ingroups representing ten of the eleven families, were selected to produce a phylogenetic inference of nepomorphan superfamilial or familial relationships via parsimony and Bayesian techniques. Our results supported the monophylies of Nepomorpha, Naucoroidea （Aphelocheiridae ＋ Naucoridae）, Nepoidea （Belostomatidae ＋ Nepidae）, Ochteroidea （Ochteridae ＋ Gelastocoridae） and Pieoidea （Pleidae ＋ Helotrephidae）; the most basal lineage of Ochteroidea; Notonectoidea contained Notonectidae only and formed a new sister relationship with （Pleoidea ＋ Naucoroidea）; and the sister relationship of （Nepoidea ＋ Corixoidea）. The Hox genes are suitable molecular markers to resolve phylogenetic relationships at superfamily or family levels in Heteroptera.展开更多
Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red rive...Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.展开更多
Weaning of piglets is generally considered as a stressor which changes intestinal ecosystem and leads to clinical implications. Microbiota inhabiting in small intestine （especially ileum） are assumed to promote heal...Weaning of piglets is generally considered as a stressor which changes intestinal ecosystem and leads to clinical implications. Microbiota inhabiting in small intestine （especially ileum） are assumed to promote health, but their functional properties are yet poody dascdbed. As indicated by the 16S rRNA gene sequences of ileal micrebiota in nursing piglets （at the age of 21 and 28 d） and 28-day-old weaned piglets （weaned at 21 d of age）, the microbiota were mainly comprised of gram-positive bacteria. There were 40 operational taxonomic units （OTUs） （from 171 clones） in the ileum of nursing piglets aged 21 d, 61 OTUs （from 194 clones） in the ileum of nursing piglets aged 28 d, and 56 OTUs （from 171 clones） in the ileum of weaned piglets aged 28 d. The flea of nursing piglets aged 21 d were dominantly occupied by Lactobacilli （87.7%） as well as Streptococ cus （ 3.5 % ）. Lactobacillus amy/ovorus （41.5 % ）, Lactobaci/lus sp. （ 19.3 % ）, Lactobaci/lus reuteri （ 12.3 % ）, Lactobacillus salivarius （ 9.4 % ） and L. mucosae （4.7%） were the predominant species among Lactobacil/L Similar results were obtained in the nursing piglets at 28 d of age ex- cept that Lactobaci/li decreased to 71.1% and Streptococcus increased to 21.1% significantly. Lactobacillus （52.0%） and Streptococcus （26.3%） were the two major groups in the ileum of weaned piglets aged 28 d. Lactobacillus amylovorus （31.6%） and Lactobaci/lus reuteri （ 16.4% ） was the two most important species in Lactobacillus. Therefore, Lactobacilli were predominant in the ileum of nursing and weaned piglets, and they had the highest diversity, followed by Streptococcus. The diversity of ileal microbiota was not different remarkably between the nursing piglets and the weaned piglets, but the composition changed significantly. These findings are helpful to understand ileal bacterial ecophysiology and further develop nutritional regimes to prevent or counteract complications during the weaning transition.展开更多
The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from ten species of Chloranthus Swartz and two outgroup species of Sarcandra Gardn. were sequenced. The regions ranged in length from 654 to 663 b...The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from ten species of Chloranthus Swartz and two outgroup species of Sarcandra Gardn. were sequenced. The regions ranged in length from 654 to 663 bp, with ITS1 (285-290 bp) slightly longer than ITS2 (205-211 bp). Of the 669 aligned positions, 109 sites (56 in ITS1, 52 in ITS2, and one in 5.8S region) were phylogenetically informative. Only one most parsimonious tree of 252 steps was obtained in PAUP analysis when gaps were treated as the fifth state. The traditional division of Chloranthus on the basis of habit seems to be quite unnatural. Evidence from the sequence of ITS region, just as that from cytology and anatomy, strongly suggested the separation of the genus into two groups according to the characteristics of androecial organs: one contains C. angustifolius, C. nervosus, C. japonicus and C. fortunei, and the other comprises the remaining species.展开更多
In order to analyze skull variation in the genus Macaca ,seventy seven craniodental variables were taken from eleven species.They were first defined seven functional units comprising three anatomical regions.Twenty s...In order to analyze skull variation in the genus Macaca ,seventy seven craniodental variables were taken from eleven species.They were first defined seven functional units comprising three anatomical regions.Twenty seven variables were finally selected to carry out the morphology of the whole skull.The data,organized in these ways,were examined to discover variations between and within the various species.The methods used were Principal Components Analysis (PCA) and Discriminant Function Analysis (DFA).PCAs of the