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
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
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
Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba pl...Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits,here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in Southern China and identified SNPs associated with five horticultural traits,based on 11704 SNPs derived from double-digest restriction-site associated DNA sequencing(ddRAD-seq).Clustering analysis revealed that these accessions were composed of three groups:C.speciosa group,C.insignis group,and hybrid group.The GWAS identified two,four,two,three,and four SNPs related to petal color,petal striation number,flowering time,trunk shape,and prickles on the trunk and branches,respectively.One to two candidate genes were found near the SNPs strongly associated with these traits.This study revealed the genetic relatedness in the Ceiba plants cultivated in Southern China and presented the first GWAS analysis for five horticultural traits for them,laying a foundation for phenotype-related marker selection and molecular breeding.展开更多
Land snails of the family Enidae(Gastropoda,Stylommatophora,Pupilloidea)exhibit specific regional distributions,primarily in southern Gansu and northwestern Sichuan,China.Although numerous morphological studies have b...Land snails of the family Enidae(Gastropoda,Stylommatophora,Pupilloidea)exhibit specific regional distributions,primarily in southern Gansu and northwestern Sichuan,China.Although numerous morphological studies have been conducted,molecular and integrative evidence remains insufficient for resolving the classification of species with uncertain taxonomic status.More rigorous phylogenetic investigations are necessary to clarify the evolutionary biology of Chinese Enidae in this biodiversity hotspot.In the present study,we examined three Enidae genera—Subzebrinus,Pupinidius,and Petraeomastus—collected from 19 localities around Wenxian and Wenchuan in the adjoining regions of Gansu and Sichuan,China.We employed genome-wide doubledigest restriction site-associated DNA sequencing(ddRAD-seq)and machine learning-based image clustering for integrative phylogenetic and morphological analyses of these genera.Phylogenetic trees constructed from genome-wide single nucleotide polymorphism(SNP)data revealed species-level monophyly but genus-level polyphyly,highlighting the need for taxonomic revision.Image clustering identified distinct shell morphology clusters that closely aligned with phylogenetic relationships,suggesting highly conserved phylogeny and morphology within species,as supported by geographical differentiation and localization within species.However,molecular and morphological divergences were also detected in certain Pupinidius and Petraeomastus species.This integrative analysis of genome-wide phylogenetic data and shell morphology clustering provides a solid foundation for future evolutionary studies of Chinese Enidae.展开更多
The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkab...The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos(PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos.However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and timecalibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing,and explored the evolutionary trends of habit,inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae,Racemobambosinae s.l.(comprising Dinochloinae,Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l.(comprising Bambusinae s.str. plus Holttumochloinae).The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.展开更多
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。
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 (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.
基金supported by the Guangzhou Landscaping Company(Grant No.2018–69).
文摘Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits,here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in Southern China and identified SNPs associated with five horticultural traits,based on 11704 SNPs derived from double-digest restriction-site associated DNA sequencing(ddRAD-seq).Clustering analysis revealed that these accessions were composed of three groups:C.speciosa group,C.insignis group,and hybrid group.The GWAS identified two,four,two,three,and four SNPs related to petal color,petal striation number,flowering time,trunk shape,and prickles on the trunk and branches,respectively.One to two candidate genes were found near the SNPs strongly associated with these traits.This study revealed the genetic relatedness in the Ceiba plants cultivated in Southern China and presented the first GWAS analysis for five horticultural traits for them,laying a foundation for phenotype-related marker selection and molecular breeding.
基金supported by the Japan Society for the Promotion of Science(KAKENHI-17H04611)National Natural Science Foundation of China(31872196)Japanese Government(MEXT)Scholarship,and PostDoc Fellowship of Anhui University。
文摘Land snails of the family Enidae(Gastropoda,Stylommatophora,Pupilloidea)exhibit specific regional distributions,primarily in southern Gansu and northwestern Sichuan,China.Although numerous morphological studies have been conducted,molecular and integrative evidence remains insufficient for resolving the classification of species with uncertain taxonomic status.More rigorous phylogenetic investigations are necessary to clarify the evolutionary biology of Chinese Enidae in this biodiversity hotspot.In the present study,we examined three Enidae genera—Subzebrinus,Pupinidius,and Petraeomastus—collected from 19 localities around Wenxian and Wenchuan in the adjoining regions of Gansu and Sichuan,China.We employed genome-wide doubledigest restriction site-associated DNA sequencing(ddRAD-seq)and machine learning-based image clustering for integrative phylogenetic and morphological analyses of these genera.Phylogenetic trees constructed from genome-wide single nucleotide polymorphism(SNP)data revealed species-level monophyly but genus-level polyphyly,highlighting the need for taxonomic revision.Image clustering identified distinct shell morphology clusters that closely aligned with phylogenetic relationships,suggesting highly conserved phylogeny and morphology within species,as supported by geographical differentiation and localization within species.However,molecular and morphological divergences were also detected in certain Pupinidius and Petraeomastus species.This integrative analysis of genome-wide phylogenetic data and shell morphology clustering provides a solid foundation for future evolutionary studies of Chinese Enidae.
基金supported by the National Natural Science Foundation of China (No. 32120103003, 31970355, 32300206)the Key R & D program of Yunnan Province, China (No. 202103AC100003)Postdoctoral Directional Training Foundation of Yunnan Province。
文摘The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos(PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos.However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and timecalibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing,and explored the evolutionary trends of habit,inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae,Racemobambosinae s.l.(comprising Dinochloinae,Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l.(comprising Bambusinae s.str. plus Holttumochloinae).The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.
