Eleocharis vivipara,an amphibious sedge in the Cyperaceae family,has several remarkable properties,most notably its alternate use of C_(3)photosynthesis underwater and C_(4)photosynthesis on land.However,the absence o...Eleocharis vivipara,an amphibious sedge in the Cyperaceae family,has several remarkable properties,most notably its alternate use of C_(3)photosynthesis underwater and C_(4)photosynthesis on land.However,the absence of genomic data has hindered its utility for evolutionary and genetic research.Here,we present a high-quality genome for E.vivipara,representing the first chromosome-level genome for the Eleocharis genus,with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes.Its Hi–C pattern,chromosome clustering results,and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n=4x=20.Phylogenetic analysis suggests that E.vivipara diverged from Cyperus esculentus approximately 32.96million years ago(Mya),and underwent a wholegenome duplication(WGD)about 3.5 Mya.Numerous fusion and fission events were identified between the chromosomes of E.vivipara and its close relatives.We demonstrate that E.vivipara has holocentromeres,a chromosomal feature which can maintain the stability of such chromosomal rearrangements.Experimental transplantation and cross-section studies showed its terrestrial culms developed C_(4)Kranz anatomy with increased number of chloroplasts in the bundle sheath(BS)cells.Gene expression and weighted gene co-expression network analysis(WGCNA)showed overall elevated expression of core genes associated with the C_(4)pathway,and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency.We found evidence of mixed nicotinamide adenine dinucleotide-malic enzyme and phosphoenolpyruvate carboxykinase type C_(4)photosynthesis in E.vivipara,and hypothesize that the evolution of C_(4)photosynthesis predates the WGD event.The mixed type is dominated by subgenome A and supplemented by subgenome B.Collectively,our findings not only shed light on the evolution of E.vivipara and karyotype within the Cyperaceae family,but also provide valuable insights into the transition between C_(3)and C_(4)photosynthesis,offering promising avenues for crop improvement and breeding.展开更多
Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to explorin...Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement.This transformation has been facilitated by the increasing adoption of whole-genome resequencing.In this review,we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding.A total of 187 land plants from 163 countries have been resequenced,comprising 54413 accessions.As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted.Economically important crops,particularly cereals,vegetables,and legumes,have dominated the resequencing efforts,leaving a gap in 49 orders,including Lycopodiales,Liliales,Acorales,Austrobaileyales,and Commelinales.The resequenced germplasm is distributed across diverse geographic locations,providing a global perspective on plant genomics.We highlight genes that have been selected during domestication,or associated with agronomic traits,and form a repository of candidate genes for future research and application.Despite the opportunities for cross-species comparative genomics,many population genomic datasets are not accessible,impeding secondary analyses.We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy.The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs,coupled with advances in analysis and computational technologies.This expansion,in terms of both scale and quality,holds promise for deeper insights into plant trait genetics and breeding design.展开更多
基金funded by the National Natural Science Foundation of China(32300217)the National Key R&D Program of China(2023YFA0914600)+2 种基金the Guangdong Basic and Applied Basic Research Foundation(2022A1515110358)the Guangdong Science and Technology Foundation,“Zhu Jiang Talent Innovation”project(2019ZT08N628)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(PT202101-01)。
文摘Eleocharis vivipara,an amphibious sedge in the Cyperaceae family,has several remarkable properties,most notably its alternate use of C_(3)photosynthesis underwater and C_(4)photosynthesis on land.However,the absence of genomic data has hindered its utility for evolutionary and genetic research.Here,we present a high-quality genome for E.vivipara,representing the first chromosome-level genome for the Eleocharis genus,with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes.Its Hi–C pattern,chromosome clustering results,and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n=4x=20.Phylogenetic analysis suggests that E.vivipara diverged from Cyperus esculentus approximately 32.96million years ago(Mya),and underwent a wholegenome duplication(WGD)about 3.5 Mya.Numerous fusion and fission events were identified between the chromosomes of E.vivipara and its close relatives.We demonstrate that E.vivipara has holocentromeres,a chromosomal feature which can maintain the stability of such chromosomal rearrangements.Experimental transplantation and cross-section studies showed its terrestrial culms developed C_(4)Kranz anatomy with increased number of chloroplasts in the bundle sheath(BS)cells.Gene expression and weighted gene co-expression network analysis(WGCNA)showed overall elevated expression of core genes associated with the C_(4)pathway,and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency.We found evidence of mixed nicotinamide adenine dinucleotide-malic enzyme and phosphoenolpyruvate carboxykinase type C_(4)photosynthesis in E.vivipara,and hypothesize that the evolution of C_(4)photosynthesis predates the WGD event.The mixed type is dominated by subgenome A and supplemented by subgenome B.Collectively,our findings not only shed light on the evolution of E.vivipara and karyotype within the Cyperaceae family,but also provide valuable insights into the transition between C_(3)and C_(4)photosynthesis,offering promising avenues for crop improvement and breeding.
基金supported by the National Key Research and Development Program of China(2020YFE0202300)Science and Technology Major Project of Guangxi(GuiKeAA20108005-2)+1 种基金Guangdong Innovation Research Team Fund(grant number:2014ZT05S078)National Key Research and Development Program of China(2019YFA0707000).No conflict of interest declared.
文摘Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement.This transformation has been facilitated by the increasing adoption of whole-genome resequencing.In this review,we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding.A total of 187 land plants from 163 countries have been resequenced,comprising 54413 accessions.As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted.Economically important crops,particularly cereals,vegetables,and legumes,have dominated the resequencing efforts,leaving a gap in 49 orders,including Lycopodiales,Liliales,Acorales,Austrobaileyales,and Commelinales.The resequenced germplasm is distributed across diverse geographic locations,providing a global perspective on plant genomics.We highlight genes that have been selected during domestication,or associated with agronomic traits,and form a repository of candidate genes for future research and application.Despite the opportunities for cross-species comparative genomics,many population genomic datasets are not accessible,impeding secondary analyses.We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy.The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs,coupled with advances in analysis and computational technologies.This expansion,in terms of both scale and quality,holds promise for deeper insights into plant trait genetics and breeding design.
