Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-05-31

AUTHORS

Xu Cai, Lichun Chang, Tingting Zhang, Haixu Chen, Lei Zhang, Runmao Lin, Jianli Liang, Jian Wu, Michael Freeling, Xiaowu Wang

ABSTRACT

BackgroundDespite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes.ResultsHerein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being “flexible.” We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation.ConclusionsThis pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement. More... »

PAGES

166

References to SciGraph publications

  • 2012-12-19. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres in NATURE
  • 2012-08-28. A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa in BMC PLANT BIOLOGY
  • 2020-01-13. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus in NATURE PLANTS
  • <error retrieving object. in <ERROR RETRIEVING OBJECT
  • 2017-02-07. Genome-wide analysis of auxin transport genes identifies the hormone responsive patterns associated with leafy head formation in Chinese cabbage in SCIENTIFIC REPORTS
  • 2017-09-25. Graphtyper enables population-scale genotyping using pangenome graphs in NATURE GENETICS
  • 2014-05-23. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes in NATURE COMMUNICATIONS
  • 2018-12-31. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance in NATURE PLANTS
  • 2018-10-01. Variation graph toolkit improves read mapping by representing genetic variation in the reference in NATURE BIOTECHNOLOGY
  • 2017-03-06. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication in NATURE GENETICS
  • 2006-12-21. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide in NATURE PROTOCOLS
  • 2019-11-14. OrthoFinder: phylogenetic orthology inference for comparative genomics in GENOME BIOLOGY
  • 2011-12-11. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes in NATURE BIOTECHNOLOGY
  • 2015-12-10. Understanding Brassicaceae evolution through ancestral genome reconstruction in GENOME BIOLOGY
  • 2006-09-20. Auxin in action: signalling, transport and the control of plant growth and development in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2018-01-15. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice in NATURE GENETICS
  • 2020-02-20. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics in NATURE COMMUNICATIONS
  • 2018-07-30. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes in NATURE GENETICS
  • 2015-06-29. Assembly and diploid architecture of an individual human genome via single-molecule technologies in NATURE METHODS
  • 2011-10-28. Mapping quantitative trait loci for leaf and heading-related traits in Chinese cabbage (Brassica rapa L. ssp. pekinesis) in HORTICULTURE, ENVIRONMENT, AND BIOTECHNOLOGY
  • 2017-07-26. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference in NATURE
  • 2019-05-13. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor in NATURE GENETICS
  • 2019-05-24. One reference genome is not enough in GENOME BIOLOGY
  • 2018-11-02. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps in NATURE PLANTS
  • 2017-05-15. The evolutionary significance of polyploidy in NATURE REVIEWS GENETICS
  • 2019-12-16. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies in GENOME BIOLOGY
  • 2016-08-15. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea in NATURE GENETICS
  • 2011-08-28. The genome of the mesopolyploid crop species Brassica rapa in NATURE GENETICS
  • 2019-12-16. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 in GENOME BIOLOGY
  • 2017-12-19. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure in NATURE COMMUNICATIONS
  • 2019-12-16. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline in GENOME BIOLOGY
  • 2018-08-15. Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies in HORTICULTURE RESEARCH
  • 2008-01-11. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments in GENOME BIOLOGY
  • 2016-08-01. Whole-genome duplication as a key factor in crop domestication in NATURE PLANTS
  • 2018-04-30. Gene retention, fractionation and subgenome differences in polyploid plants in NATURE PLANTS
  • 2016-11-11. The pangenome of an agronomically important crop plant Brassica oleracea in NATURE COMMUNICATIONS
  • 2020-08-10. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome in NATURE PLANTS
  • 2015-03-09. HISAT: a fast spliced aligner with low memory requirements in NATURE METHODS
  • 2004-01-30. Versatile and open software for comparing large genomes in GENOME BIOLOGY
  • 2020-08-09. Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes in THEORETICAL AND APPLIED GENETICS
  • 2011-05-15. Full-length transcriptome assembly from RNA-Seq data without a reference genome in NATURE BIOTECHNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-021-02383-2

    DOI

    http://dx.doi.org/10.1186/s13059-021-02383-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1138487683