functional units anatomical regions,and the whole skull provided similar,though not identical,separations of species clusters in both sexes separately.These differences in structure could be related to size,sexual dimorphism,diet,ecology,classification and phylogeny.The question of size should have been easy to settle.Unfortunately,this is not the case.In this study where the raw data are measurements of the specimens,the main differences should be size.However,the size differences seem to occur in both the first and second (independent) multivariate axes.In some analyses the size differences between the species are biggest and appear in the first axis.In other analyses it is the separation between the sexes (and these too are largely size) that are the biggest and appear in the first axis.Yet in other analyses,both of these size separations,though still orthogonal to one another,present in the combination of the first two axes.This certainly implies that a single axis of body size is not present and that shape differences have not been isolated form size differences.It also implies that sexual dimorphism is a complex matter.As a result,the question of the relationships between the species is therefore also complex.One cluster of species that includes M fascicularis,M sinica and M radiata was significantly isolated from all others regardless of level of analysis.This relationship is quite different from that proposed on the anatomy of the reproductive organs (Delson,1980;Fooden,1976,1980).展开更多
Nucleotide sequences of segments of the mitochondrial control regions were analyzed to infer the phylogenetic relationships among 7 macaques.High nucleotide diversity in Macaca assamensis and relatively low diversity ...Nucleotide sequences of segments of the mitochondrial control regions were analyzed to infer the phylogenetic relationships among 7 macaques.High nucleotide diversity in Macaca assamensis and relatively low diversity in M.thibetana were found.Based on the ML tree from control regions,species in our study can roughly be sorted into three species groups except for the phylogenetic position of M.fascicularis,i.e.,silenus group,including M.leonina;sinica group,including M.arctoides,M.assamensis,and M.thibetana;and fascicularis group,including M.mulatta and M.cyclopis.A discrepancy between earlier studies (Fooden & Lanyon,1989;Tosi et al,2003a;Deinard & Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales & Melnick,1998),our result supported the hypothesis that M.fascicularis diverged earlier than M.leonina.Mitochondrial paraphyly in eastern M.mulatta (with respect to M.cyclopis) and eastern M.assamensis (with respect to M.thibetana) were clearly observed in our study.In accordance with the results of Y chromosome,allozyme,nuclear genes and some morphological data (Delson,1980;Fooden & Lanyon,1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard & Smith,2001),our study on control region sequences supported M.arctoides to be classified into the sinica group.However,this result disagreed with the previous mtDNA studies (Hayasaka et al,1996;Morales & Melnick,1998;Tosi et al,2003a).展开更多
Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strai...Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10 236 715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9 228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel ＇quasicore＇ with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.展开更多
To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA geneare sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining ...To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA geneare sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining method.Coleoids are divided into two main lineages, Decabrachia and Octobrachia. The monophyly of the order Sepioidea,which includes the families Sepiidae, Sepiolidae and Idiosepiidae , is not supported. From the two families ofSepioidea examined, the Sepiolidae are polyphyletic and are excluded from the order. On the basis of 16S rRNA andamino acid of COI gene sequences data, the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished, butdo not have a visible boundary using COI gene sequences. The reason is explained. This suggests that the 16S rDNAof cephalopods is a precious tool to analyze taxonomic relationships at the genus level, and COI gene is fitter at ahigher taxonomic level (i.e., family).展开更多
基金Supported by the Research and Development Program of Shandong Province,China(Major Science and Technology Innovation Project)(No.2021CXGC011306)the MNR Key Laboratory of Eco-Environmental Science and Technology,China(No.MEEST-2021-05)+2 种基金the Natural Science Foundation of Shandong Province(No.ZR2020MD002)the Doctoral Science Research Foundation of Yantai University(Nos.SM15B01,SM19B70,SM19B28)the“Double-Hundred Action”of Yantai City(No.2320004-SM20RC02)。
文摘Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.
