东帕米尔高原作为生物多样性丰富的区域之一,喜马拉雅雪鸡和藏雪鸡在此混群分布。以东帕米尔高原喜马拉雅雪鸡为研究对象,采用PCR和测序技术,研究了mt DNA D-loop区序列特征,下载Gen Bank已提交的雪鸡序列,利用最大似然法构建系统发育...东帕米尔高原作为生物多样性丰富的区域之一,喜马拉雅雪鸡和藏雪鸡在此混群分布。以东帕米尔高原喜马拉雅雪鸡为研究对象,采用PCR和测序技术,研究了mt DNA D-loop区序列特征,下载Gen Bank已提交的雪鸡序列,利用最大似然法构建系统发育树和中介网络关系,以阐明东帕米尔高原喜马拉雅雪鸡遗传多样性水平和系统进化地位。结果表明:东帕米尔高原喜马拉雅雪鸡mt DNA D-loop序列富含A、T碱基,含量为59.8%,存在64个多态位点,占核苷酸总数的5.5%,其中单一多态位点29个,简约信息位点33个,两处插入或缺失,转换发生的频率远远高于颠换;25个个体存在23种单倍型,平均单倍型多样度(Hd)为0.92±0.0001,平均核苷酸多样度(π)为0.00958,平均核苷酸差异度(K)为11.067,说明东帕米尔高原喜马拉雅雪鸡核苷酸多样性较低,单倍型多样性高,具有较为丰富的遗传多样性;系统发育分析显示喜马拉雅雪鸡与藏雪鸡分为明显的两大簇群,本研究涉及的东帕米尔高原喜马拉雅雪鸡出现遗传分化,呈现明显的2个进化支;中介网络关系分析显示雪鸡具有明显的地理分布特征,本研究雪鸡84%的单倍型聚在以东帕米尔高原为中心的进化支上。因此,建议扩大塔什库尔干野生动物自然保护区(位于东帕米尔高原境内)范围,建立国家级自然保护区,恢复生态环境,以提高雪鸡栖息地的生存适宜性。展开更多
This study addressed three important aims:(1) undermining the previously obtained raw data about wood-decaying fungi(WDF) distribution and continuously investigating permanent plots to address certain scientific quest...This study addressed three important aims:(1) undermining the previously obtained raw data about wood-decaying fungi(WDF) distribution and continuously investigating permanent plots to address certain scientific questions in ecology,(2) resolving the higher-level phylogeny of WDF with the help of multiple loci,and(3) testing and estimating the medicinal values of species that are closely related to well-known medicinal species.More than 1200 species and 2469 strains of WDF in China were identified from 28908 specimens collected from a series of field investigations.Using these materials,studies in multiple disciplines,such as ecology,taxonomy and phylogeny,and medicine,have been performed.With respect to ecology,the diversity of wood-decaying polypores significantly differed among a boreal forest zone,a temperate and warm temperate forest zone,and a tropical and subtropical forest zone.For instance,from north to south,the number and proportion of brown-rot species and the proportion of species found on fallen trunks were both decreased.The ecological patterns of wood-decaying polypores on gymnosperm and angiosperm trees were also explored by a case study in Northeast China.Although the total species richness was similar between the two tree groups,several other characteristics were significantly different,such as community structure and richness in certain substrates.The taxonomy and phylogeny of wide samples were referred to and their phylogenetic positions were resolved or at least partially established.In particular,phylogenetic knowledge about four genera,Fomitiporia,Ganoderma,Inonotus and Perenniporia,which include medicinal species,was essential for further research to determine the medicinal values of these types of fungi.Among these medicinal species,we mainly focused on Inonotus obliquus for its medicinal purposes.Polyphenols,polysaccharides and lanostane-type triterpenoids,extracted from the sterile conk of this species,could dramatically decrease levels of free radicals,DPPH and hydroxyl radicals,respectively.The metabolic profiles(both production and composition) of cultured I.obliquus mycelia could be altered by co-culture with other medicinal species or by induction of S-nitrosylation and denitrosylation,which may enhance the antioxidant capacity of I.obliquus.展开更多
