Extra-pair paternity(EPP)is commonly found in socially monogamous birds,especially in small passerine birds,and there are interspecific and intraspecific variations in the extent of EPP.The Chestnut-vented Nuthatch(Si...Extra-pair paternity(EPP)is commonly found in socially monogamous birds,especially in small passerine birds,and there are interspecific and intraspecific variations in the extent of EPP.The Chestnut-vented Nuthatch(Sitta nagaensis)is a socially monogamous passerine bird,and verifying whether this species has EPP relies on parentage testing-S.nagaensis is not known to have EPP.In this study,we developed SNP markers of this species that are informative for parentage analysis from double digest restriction site-associated DNA sequencing(ddRAD-seq)data.A panel consisting of 50 SNP markers,with a mean heterozygosity of 0.343,was used to resolve 95% of nestlings to fathers.The combined exclusion probabilities for the first parent and second parent were 0.991 and 0.9999,respectively.This panel of SNP markers is a powerful tool for parentage assignments in S.nagaensis.In addition,we found that three offspring(7.9%)from three nests(23.1%)were the result of extra-pair fertilization out of 38 offspring in 13 nests.Our study provided information on parentage analysis that has not been reported before in S.nagaensis.It also supplemented the understudied EPP behavior of birds in Asia,contributing to a general understanding of the EPP behaviors of birds.展开更多
Obtaining high-quality plant materials for experiments is challenging for many research projects.Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, w...Obtaining high-quality plant materials for experiments is challenging for many research projects.Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on dd RADseq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species(Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the dd RAD-seq technique(Midd RAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA,regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The dd RAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by dd RAD-seq.展开更多
Pm48为本实验室鉴定的一个抗白粉病新基因。为精细定位该基因,利用混池ddRAD测序鉴定了81个与该基因关联的序列,开发了STS标记Xmp931,转化了CAPS标记Xmp928、Xmp930和Xmp936;同时,利用粗山羊草基因组序列开发了71个基因组SSR标记,定位...Pm48为本实验室鉴定的一个抗白粉病新基因。为精细定位该基因,利用混池ddRAD测序鉴定了81个与该基因关联的序列,开发了STS标记Xmp931,转化了CAPS标记Xmp928、Xmp930和Xmp936;同时,利用粗山羊草基因组序列开发了71个基因组SSR标记,定位了其中的Xmp1089和Xmp1112。在115个宁糯麦1号′Tabasco衍生的F2:3家系中,Xmp928与目的基因共分离,Xmp1112位于近着丝粒方向处距抗病基因3.1 c M。在671个纯合感病家系中,标记Xmp928仍与目的基因共分离。利用3个中国春5DS缺失系,最终将Pm48定位在小麦5DS上0.63–0.67的臂区段中。展开更多
Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单,不受有无参考基因组的限制,可大大简化基因组的复杂性,减少实验费用,通过...Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单,不受有无参考基因组的限制,可大大简化基因组的复杂性,减少实验费用,通过一次测序就可以获得数以万计的多态性标记。目前,RAD-seq技术已成功应用于超高密度遗传图谱的构建、重要性状的精细定位、辅助基因组序列组装、群体基因组学以及系统发生学等基因组研究热点领域。文章主要介绍了RAD-seq的技术原理、技术发展及其在基因组研究中的广泛应用。鉴于RAD-seq方法的独特性,该技术必将在复杂基因组研究领域具有广泛的应用前景。展开更多
Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations.In this study,we used double digest restriction-siteassociated DNA...Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations.In this study,we used double digest restriction-siteassociated DNA sequencing(ddRAD)technology to assess the genetic diversity,genetic structure and demographic history of the three extant populations of R.meddianum.Analysis of SNPs indicated that R.meddianum populations have a high genetic diversity(p?0.0772±0.0024,HE?0.0742±0.002).Both FST values(0.1582e0.2388)and AMOVA showed a moderate genetic differentiation among the R.meddianum populations.Meanwhile,STRUCTURE,PCoA and NJ trees indicated that the R.meddianum samples were clustered into three distinct genetic groups.Using the stairway plot,we found that R.meddianum underwent a population bottleneck about 70,000 years ago.Furthermore,demographic models of R.meddianum and its relative,Rhododendron cyanocarpum,revealed that these species diverged about 3.05(2.21e5.03)million years ago.This divergence may have been caused by environmental changes that occurred after the late Pliocene,e.g.,the Asian winter monsoon intensified,leading to a drier climate.Based on these findings,we recommend that R.meddianum be conserved through in situ,ex situ approaches and that its seeds be collected for germplasm.展开更多
Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bam...Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.展开更多
Three woody bamboo species collected in Hainan,China in 1940 have been described as Dinochloa based on vegetative specimens.However,the identity of these species has long been in doubt,largely because the vegetative p...Three woody bamboo species collected in Hainan,China in 1940 have been described as Dinochloa based on vegetative specimens.However,the identity of these species has long been in doubt,largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus,a climbing or scrambling bamboo genus of the paleotropical woody bamboos(Poaceae:Bambusoideae)that consists of about 15 species and one variety.To determine the phylogenetic affinity of the three Dinochloa species from Hainan,we sampled almost all recognized Chinese species of Melocalamus and representative species of Dinochloa as well as other closely related genera,performed molecular phylogenetic analysis,and compared their morphology based on herbarium and fieldwork investigation.Our ddRAD data indicate that the three species from Hainan are closely related to Melocalamus,not Dinochloa.Morphological analysis showed that these three species have a climbing habit but do not grow spirally,their culm leaves have smooth bases,and there is a ring of powder and/or tomenta above and below the nodes.Taken together our findings indicate that the three species from Hainan originally published in Dinochloa should be transferred to Melocalamus,i.e.,Melocalamus orenudus(McClure) D.Z.Li& J.X.Liu,Melocalamus puberulus(McClure) D.Z.Li & J.X.Liu,and Melocalamus utilis(McClure) D.Z.Li &J.X.Liu,respectively.This study concludes with an enumeration of Chinese species of Melocalamus,with a key to nine recognized species and one variety,and a lectotypification for M. compatiflorus.展开更多
基金supported by the Science and Technology Project of Yunnan(202101AT070040)the National Natural Science Foundation of China(U23A20162)+1 种基金the Yunnan Provincial Department of Education Fund for Scientific Research Project(2023Y0722)the First Class Forestry Academic Subject in Yunnan Province.
文摘Extra-pair paternity(EPP)is commonly found in socially monogamous birds,especially in small passerine birds,and there are interspecific and intraspecific variations in the extent of EPP.The Chestnut-vented Nuthatch(Sitta nagaensis)is a socially monogamous passerine bird,and verifying whether this species has EPP relies on parentage testing-S.nagaensis is not known to have EPP.In this study,we developed SNP markers of this species that are informative for parentage analysis from double digest restriction site-associated DNA sequencing(ddRAD-seq)data.A panel consisting of 50 SNP markers,with a mean heterozygosity of 0.343,was used to resolve 95% of nestlings to fathers.The combined exclusion probabilities for the first parent and second parent were 0.991 and 0.9999,respectively.This panel of SNP markers is a powerful tool for parentage assignments in S.nagaensis.In addition,we found that three offspring(7.9%)from three nests(23.1%)were the result of extra-pair fertilization out of 38 offspring in 13 nests.Our study provided information on parentage analysis that has not been reported before in S.nagaensis.It also supplemented the understudied EPP behavior of birds in Asia,contributing to a general understanding of the EPP behaviors of birds.
基金supported by the National Natural Science Foundation of China (Grant No. 31470322 and 31430011)
文摘Obtaining high-quality plant materials for experiments is challenging for many research projects.Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on dd RADseq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species(Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the dd RAD-seq technique(Midd RAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA,regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The dd RAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by dd RAD-seq.