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34059118


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Base Sequence", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Brassica rapa", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Domestication", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomic Structural Variation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Molecular Sequence Annotation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polyploidy", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Species Specificity", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Synteny", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Cai", 
            "givenName": "Xu", 
            "id": "sg:person.011160644607.85", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011160644607.85"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chang", 
            "givenName": "Lichun", 
            "id": "sg:person.016547616441.54", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016547616441.54"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhang", 
            "givenName": "Tingting", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chen", 
            "givenName": "Haixu", 
            "id": "sg:person.014535452473.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014535452473.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhang", 
            "givenName": "Lei", 
            "id": "sg:person.014007700254.13", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014007700254.13"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lin", 
            "givenName": "Runmao", 
            "id": "sg:person.01243562522.29", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01243562522.29"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Liang", 
            "givenName": "Jianli", 
            "id": "sg:person.01144553733.83", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01144553733.83"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wu", 
            "givenName": "Jian", 
            "id": "sg:person.01076440533.87", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01076440533.87"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.47840.3f", 
              "name": [
                "Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Freeling", 
            "givenName": "Michael", 
            "id": "sg:person.0634660645.76", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634660645.76"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China", 
              "id": "http://www.grid.ac/institutes/grid.464357.7", 
              "name": [
                "Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wang", 
            "givenName": "Xiaowu", 
            "id": "sg:person.01111134275.07", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01111134275.07"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/s13580-011-0031-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022560577", 
              "https://doi.org/10.1007/s13580-011-0031-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.3317", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005140994", 
              "https://doi.org/10.1038/nmeth.3317"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3964", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091911912", 
              "https://doi.org/10.1038/ng.3964"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.2050", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001125924", 
              "https://doi.org/10.1038/nbt.2050"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-019-1717-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1115634496", 
              "https://doi.org/10.1186/s13059-019-1717-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.3454", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013577548", 
              "https://doi.org/10.1038/nmeth.3454"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-020-14779-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1125025012", 
              "https://doi.org/10.1038/s41467-020-14779-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature23264", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1090898815", 
              "https://doi.org/10.1038/nature23264"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41477-018-0289-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1107829107", 
              "https://doi.org/10.1038/s41477-018-0289-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41588-018-0041-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1100275618", 
              "https://doi.org/10.1038/s41588-018-0041-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2008-9-1-r7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029779393", 
              "https://doi.org/10.1186/gb-2008-9-1-r7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-019-1911-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123449994", 
              "https://doi.org/10.1186/s13059-019-1911-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2004-5-2-r12", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022585853", 
              "https://doi.org/10.1186/gb-2004-5-2-r12"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41477-020-0735-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1130021304", 
              "https://doi.org/10.1038/s41477-020-0735-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41438-018-0071-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1105814076", 
              "https://doi.org/10.1038/s41438-018-0071-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41588-019-0410-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1114164300", 
              "https://doi.org/10.1038/s41588-019-0410-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41477-018-0136-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103640986", 
              "https://doi.org/10.1038/s41477-018-0136-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.919", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035519342", 
              "https://doi.org/10.1038/ng.919"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11798", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038528047", 
              "https://doi.org/10.1038/nature11798"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2006.384", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045693921", 
              "https://doi.org/10.1038/nprot.2006.384"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms13390", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005082733", 
              "https://doi.org/10.1038/ncomms13390"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-017-02292-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1099705896", 
              "https://doi.org/10.1038/s41467-017-02292-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg.2017.26", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085409542", 