基金partially supported by the Natural Science Foundation of China (#31900186,#32260050)Yunnan Fundamental Research Projects (Grant NO.202301BF07001-016)the Glory Light International Fellowship for Chinese Botanists at Missouri Botanical Garden (MO) to X.M.Zhou
文摘Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74%increase of the earlier largest sampling)representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylogenetic context.Our major results include:(1)the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades;(2)the Sinensis group is resolved as sister to S.subg.Pulviniella with strong support in two of the three analyses;(3)most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family;and(4)an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l.is split into seven subfamilies(corresponding to the current six subgenera t the Sinensis group)and 19 genera(the major diagnosable clades)with nine new species-poor genera.We support the conservation of Selaginella with a new type,S.flabellata,to minimize nomenclatural instability.We provide a key to subfamilies and genera,images illustrating their morphology,their morphological and geographical synopses,a list of constituent species,and necessary new combinations.This new classification will hopefully facilitate communication,promote further studies,and help conservation.
基金supported by the National Key Research and Development Projects of the Ministry of Science and Technology of China (2021YFC2301300)National Natural Science Foundation of China (82050002,32070528,32100335,32000287)Beijing Natural Sciences Foundation for Distinguished Young Scholars (JQ19022)。
文摘The timing of mammalian diversification in relation to the Cretaceous-Paleogene(KPg)mass extinction continues to be a subject of substantial debate.Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples.In the present study,we improved an existing dataset from the landmark study of Meredith et al.(2011)by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers.Using these two datasets,we then constructed phylogenies for extant mammalian families,providing improved resolution of many conflicting relationships.Moreover,the timetrees generated,which were calibrated using appropriate molecular clock models and multiple fossil records,indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period.Additionally,intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary,supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification.Thus,our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.
基金the National Natural Science Foundation of China(Nos.41871037,31800172,32170204)the Fund for Shanxi‘1331 Project’.
文摘The marine and freshwater Hildenbrandia samples were collected from diverse locations of China and Japan,and mor-phological characterization and molecular phylogenetic analysis were conducted on these samples.Morphological measurements of freshwater specimens were consistent with the results of H.jigongshanensis,whereas cell dimensions of marine specimens were slightly larger than those of widely distributed H.rubra and H.crouanii.Phylogenetic trees based on rbcL,psbA and UPA sequences were consistent.Freshwater specimens collected in this study formed an independent clade with H.jigongshanensis supported by high values.Species attribution was confirmed further by the similar ITS2 secondary structures among the samples of H.jigongshan-ensis.It was found that the intraspecific divergence of rbcL gene in H.jigongshanensis was smaller than other two freshwater species H.rivularis and H.angolensis.Phylogenetic trees showed that marine specimens in this study grouped together with H.rubra samples of North America,and were different with the H.rubra samples of Europe.Combining the comparison results of CBC numbers in ITS2 secondary structure,we propose the marine samples collected in this study to be a new species Hildenbrandia qingdaoensis sp.nov.The separation of the marine and freshwater specimens was supported by the rbcL,UPA and psbA phylogeny as well as ITS2 se-condary structure inference.Biogeographical reconstruction showed the ancestor of freshwater Hildenbrandia might derive from South America and dispersed from North America to Europe and then to Asian countries,which needs to be verified further with more sam-ples and molecular evidences from South America.