文摘Pm48为本实验室鉴定的一个抗白粉病新基因。为精细定位该基因,利用混池ddRAD测序鉴定了81个与该基因关联的序列,开发了STS标记Xmp931,转化了CAPS标记Xmp928、Xmp930和Xmp936;同时,利用粗山羊草基因组序列开发了71个基因组SSR标记,定位了其中的Xmp1089和Xmp1112。在115个宁糯麦1号′Tabasco衍生的F2:3家系中,Xmp928与目的基因共分离,Xmp1112位于近着丝粒方向处距抗病基因3.1 c M。在671个纯合感病家系中,标记Xmp928仍与目的基因共分离。利用3个中国春5DS缺失系,最终将Pm48定位在小麦5DS上0.63–0.67的臂区段中。
文摘Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单,不受有无参考基因组的限制,可大大简化基因组的复杂性,减少实验费用,通过一次测序就可以获得数以万计的多态性标记。目前,RAD-seq技术已成功应用于超高密度遗传图谱的构建、重要性状的精细定位、辅助基因组序列组装、群体基因组学以及系统发生学等基因组研究热点领域。文章主要介绍了RAD-seq的技术原理、技术发展及其在基因组研究中的广泛应用。鉴于RAD-seq方法的独特性,该技术必将在复杂基因组研究领域具有广泛的应用前景。
基金supported by the Fundamental Research Funds for the Central Non-profit Research Institution of the Chinese Academy of Forestry(Grant No.CAFYBB2019ZB007)the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment,China(Grant No.2019HJ2096001006)+2 种基金the Ten Thousand Talent Program of Yunnan Province(Grant No.YNWRQNBJ-2019-010YNWR-QNBJ-2018-174)the Young and Middle-aged Academic and Technical Leader Reserve Talent Project of Yunnan Province(Grant No.2018HB066).
文摘Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations.In this study,we used double digest restriction-siteassociated DNA sequencing(ddRAD)technology to assess the genetic diversity,genetic structure and demographic history of the three extant populations of R.meddianum.Analysis of SNPs indicated that R.meddianum populations have a high genetic diversity(p?0.0772±0.0024,HE?0.0742±0.002).Both FST values(0.1582e0.2388)and AMOVA showed a moderate genetic differentiation among the R.meddianum populations.Meanwhile,STRUCTURE,PCoA and NJ trees indicated that the R.meddianum samples were clustered into three distinct genetic groups.Using the stairway plot,we found that R.meddianum underwent a population bottleneck about 70,000 years ago.Furthermore,demographic models of R.meddianum and its relative,Rhododendron cyanocarpum,revealed that these species diverged about 3.05(2.21e5.03)million years ago.This divergence may have been caused by environmental changes that occurred after the late Pliocene,e.g.,the Asian winter monsoon intensified,leading to a drier climate.Based on these findings,we recommend that R.meddianum be conserved through in situ,ex situ approaches and that its seeds be collected for germplasm.
基金supported by the National Natural Science Foundation of China (Grant No. 31470322 and 31430011)
文摘Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.
基金supported by the National Natural Science Foundation of China (31670396 and 31800181)Postdoctoral Directional Training Foundation of Yunnan Province,China (E2317482)the Key R & D program of Yunnan Province,China (202103AC100003)。
文摘Three woody bamboo species collected in Hainan,China in 1940 have been described as Dinochloa based on vegetative specimens.However,the identity of these species has long been in doubt,largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus,a climbing or scrambling bamboo genus of the paleotropical woody bamboos(Poaceae:Bambusoideae)that consists of about 15 species and one variety.To determine the phylogenetic affinity of the three Dinochloa species from Hainan,we sampled almost all recognized Chinese species of Melocalamus and representative species of Dinochloa as well as other closely related genera,performed molecular phylogenetic analysis,and compared their morphology based on herbarium and fieldwork investigation.Our ddRAD data indicate that the three species from Hainan are closely related to Melocalamus,not Dinochloa.Morphological analysis showed that these three species have a climbing habit but do not grow spirally,their culm leaves have smooth bases,and there is a ring of powder and/or tomenta above and below the nodes.Taken together our findings indicate that the three species from Hainan originally published in Dinochloa should be transferred to Melocalamus,i.e.,Melocalamus orenudus(McClure) D.Z.Li& J.X.Liu,Melocalamus puberulus(McClure) D.Z.Li & J.X.Liu,and Melocalamus utilis(McClure) D.Z.Li &J.X.Liu,respectively.This study concludes with an enumeration of Chinese species of Melocalamus,with a key to nine recognized species and one variety,and a lectotypification for M. compatiflorus.