              "https://doi.org/10.1038/nrg.2017.26"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-020-03664-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1130003123", 
              "https://doi.org/10.1007/s00122-020-03664-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms4930", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005748112", 
              "https://doi.org/10.1038/ncomms4930"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2229-12-151", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015231367", 
              "https://doi.org/10.1186/1471-2229-12-151"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41588-018-0182-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1105781352", 
              "https://doi.org/10.1038/s41588-018-0182-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-019-1905-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123449991", 
              "https://doi.org/10.1186/s13059-019-1905-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.4227", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1106252579", 
              "https://doi.org/10.1038/nbt.4227"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm2020", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010209092", 
              "https://doi.org/10.1038/nrm2020"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06250", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036876479", 
              "https://doi.org/10.1038/nature06250"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-019-1910-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123449993", 
              "https://doi.org/10.1186/s13059-019-1910-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-019-1832-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1122590823", 
              "https://doi.org/10.1186/s13059-019-1832-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41477-018-0329-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1110510291", 
              "https://doi.org/10.1038/s41477-018-0329-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3807", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084129147", 
              "https://doi.org/10.1038/ng.3807"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3634", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050487125", 
              "https://doi.org/10.1038/ng.3634"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-015-0814-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030717308", 
              "https://doi.org/10.1186/s13059-015-0814-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nplants.2016.115", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032757438", 
              "https://doi.org/10.1038/nplants.2016.115"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1883", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015803168", 
              "https://doi.org/10.1038/nbt.1883"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41477-019-0577-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1124047707", 
              "https://doi.org/10.1038/s41477-019-0577-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep42229", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1083688654", 
              "https://doi.org/10.1038/srep42229"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2021-05-31", 
        "datePublishedReg": "2021-05-31", 
        "description": "BackgroundDespite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes.ResultsHerein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being \u201cflexible.\u201d We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation.ConclusionsThis pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s13059-021-02383-2", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.8194602", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.5540638", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023439", 
            "issn": [
              "1474-760X", 
              "1465-6906"
            ], 
            "name": "Genome Biology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "22"
          }
        ], 
        "keywords": [
          "whole genome triplication", 
          "intraspecific diversification", 
          "leafy head formation", 
          "structural variations", 
          "pan-genome analysis", 
          "more transposable elements", 
          "non-synonymous mutations", 
          "dominant subgenome", 
          "genome evolution", 
          "syntenic genes", 
          "phytohormone auxin", 
          "rapa genome", 
          "ancestral genomes", 
          "genome diversification", 
          "gene content", 
          "B. rapa", 
          "transposable elements", 
          "Brassica rapa", 
          "such genes", 
          "candidate genes", 
          "genome", 
          "distinctive morphotypes", 
          "genes", 
          "head formation", 
          "domestication", 
          "allopolyploidization", 
          "subgenomes", 
          "diversification", 
          "rapa", 
          "rich resource", 
          "polyploidization", 
          "auxin", 
          "Brassica", 
          "subspecies", 
          "morphotypes", 
          "species", 
          "plants", 
          "underexplored role", 
          "speciation", 
          "mutations", 
          "novo", 
          "triplication", 
          "uncovers", 
          "variation", 
          "possible contribution", 
          "adaptation", 
          "ResultsHerein", 
          "evolution", 
          "role", 
          "contrast", 
          "response", 
          "formation", 
          "consequences", 
          "environment", 
          "stimuli", 
          "content", 
          "analysis", 
          "elements", 
          "impact", 
          "resources", 
          "contribution", 
          "flexibility", 
          "LF", 
          "influence", 
          "work", 
          "prevalence", 
          "improvement", 
          "BackgroundDespite", 
          "recurrence"
        ], 
        "name": "Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa", 
        "pagination": "166", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1138487683"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13059-021-02383-2"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "34059118"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13059-021-02383-2", 
          "https://app.dimensions.ai/details/publication/pub.1138487683"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-11-24T21:08", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_896.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s13059-021-02383-2"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02383-2'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02383-2'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02383-2'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02383-2'