文摘Cholera is a significant public health threat across the globe, especially in coastal regions with poor water supply. This study was carried out to determine the antibiogram, genomic, and phylogeny of stool and seafood isolates from some cholera-prone coastal communities in Rivers State, Nigeria. A total of 400 stool samples and 42 different seafood were aseptically collected and examined using standard microbiology and molecular techniques. An antibiogram of isolates from seafood and stool samples was assayed. Genes for virulence, resistance, and relatedness of bacteria identified were also determined. The isolates from the stool and seafood were examined for susceptibility to some selected antibiotics. The findings showed the prevalence rate of cholera in the communities as follows: 16% in Kaa, 30% in Andoni, 4% in Ogu/Bolo, and 10% in Abua/Odual. The isolates from stool were susceptible to Ciprofloxacin and Gentamycin with a susceptibility rate of 94.12% each while 100% resistance was recorded against Amoxicillin-clavulanic acid, 94.12% against Amikacin and 88.24% against Colistin. For the sea foods, the isolates were susceptible to gentamycin and ciprofloxacin with a susceptibility rate of 91.43% and 82.86% respectively. Resistance was also recorded against Colistin (88.57%) and Azithromycin (82.86%). Testing the isolates for the presence of 16SrRNA genes showed that all were positive with 1500 bp 16SrRNA gene band size. TEM, OXA, SHV, and CTX-M resistant genes were detected whereas the virulence genes were TDH and AcrB. The phylogenetic analysis revealed isolates from seafood to be Aeromonas dhakensis, Vibrio parahaemolyticus, Vibrio azureus, and Providencia rettgeri, while in stool samples they were Enterobacter sichuanensis, Enterobacter hormaechei, Providencia sneebia, and Proteus vulgaris. Providencia stuartii, Proteus mirabilis, Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae were common isolates from both seafood and stool samples. This study has shown that not all reported cases of cholera are caused by Vibrio cholerae. Therefore, attention should be paid to other water-borne bacteria in every outbreak, especially in coastal communities.
基金This work was supported by National Natural Science Foundation of China (No. 30570247)the Natural Science Foundation of Shanxi Province (No. 2003-1087)
文摘The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.
基金Supported by National Natural Science Foundation of China(30160015)
文摘The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as sample taxa. The sequence constitutions and variations were analyzed and the molecular phylogenetic trees were reconstructed based on the combined sequence data （795bp length in total） of 12S rDNA and 16S rDNA, using the grasshopper Pyrgomorpha conica of Pyrgomorphidae as the outgroup. The results showed that the rates of the two kinds of transitions are obviously much higher than that of the four kinds of Wansversions in these combined 12S＋16S rDNA sequence data. The saturation ofnucleotide substitutions happened in 12S and 16S rDNA sequence data. The molecular phylogenetic trees indicated that Oedipodinae is a monophyletic group and this subfamily is a natural one, but Catantopinae and Acridinae are non-monophyletic. Oedipodnae is a relatively primitive group within the Acrididae, whereas the Oxyinae may have diverged later than Oedipodinae, but earlier than most other species of Acridide.
文摘The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trn L-F region were sequenced for 41 species of the Aceraceae, representing both genera Acer and Dipteronia, to reconstruct phylogeny of this family, especially within Acer. The analyses were performed in separate and combined sequence data sets, with the Sapindaceae and Hippocastanaceae being selected as outgroups. It was indicated that the Aceraceae was monophyletic and D. sinensis was basal to the rest of the family but the two genera of it might be not monophyletic because Dipteronia dyerana was nested within Acer. The result inferred from the combined data showed greater resolution within Acer than that from the two separate data sets. The monophyly of most sections in Xu's system (1996) were supported with high bootstrap values, and some relationships between (or among) sections were also inferred, such as sect. Palmata and sect. Microcarpa; sect. Platanoidea, sect. Lithocarpa and sect. Macrophylla; sect. Integrifolia, sect. Trifoliata and sect. Pentaphylla; and sect. Acer, sect. Goniocarpa and sect. Saccharina (sensu Ogata). However, the sectional status and circumscriptions of some of the above-mentioned sections should be further adjusted. It seemed that the Xu's delimitations of sect. Rubra and sect. Saccharodendran should be revaluated.