The mitochondrial genome complete sequence of Achalinus meiguensis was reported for the first time in the present study. The complete mitochondrial genome of A. meiguensis is 17239 bp in length and contains 13 protein...The mitochondrial genome complete sequence of Achalinus meiguensis was reported for the first time in the present study. The complete mitochondrial genome of A. meiguensis is 17239 bp in length and contains 13 protein-coding genes, 22 tRNA, 2 rRNA, and 2 non-coding regions (Control regions). On the basis of comparison with the other complete mitochondrial sequences reported, we explored the characteristic of structure and evolution. For example, duplication control regions independently occurred in the evolutionary history of reptiles; the pseudo-tRNA of snakes occurred in the Caenophidia; snake is shorter than other vertebrates in the length of tRNA because of the truncations of TΨC arm (less than 5 bp) and "DHU" arm. The phylogenic analysis by MP and BI analysis showed that the phylogenetic position of A. meiguensis was placed in Caenophidia as a sister group to other advanced snakes with the exclusion of Acrochordus granulatus which was rooted in the Caenophidia. Therefore we suggested that the subfamily Xenodermatinae, which contains A. meiguensis, should be raised to a family rank or higher rank. At the same time, based on the phylogenic statistic test, the tree of Bayesian was used for estimating the divergence time. The results showed that the divergence time between Henophidia and Caenophidia was 109.50 Mya; 106.18 Mya for divergence between Acrochordus granulatus and the other snakes of the Caenophidia; the divergence time of A. meiguensis was 103 Mya, and Viperidae diverged from the unilateral of Elapidae and Colubridae was 96.06 Mya.展开更多
Bacteria need a high degree of genetic stability to maintain their species identities over long evolutionary times while retaining some mutability to adapt to the changing environment.It is a long unanswered question ...Bacteria need a high degree of genetic stability to maintain their species identities over long evolutionary times while retaining some mutability to adapt to the changing environment.It is a long unanswered question that how bacteria reconcile these seemingly contradictory biological properties.We hypothesized that certain mechanisms must maintain a dynamic balance between genetic stability and mutability for the survival and evolution of bacterial species.To identify such mechanisms,we analyzed bacterial genomes,focusing on the Salmonella mismatch repair(MMR)system.We found that the MMR gene mutL functions as a genetic switch through a slipped-strand mispairing mechanism,modulating and maintaining a dynamic balance between genetic stability and mutability during bacterial evolution.This mechanism allows bacteria to maintain their phylogenetic status,while also adapting to changing environments by acquiring novel traits.In this review,we outline the history of research into this genetic switch,from its discovery to the latest findings,and discuss its potential roles in the genomic evolution of bacteria.展开更多
In order to elucidate the genetic diversity and taxonomic status of Siberian roe deer(Capreolus pygargus)from the Korean peninsula,partial sequences of the mitochondrial cytochrome b gene were analyzed.We collected 57...In order to elucidate the genetic diversity and taxonomic status of Siberian roe deer(Capreolus pygargus)from the Korean peninsula,partial sequences of the mitochondrial cytochrome b gene were analyzed.We collected 57 roe deer samples from Mainland and Jeju Island between July 2004 and June 2009.A total of 50 sequences(1,070 bp)were obtained,and seven haplotypes were defined.Five haplotypes were found from Mainland,and two were discovered from Jeju Island.The genetic diversity was lower in the Jeju Island population than in the Mainland population.In addition,both the consensus neighbor-joining tree and