     

    This table displays all metadata directly associated to this object as RDF triples.

    403 TRIPLES      21 PREDICATES      145 URIs      96 LITERALS      17 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13059-021-02383-2 schema:about N0178a727ffe548ceb2f67abe2507ed5d
    2 N0c96b80e40df4dbca64c977a8b58b04c
    3 N6b45a2e00726417990b81adf2c79129e
    4 N70783a48dea44e1fa270d4b2a0349cde
    5 N7d213ad601c74bfe8fa7e228a6dead08
    6 N8f213383460f4b5184e1fcd77ccd4616
    7 Nbdfd80946aec48a5a31257620be9a3ff
    8 Nd0e0ea3ffb6a4c02bbad9621e80f622d
    9 Ndb313384961b46fca5d73810a04c9b56
    10 Nde03870022c74ef7bb70b61b296bd25e
    11 anzsrc-for:06
    12 anzsrc-for:0604
    13 schema:author N661228bf372648c58436b03d8e68b7bb
    14 schema:citation sg:pub.10.1007/s00122-020-03664-3
    15 sg:pub.10.1007/s13580-011-0031-x
    16 sg:pub.10.1038/nature06250
    17 sg:pub.10.1038/nature11798
    18 sg:pub.10.1038/nature23264
    19 sg:pub.10.1038/nbt.1883
    20 sg:pub.10.1038/nbt.2050
    21 sg:pub.10.1038/nbt.4227
    22 sg:pub.10.1038/ncomms13390
    23 sg:pub.10.1038/ncomms4930
    24 sg:pub.10.1038/ng.3634
    25 sg:pub.10.1038/ng.3807
    26 sg:pub.10.1038/ng.3964
    27 sg:pub.10.1038/ng.919
    28 sg:pub.10.1038/nmeth.3317
    29 sg:pub.10.1038/nmeth.3454
    30 sg:pub.10.1038/nplants.2016.115
    31 sg:pub.10.1038/nprot.2006.384
    32 sg:pub.10.1038/nrg.2017.26
    33 sg:pub.10.1038/nrm2020
    34 sg:pub.10.1038/s41438-018-0071-9
    35 sg:pub.10.1038/s41467-017-02292-8
    36 sg:pub.10.1038/s41467-020-14779-y
    37 sg:pub.10.1038/s41477-018-0136-7
    38 sg:pub.10.1038/s41477-018-0289-4
    39 sg:pub.10.1038/s41477-018-0329-0
    40 sg:pub.10.1038/s41477-019-0577-7
    41 sg:pub.10.1038/s41477-020-0735-y
    42 sg:pub.10.1038/s41588-018-0041-z
    43 sg:pub.10.1038/s41588-018-0182-0
    44 sg:pub.10.1038/s41588-019-0410-2
    45 sg:pub.10.1038/srep42229
    46 sg:pub.10.1186/1471-2229-12-151
    47 sg:pub.10.1186/gb-2004-5-2-r12
    48 sg:pub.10.1186/gb-2008-9-1-r7
    49 sg:pub.10.1186/s13059-015-0814-y
    50 sg:pub.10.1186/s13059-019-1717-0
    51 sg:pub.10.1186/s13059-019-1832-y
    52 sg:pub.10.1186/s13059-019-1905-y
    53 sg:pub.10.1186/s13059-019-1910-1
    54 sg:pub.10.1186/s13059-019-1911-0
    55 schema:datePublished 2021-05-31
    56 schema:datePublishedReg 2021-05-31
    57 schema:description BackgroundDespite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes.ResultsHerein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being “flexible.” We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation.ConclusionsThis pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.
    58 schema:genre article
    59 schema:isAccessibleForFree true
    60 schema:isPartOf N69bf74b749064444ae0ed279f3861b1f
    61 Nde439cdbe4184431bf28cb992e009d2f
    62 sg:journal.1023439
    63 schema:keywords B. rapa
    64 BackgroundDespite
    65 Brassica
    66 Brassica rapa
    67 LF
    68 ResultsHerein
    69 adaptation
    70 allopolyploidization
    71 analysis
    72 ancestral genomes
    73 auxin
    74 candidate genes
    75 consequences
    76 content
    77 contrast
    78 contribution
    79 distinctive morphotypes
    80 diversification
    81 domestication
    82 dominant subgenome
    83 elements
    84 environment
    85 evolution
    86 flexibility
    87 formation
    88 gene content
    89 genes
    90 genome
    91 genome diversification
    92 genome evolution
    93 head formation
    94 impact
    95 improvement
    96 influence
    97 intraspecific diversification
    98 leafy head formation
    99 more transposable elements
    100 morphotypes
    101 mutations
    102 non-synonymous mutations
    103 novo
    104 pan-genome analysis
    105 phytohormone auxin
    106 plants
    107 polyploidization
    108 possible contribution
    109 prevalence
    110 rapa
    111 rapa genome
    112 recurrence
    113 resources
    114 response
    115 rich resource
    116 role
    117 speciation
    118 species
    119 stimuli
    120 structural variations
    121 subgenomes
    122 subspecies
    123 such genes
    124 syntenic genes
    125 transposable elements
    126 triplication
    127 uncovers
    128 underexplored role
    129 variation
    130 whole genome triplication
    131 work
    132 schema:name Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa
    133 schema:pagination 166
    134 schema:productId N3290929554544355bce91748b3acbe91
    135 N530bbfe4d82e4d88ab7379bc133e3f0e