文摘The molecular phylogeny of the Lardizabalaceae is reconstructed based on chloroplast trn L_F sequences alone and combined trn L_F and rbc L sequences. The phylogenetic topologies agree well with Qin's and Takhtajan's tribal classification in both analyses. Decaisneae and Sinofranchetieae are basal clades in the phylogenetic trees and external to all other taxa in the family. Lardizabaleae consisting of Boquila and Lardizabala are well supported in both trn L_F (100%) analysis and trn L_F and rbc L combined analysis (99%). Tribe Akebieae are strongly supported by a bootstrap value of 100% in both trn L_F analysis and trn L_F and rbc L combined analysis. However, the new genus Archakebia is nested within the genus Akebia in the trn L_F trees. In the combined trees, Archakebia is sister to Akebia with high bootstrap support. The inter_relationships among three closely related genera Parvatia , Holboellia and Stauntonia are still problematic. P. brunoniana ssp. elliptica is sister to H. latifolia in both analyses with low bootstrap support. H. parviflora is nested within the Stauntonia and sister to S. cavalerieana . Therefore, these three genera of tribe Akebieae may not be monophylytic and their generic boundary and delimitation need to be further studied, by exploring more molecular data, together with more morphological characters.
基金Supported by National Natural Science Foundation of China(30770263)~~
文摘[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homologous sequences between them and 11 relative species of Artemia from GenBank were compared;the molecular phylogenetic tree was constructed by Mega Microsoft using Artemiopsis stefanssoni as outgroup.[Result] Artemia persimilis was the primal group in genus Artemia;Artemia franciscana and Artemia monica were the evolved groups;Artemia urmiana,Artemia sinica and other Artemia species from China shared a close genetic relationship.[Conclusion] Based on the 16S rDNA sequence of them,the phylogenetic relationships of these bisexual Artemia species were A.persimilis→A.urmiana,A.sinica and A.tibetiana→A.tunisiana→A.monica→A.Franciscan.
文摘The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fishes. Sister groups A (S. hollandi) and B-E (S. sinensis + S. denticulatus + S. yunnanensis + S. polylepis) represent the first phyletic branching within the genus Spinibarbus. The phyletic division of second sister groups B (S. sinensis) and C-E (S. denticulatus + S. yunnanensis + S. polylepis) is supposed to be resulted from the upheaval of Yunnan-Guizhou Plateau and the subsequent drainages' division. The phyletic division of third sister groups C (S. denticulatus) and D^E (S. yunnanensis + S. polylepis) is supposed to be resulted from the environmental differentiation between Yunnan-Guizhou Plateau and the lowlands of middle and lower Pearl and Yuanjiang Rivers.
基金supported by the Natural Science Foundation of China(Nos.30725005,31071959,J0930005)supported by the Ministry of Education of China(No.20100031110026)
文摘The phylogenetic relationships among the Nepomorpha （Hemiptera： Heteroptera） were analyzed based on nuclear protein coding genes-partial sequences of four Hox genes： abd-A, Dfd, Ubx and pb. Fifteen taxa, of which eleven were ingroups representing ten of the eleven families, were selected to produce a phylogenetic inference of nepomorphan superfamilial or familial relationships via parsimony and Bayesian techniques. Our results supported the monophylies of Nepomorpha, Naucoroidea （Aphelocheiridae ＋ Naucoridae）, Nepoidea （Belostomatidae ＋ Nepidae）, Ochteroidea （Ochteridae ＋ Gelastocoridae） and Pieoidea （Pleidae ＋ Helotrephidae）; the most basal lineage of Ochteroidea; Notonectoidea contained Notonectidae only and formed a new sister relationship with （Pleoidea ＋ Naucoroidea）; and the sister relationship of （Nepoidea ＋ Corixoidea）. The Hox genes are suitable molecular markers to resolve phylogenetic relationships at superfamily or family levels in Heteroptera.