maximum parsimony tree showed an identical topology between the Mainland and Jeju Island clades.Based on the results,two subspecies of the Korean roe deer were confirmed.Siberian roe deer in Jeju Island showed a distinct difference in the cytochrome b gene compared with other Siberian roe deer,being aunique native species inhabiting only Jeju Island in Korea.Because Siberian roe deer in Jeju Island can be classified at subspecies level,the new subspecies in Jeju was named Capreolus pygargus jejuensis in this study.For this new subspecies,reasonable conservation and management effort is needed in the future.展开更多
文摘东帕米尔高原作为生物多样性丰富的区域之一,喜马拉雅雪鸡和藏雪鸡在此混群分布。以东帕米尔高原喜马拉雅雪鸡为研究对象,采用PCR和测序技术,研究了mt DNA D-loop区序列特征,下载Gen Bank已提交的雪鸡序列,利用最大似然法构建系统发育树和中介网络关系,以阐明东帕米尔高原喜马拉雅雪鸡遗传多样性水平和系统进化地位。结果表明:东帕米尔高原喜马拉雅雪鸡mt DNA D-loop序列富含A、T碱基,含量为59.8%,存在64个多态位点,占核苷酸总数的5.5%,其中单一多态位点29个,简约信息位点33个,两处插入或缺失,转换发生的频率远远高于颠换;25个个体存在23种单倍型,平均单倍型多样度(Hd)为0.92±0.0001,平均核苷酸多样度(π)为0.00958,平均核苷酸差异度(K)为11.067,说明东帕米尔高原喜马拉雅雪鸡核苷酸多样性较低,单倍型多样性高,具有较为丰富的遗传多样性;系统发育分析显示喜马拉雅雪鸡与藏雪鸡分为明显的两大簇群,本研究涉及的东帕米尔高原喜马拉雅雪鸡出现遗传分化,呈现明显的2个进化支;中介网络关系分析显示雪鸡具有明显的地理分布特征,本研究雪鸡84%的单倍型聚在以东帕米尔高原为中心的进化支上。因此,建议扩大塔什库尔干野生动物自然保护区(位于东帕米尔高原境内)范围,建立国家级自然保护区,恢复生态环境,以提高雪鸡栖息地的生存适宜性。
基金supported by the National Natural Science Foundation of China (30910103907,31070022)
文摘This study addressed three important aims:(1) undermining the previously obtained raw data about wood-decaying fungi(WDF) distribution and continuously investigating permanent plots to address certain scientific questions in ecology,(2) resolving the higher-level phylogeny of WDF with the help of multiple loci,and(3) testing and estimating the medicinal values of species that are closely related to well-known medicinal species.More than 1200 species and 2469 strains of WDF in China were identified from 28908 specimens collected from a series of field investigations.Using these materials,studies in multiple disciplines,such as ecology,taxonomy and phylogeny,and medicine,have been performed.With respect to ecology,the diversity of wood-decaying polypores significantly differed among a boreal forest zone,a temperate and warm temperate forest zone,and a tropical and subtropical forest zone.For instance,from north to south,the number and proportion of brown-rot species and the proportion of species found on fallen trunks were both decreased.The ecological patterns of wood-decaying polypores on gymnosperm and angiosperm trees were also explored by a case study in Northeast China.Although the total species richness was similar between the two tree groups,several other characteristics were significantly different,such as community structure and richness in certain substrates.The taxonomy and phylogeny of wide samples were referred to and their phylogenetic positions were resolved or at least partially established.In particular,phylogenetic knowledge about four genera,Fomitiporia,Ganoderma,Inonotus and Perenniporia,which include medicinal species,was essential for further research to determine the medicinal values of these types of fungi.Among these medicinal species,we mainly focused on Inonotus obliquus for its medicinal purposes.Polyphenols,polysaccharides and lanostane-type triterpenoids,extracted from the sterile conk of this species,could dramatically decrease levels of free radicals,DPPH and hydroxyl radicals,respectively.The metabolic profiles(both production and composition) of cultured I.obliquus mycelia could be altered by co-culture with other medicinal species or by induction of S-nitrosylation and denitrosylation,which may enhance the antioxidant capacity of I.obliquus.
