The largemouth bronze gudgeon(Coreius guichenoti),an endemic fish species,is distributed in the upper Yangtze River drainage.Due to anthropogenetic factors such as water pollution,overfishing,and dam construction,the ...The largemouth bronze gudgeon(Coreius guichenoti),an endemic fish species,is distributed in the upper Yangtze River drainage.Due to anthropogenetic factors such as water pollution,overfishing,and dam construction,the wild populations of C.guichenoti have dramatically declined in recent decades.In this study,we generated a reference chromosomal-level genome assembly of C.guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies.The final genome assembly was 1.10 Gb in length(contig N50:28.64 Mb;scaffold N50:42.39 Mb)with 25 chromosomes.The completeness score of the C.guichenoti genome was 96.4%,and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes.A total of 24325 PCGs were annotated for the C.guichenoti genome.Comparative genomics analysis identified 986 expanded gene families in C.guichenoti,which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity.Furthermore,positively selected genes(PSGs)detected in C.guichenoti were mainly associated with DNA repair,ATP binding,mitochondrion,and lipid homeostasis.Based on the reference genome and resequencing data,the polymorphic microsatellite(SSR)loci were comprehensively analyzed for C.guichenoti,and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping.All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium(HWE)deviation showed high polymorphism,good amplification stability,and selective neutrality.The PID(sibs)curves revealed that the subset of four tetra-nucleotide SSR loci(cgui1,cgui5,cgui3,cgui13)was sufficient for accurate identification of C.guichenoti individuals(PIDsib<0.01).These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis.The chromosome-level genome assembly and findings laid solid foundations for molecular breeding,genomic research,and biological conservation of C.guichenoti.展开更多
Local adaptation is critical for plant survivals and reproductions in the context of global environmental change.Heterogeneous environments impose various selection pressures that influence the fitness of organisms an...Local adaptation is critical for plant survivals and reproductions in the context of global environmental change.Heterogeneous environments impose various selection pressures that influence the fitness of organisms and leave genomic signatures during the process of adaptation to local environments.However,unveiling the genomic signatures of adaptation still poses a major challenge especially for perennials due to limited genomic resources.Here,we utilized Actinidia eriantha,a Chinese endemic liana,as a model case to detect drivers of local adaptation and adaptive signals through landscape genomics for 311 individuals collected from 25 populations.Our results demonstrated precipitation and solar radiation were two crucial factors influencing the patterns of genetic variations and driving adaptive processes.We further uncovered a set of genes involved in adaptation to heterogeneous environments.Among them,AeERF110 showed high genetic differentiation between populations and was confirmed to be involved in local adaptation via changes in allele frequency along with precipitation(Prec_03)and solar radiation(Srad_03)in native habitats separately,implying that adaptive loci frequently exhibited environmental and geographic signals.In addition,we assessed genetic offsets of populations under four future climate models and revealed that populations from middle and east clusters faced higher risks in adapting to future environments,which should address more attentions.Taken together,our study opens new perspectives for understanding the genetic underpinnings of local adaptation in plants to environmental changes in a more comprehensive fashion and offered the guides on applications in conservation efforts.展开更多
基金supported by the Postdoctoral Research and Development Fund of Sichuan University(2023SCU12111)the China Postdoctoral Science Foundation(2023M732476).
文摘The largemouth bronze gudgeon(Coreius guichenoti),an endemic fish species,is distributed in the upper Yangtze River drainage.Due to anthropogenetic factors such as water pollution,overfishing,and dam construction,the wild populations of C.guichenoti have dramatically declined in recent decades.In this study,we generated a reference chromosomal-level genome assembly of C.guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies.The final genome assembly was 1.10 Gb in length(contig N50:28.64 Mb;scaffold N50:42.39 Mb)with 25 chromosomes.The completeness score of the C.guichenoti genome was 96.4%,and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes.A total of 24325 PCGs were annotated for the C.guichenoti genome.Comparative genomics analysis identified 986 expanded gene families in C.guichenoti,which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity.Furthermore,positively selected genes(PSGs)detected in C.guichenoti were mainly associated with DNA repair,ATP binding,mitochondrion,and lipid homeostasis.Based on the reference genome and resequencing data,the polymorphic microsatellite(SSR)loci were comprehensively analyzed for C.guichenoti,and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping.All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium(HWE)deviation showed high polymorphism,good amplification stability,and selective neutrality.The PID(sibs)curves revealed that the subset of four tetra-nucleotide SSR loci(cgui1,cgui5,cgui3,cgui13)was sufficient for accurate identification of C.guichenoti individuals(PIDsib<0.01).These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis.The chromosome-level genome assembly and findings laid solid foundations for molecular breeding,genomic research,and biological conservation of C.guichenoti.
基金funded by the National Natural Science Foundation of China(grants number 32070377 and 31770374)Science Fund for Creative Research Groups of the Natural Science Foundation of Hubei Province(2024AFA035).
文摘Local adaptation is critical for plant survivals and reproductions in the context of global environmental change.Heterogeneous environments impose various selection pressures that influence the fitness of organisms and leave genomic signatures during the process of adaptation to local environments.However,unveiling the genomic signatures of adaptation still poses a major challenge especially for perennials due to limited genomic resources.Here,we utilized Actinidia eriantha,a Chinese endemic liana,as a model case to detect drivers of local adaptation and adaptive signals through landscape genomics for 311 individuals collected from 25 populations.Our results demonstrated precipitation and solar radiation were two crucial factors influencing the patterns of genetic variations and driving adaptive processes.We further uncovered a set of genes involved in adaptation to heterogeneous environments.Among them,AeERF110 showed high genetic differentiation between populations and was confirmed to be involved in local adaptation via changes in allele frequency along with precipitation(Prec_03)and solar radiation(Srad_03)in native habitats separately,implying that adaptive loci frequently exhibited environmental and geographic signals.In addition,we assessed genetic offsets of populations under four future climate models and revealed that populations from middle and east clusters faced higher risks in adapting to future environments,which should address more attentions.Taken together,our study opens new perspectives for understanding the genetic underpinnings of local adaptation in plants to environmental changes in a more comprehensive fashion and offered the guides on applications in conservation efforts.