文摘Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.
基金Supported by grants from Knowledge Innovation Project of Chinese Academy of Sciences (KSCX2-YW-N-051 and SW-323)NSFC(30901040, 30901041, 30928018, 30828025, 30700581, and 30771558)+2 种基金National Basic Research Program of China(2009CB118800)National 863 project (2008AA10Z316)National Scientific and Technological Supporting Project(2007BAQ01047 and 2006BAD12B07)~~
文摘Weaning of piglets is generally considered as a stressor which changes intestinal ecosystem and leads to clinical implications. Microbiota inhabiting in small intestine （especially ileum） are assumed to promote health, but their functional properties are yet poody dascdbed. As indicated by the 16S rRNA gene sequences of ileal micrebiota in nursing piglets （at the age of 21 and 28 d） and 28-day-old weaned piglets （weaned at 21 d of age）, the microbiota were mainly comprised of gram-positive bacteria. There were 40 operational taxonomic units （OTUs） （from 171 clones） in the ileum of nursing piglets aged 21 d, 61 OTUs （from 194 clones） in the ileum of nursing piglets aged 28 d, and 56 OTUs （from 171 clones） in the ileum of weaned piglets aged 28 d. The flea of nursing piglets aged 21 d were dominantly occupied by Lactobacilli （87.7%） as well as Streptococ cus （ 3.5 % ）. Lactobacillus amy/ovorus （41.5 % ）, Lactobaci/lus sp. （ 19.3 % ）, Lactobaci/lus reuteri （ 12.3 % ）, Lactobacillus salivarius （ 9.4 % ） and L. mucosae （4.7%） were the predominant species among Lactobacil/L Similar results were obtained in the nursing piglets at 28 d of age ex- cept that Lactobaci/li decreased to 71.1% and Streptococcus increased to 21.1% significantly. Lactobacillus （52.0%） and Streptococcus （26.3%） were the two major groups in the ileum of weaned piglets aged 28 d. Lactobacillus amylovorus （31.6%） and Lactobaci/lus reuteri （ 16.4% ） was the two most important species in Lactobacillus. Therefore, Lactobacilli were predominant in the ileum of nursing and weaned piglets, and they had the highest diversity, followed by Streptococcus. The diversity of ileal microbiota was not different remarkably between the nursing piglets and the weaned piglets, but the composition changed significantly. These findings are helpful to understand ileal bacterial ecophysiology and further develop nutritional regimes to prevent or counteract complications during the weaning transition.
文摘The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from ten species of Chloranthus Swartz and two outgroup species of Sarcandra Gardn. were sequenced. The regions ranged in length from 654 to 663 bp, with ITS1 (285-290 bp) slightly longer than ITS2 (205-211 bp). Of the 669 aligned positions, 109 sites (56 in ITS1, 52 in ITS2, and one in 5.8S region) were phylogenetically informative. Only one most parsimonious tree of 252 steps was obtained in PAUP analysis when gaps were treated as the fifth state. The traditional division of Chloranthus on the basis of habit seems to be quite unnatural. Evidence from the sequence of ITS region, just as that from cytology and anatomy, strongly suggested the separation of the genus into two groups according to the characteristics of androecial organs: one contains C. angustifolius, C. nervosus, C. japonicus and C. fortunei, and the other comprises the remaining species.