文摘The mitochondrial genome complete sequence of Achalinus meiguensis was reported for the first time in the present study. The complete mitochondrial genome of A. meiguensis is 17239 bp in length and contains 13 protein-coding genes, 22 tRNA, 2 rRNA, and 2 non-coding regions (Control regions). On the basis of comparison with the other complete mitochondrial sequences reported, we explored the characteristic of structure and evolution. For example, duplication control regions independently occurred in the evolutionary history of reptiles; the pseudo-tRNA of snakes occurred in the Caenophidia; snake is shorter than other vertebrates in the length of tRNA because of the truncations of TΨC arm (less than 5 bp) and "DHU" arm. The phylogenic analysis by MP and BI analysis showed that the phylogenetic position of A. meiguensis was placed in Caenophidia as a sister group to other advanced snakes with the exclusion of Acrochordus granulatus which was rooted in the Caenophidia. Therefore we suggested that the subfamily Xenodermatinae, which contains A. meiguensis, should be raised to a family rank or higher rank. At the same time, based on the phylogenic statistic test, the tree of Bayesian was used for estimating the divergence time. The results showed that the divergence time between Henophidia and Caenophidia was 109.50 Mya; 106.18 Mya for divergence between Acrochordus granulatus and the other snakes of the Caenophidia; the divergence time of A. meiguensis was 103 Mya, and Viperidae diverged from the unilateral of Elapidae and Colubridae was 96.06 Mya.
基金supported by a Heilongjiang Innovation Endowment Award for graduate studies(YJSCX2012-197HLJ)to Tang Lea grant from the National Natural Science Foundation of China(NSFC30970078)+1 种基金the Natural Science Foundation of Heilongjiang Province to Liu GuiRongthe National Natural Science Foundation of China(NSFC30970119,81030029,81271786,NSFC-NIH 81161120416)to Liu ShuLin
文摘Bacteria need a high degree of genetic stability to maintain their species identities over long evolutionary times while retaining some mutability to adapt to the changing environment.It is a long unanswered question that how bacteria reconcile these seemingly contradictory biological properties.We hypothesized that certain mechanisms must maintain a dynamic balance between genetic stability and mutability for the survival and evolution of bacterial species.To identify such mechanisms,we analyzed bacterial genomes,focusing on the Salmonella mismatch repair(MMR)system.We found that the MMR gene mutL functions as a genetic switch through a slipped-strand mispairing mechanism,modulating and maintaining a dynamic balance between genetic stability and mutability during bacterial evolution.This mechanism allows bacteria to maintain their phylogenetic status,while also adapting to changing environments by acquiring novel traits.In this review,we outline the history of research into this genetic switch,from its discovery to the latest findings,and discuss its potential roles in the genomic evolution of bacteria.
文摘In order to elucidate the genetic diversity and taxonomic status of Siberian roe deer(Capreolus pygargus)from the Korean peninsula,partial sequences of the mitochondrial cytochrome b gene were analyzed.We collected 57 roe deer samples from Mainland and Jeju Island between July 2004 and June 2009.A total of 50 sequences(1,070 bp)were obtained,and seven haplotypes were defined.Five haplotypes were found from Mainland,and two were discovered from Jeju Island.The genetic diversity was lower in the Jeju Island population than in the Mainland population.In addition,both the consensus neighbor-joining tree and maximum parsimony tree showed an identical topology between the Mainland and Jeju Island clades.Based on the results,two subspecies of the Korean roe deer were confirmed.Siberian roe deer in Jeju Island showed a distinct difference in the cytochrome b gene compared with other Siberian roe deer,being aunique native species inhabiting only Jeju Island in Korea.Because Siberian roe deer in Jeju Island can be classified at subspecies level,the new subspecies in Jeju was named Capreolus pygargus jejuensis in this study.For this new subspecies,reasonable conservation and management effort is needed in the future.
