Lobularia maritima(L.)Desv.is an ornamental plant cultivated across the world.It belongs to the family Brassicaceae and can tolerate dry,poor and contaminated habitats.Here,we present a chromosome-scale,high-quality g...Lobularia maritima(L.)Desv.is an ornamental plant cultivated across the world.It belongs to the family Brassicaceae and can tolerate dry,poor and contaminated habitats.Here,we present a chromosome-scale,high-quality genome assembly of L.maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data.The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length,and it includes 25,813 protein-coding genes.Approximately 41.94%of the genome consists of repetitive sequences,with abundant long terminal repeat transposable elements.Comparative genomic analysis confirmed that L.maritima underwent a species-specific whole-genome duplication(WGD)event~22.99 million years ago.We identified~1900 species-specific genes,25 expanded gene families,and 50 positively selected genes in L.maritima.Functional annotations of these genes indicated that they are mainly related to stress tolerance.These results provide new insights into the stress tolerance of L.maritima,and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.展开更多
The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However...The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.展开更多
The rapid growth of population-scale whole-genome resequencing,RNA sequencing,bisulfite sequencing,and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data.Asso-ciation analys...The rapid growth of population-scale whole-genome resequencing,RNA sequencing,bisulfite sequencing,and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data.Asso-ciation analyses of omics data,such as genome-,transcriptome-,proteome-,and methylome-wide associ-ation studies,along with integrative analyses of multiple omics datasets,require various bioinformatics tools,which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists.Here,we present EasyOmics,a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association,integration,and visualization.The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses,including data quality control,heritability estimation,genome-wide association analysis,conditional association analysis,omics quantitative trait locus mapping,omics-wide association analysis,omics data integration,and visualization.A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking.EasyOmics is a platform-independent software that can be run under all operating systems,with a docker container for quick installation.It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.展开更多
基金supported by the National Key Research and Development Program of China(2017YFC0505203)National Natural Science Foundation of China(31590821)+2 种基金Fundamental Research Funds for the Central Universities(2018CDDY-S02-SCU and SCU2019D013)National High-Level Talents Special Support Plan(10 Thousand of People Plan)985 and 211 Projects of Sichuan University.
文摘Lobularia maritima(L.)Desv.is an ornamental plant cultivated across the world.It belongs to the family Brassicaceae and can tolerate dry,poor and contaminated habitats.Here,we present a chromosome-scale,high-quality genome assembly of L.maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data.The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length,and it includes 25,813 protein-coding genes.Approximately 41.94%of the genome consists of repetitive sequences,with abundant long terminal repeat transposable elements.Comparative genomic analysis confirmed that L.maritima underwent a species-specific whole-genome duplication(WGD)event~22.99 million years ago.We identified~1900 species-specific genes,25 expanded gene families,and 50 positively selected genes in L.maritima.Functional annotations of these genes indicated that they are mainly related to stress tolerance.These results provide new insights into the stress tolerance of L.maritima,and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research program (No. 2019QZKK0502)Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB31010300)+1 种基金Fundamental Research Funds for the Central UniversitiesInternational Collaboration 111 Program (BP0719040)。
文摘The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
基金funded by the State Key Research&Development Project-Youth Scientist program(2023YFD1202400)the National Science Foundation of China(32030006 and 32200503)+1 种基金the Taishan Young Scholar Program and Distinguished Overseas Young Talents Program from Shandong province(2024HWYQ-079)the Agricultural Science and Technology Innovation Program(ASTIP-TRIC01)from the Chinese Academy of Agricultural Sciences.
文摘The rapid growth of population-scale whole-genome resequencing,RNA sequencing,bisulfite sequencing,and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data.Asso-ciation analyses of omics data,such as genome-,transcriptome-,proteome-,and methylome-wide associ-ation studies,along with integrative analyses of multiple omics datasets,require various bioinformatics tools,which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists.Here,we present EasyOmics,a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association,integration,and visualization.The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses,including data quality control,heritability estimation,genome-wide association analysis,conditional association analysis,omics quantitative trait locus mapping,omics-wide association analysis,omics data integration,and visualization.A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking.EasyOmics is a platform-independent software that can be run under all operating systems,with a docker container for quick installation.It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.