文摘In order to analyze skull variation in the genus Macaca ,seventy seven craniodental variables were taken from eleven species.They were first defined seven functional units comprising three anatomical regions.Twenty seven variables were finally selected to carry out the morphology of the whole skull.The data,organized in these ways,were examined to discover variations between and within the various species.The methods used were Principal Components Analysis (PCA) and Discriminant Function Analysis (DFA).PCAs of the functional units anatomical regions,and the whole skull provided similar,though not identical,separations of species clusters in both sexes separately.These differences in structure could be related to size,sexual dimorphism,diet,ecology,classification and phylogeny.The question of size should have been easy to settle.Unfortunately,this is not the case.In this study where the raw data are measurements of the specimens,the main differences should be size.However,the size differences seem to occur in both the first and second (independent) multivariate axes.In some analyses the size differences between the species are biggest and appear in the first axis.In other analyses it is the separation between the sexes (and these too are largely size) that are the biggest and appear in the first axis.Yet in other analyses,both of these size separations,though still orthogonal to one another,present in the combination of the first two axes.This certainly implies that a single axis of body size is not present and that shape differences have not been isolated form size differences.It also implies that sexual dimorphism is a complex matter.As a result,the question of the relationships between the species is therefore also complex.One cluster of species that includes M fascicularis,M sinica and M radiata was significantly isolated from all others regardless of level of analysis.This relationship is quite different from that proposed on the anatomy of the reproductive organs (Delson,1980;Fooden,1976,1980).
文摘Nucleotide sequences of segments of the mitochondrial control regions were analyzed to infer the phylogenetic relationships among 7 macaques.High nucleotide diversity in Macaca assamensis and relatively low diversity in M.thibetana were found.Based on the ML tree from control regions,species in our study can roughly be sorted into three species groups except for the phylogenetic position of M.fascicularis,i.e.,silenus group,including M.leonina;sinica group,including M.arctoides,M.assamensis,and M.thibetana;and fascicularis group,including M.mulatta and M.cyclopis.A discrepancy between earlier studies (Fooden & Lanyon,1989;Tosi et al,2003a;Deinard & Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales & Melnick,1998),our result supported the hypothesis that M.fascicularis diverged earlier than M.leonina.Mitochondrial paraphyly in eastern M.mulatta (with respect to M.cyclopis) and eastern M.assamensis (with respect to M.thibetana) were clearly observed in our study.In accordance with the results of Y chromosome,allozyme,nuclear genes and some morphological data (Delson,1980;Fooden & Lanyon,1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard & Smith,2001),our study on control region sequences supported M.arctoides to be classified into the sinica group.However,this result disagreed with the previous mtDNA studies (Hayasaka et al,1996;Morales & Melnick,1998;Tosi et al,2003a).
基金This paper is dedicated to the late Professor JS Chiao, who initiated the research in China for rifamycin production employing A. mediterranei more than 30 years ago and who continued the endeavor to resolve the mechanism of the ＇nitrate stimulating effect＇ up to the last breath of his life. This work was supported by the National Natural Science Foundation of China （30830002）, the National High Technology Research and Development Program of China （2007AA021301, 2007AA021503）, and the Research Unit Fund of Li Ka Shing Institute of Health Sciences （7103506）.
文摘Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10 236 715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9 228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel ＇quasicore＇ with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.
文摘To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA geneare sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining method.Coleoids are divided into two main lineages, Decabrachia and Octobrachia. The monophyly of the order Sepioidea,which includes the families Sepiidae, Sepiolidae and Idiosepiidae , is not supported. From the two families ofSepioidea examined, the Sepiolidae are polyphyletic and are excluded from the order. On the basis of 16S rRNA andamino acid of COI gene sequences data, the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished, butdo not have a visible boundary using COI gene sequences. The reason is explained. This suggests that the 16S rDNAof cephalopods is a precious tool to analyze taxonomic relationships at the genus level, and COI gene is fitter at ahigher taxonomic level (i.e., family).