    136 N7facd8e93b1f4643820304f8b2ed38dc
    137 schema:sameAs https://app.dimensions.ai/details/publication/pub.1138487683
    138 https://doi.org/10.1186/s13059-021-02383-2
    139 schema:sdDatePublished 2022-11-24T21:08
    140 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    141 schema:sdPublisher Naf6e69a3ccca4d83a22f7ee2e5660852
    142 schema:url https://doi.org/10.1186/s13059-021-02383-2
    143 sgo:license sg:explorer/license/
    144 sgo:sdDataset articles
    145 rdf:type schema:ScholarlyArticle
    146 N0178a727ffe548ceb2f67abe2507ed5d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    147 schema:name Synteny
    148 rdf:type schema:DefinedTerm
    149 N0466c2f2382c4a768ba2d70220272601 rdf:first sg:person.01243562522.29
    150 rdf:rest Nbfc60c8e499f49bf9ecf17ec1cd3c6f5
    151 N04e61ba8d80749e4b39a2c187f57262c schema:affiliation grid-institutes:grid.464357.7
    152 schema:familyName Zhang
    153 schema:givenName Tingting
    154 rdf:type schema:Person
    155 N0c96b80e40df4dbca64c977a8b58b04c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    156 schema:name Molecular Sequence Annotation
    157 rdf:type schema:DefinedTerm
    158 N2d08973bfc9d47e7b809a4ef7d8ef213 rdf:first sg:person.014007700254.13
    159 rdf:rest N0466c2f2382c4a768ba2d70220272601
    160 N3290929554544355bce91748b3acbe91 schema:name pubmed_id
    161 schema:value 34059118
    162 rdf:type schema:PropertyValue
    163 N3abcceaf708645b5a0df4d4f9dc03299 rdf:first sg:person.016547616441.54
    164 rdf:rest Ne364658a11994f49b55e469e50aafbc5
    165 N530bbfe4d82e4d88ab7379bc133e3f0e schema:name doi
    166 schema:value 10.1186/s13059-021-02383-2
    167 rdf:type schema:PropertyValue
    168 N5a1e3c337dcf42c799bf6e1476063aac rdf:first sg:person.014535452473.18
    169 rdf:rest N2d08973bfc9d47e7b809a4ef7d8ef213
    170 N661228bf372648c58436b03d8e68b7bb rdf:first sg:person.011160644607.85
    171 rdf:rest N3abcceaf708645b5a0df4d4f9dc03299
    172 N69bf74b749064444ae0ed279f3861b1f schema:volumeNumber 22
    173 rdf:type schema:PublicationVolume
    174 N6b45a2e00726417990b81adf2c79129e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    175 schema:name Domestication
    176 rdf:type schema:DefinedTerm
    177 N70783a48dea44e1fa270d4b2a0349cde schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    178 schema:name Genome, Plant
    179 rdf:type schema:DefinedTerm
    180 N7d213ad601c74bfe8fa7e228a6dead08 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    181 schema:name Brassica rapa
    182 rdf:type schema:DefinedTerm
    183 N7facd8e93b1f4643820304f8b2ed38dc schema:name dimensions_id
    184 schema:value pub.1138487683
    185 rdf:type schema:PropertyValue
    186 N86d41bb72d0f4a00886c50bcca11cfc0 rdf:first sg:person.0634660645.76
    187 rdf:rest N97f49e98c9c240898a1178e4bf77a20c
    188 N8f213383460f4b5184e1fcd77ccd4616 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Genomic Structural Variation
    190 rdf:type schema:DefinedTerm
    191 N97f49e98c9c240898a1178e4bf77a20c rdf:first sg:person.01111134275.07
    192 rdf:rest rdf:nil
    193 Naf6e69a3ccca4d83a22f7ee2e5660852 schema:name Springer Nature - SN SciGraph project
    194 rdf:type schema:Organization
    195 Nbdfd80946aec48a5a31257620be9a3ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    196 schema:name Polyploidy
    197 rdf:type schema:DefinedTerm
    198 Nbfc60c8e499f49bf9ecf17ec1cd3c6f5 rdf:first sg:person.01144553733.83
    199 rdf:rest Nd764bc570da946d7972262c2134145f5
    200 Nd0e0ea3ffb6a4c02bbad9621e80f622d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    201 schema:name Phylogeny
    202 rdf:type schema:DefinedTerm
    203 Nd764bc570da946d7972262c2134145f5 rdf:first sg:person.01076440533.87
    204 rdf:rest N86d41bb72d0f4a00886c50bcca11cfc0
    205 Ndb313384961b46fca5d73810a04c9b56 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    206 schema:name Base Sequence
    207 rdf:type schema:DefinedTerm
    208 Nde03870022c74ef7bb70b61b296bd25e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    209 schema:name Species Specificity
    210 rdf:type schema:DefinedTerm
    211 Nde439cdbe4184431bf28cb992e009d2f schema:issueNumber 1
    212 rdf:type schema:PublicationIssue
    213 Ne364658a11994f49b55e469e50aafbc5 rdf:first N04e61ba8d80749e4b39a2c187f57262c
    214 rdf:rest N5a1e3c337dcf42c799bf6e1476063aac
    215 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    216 schema:name Biological Sciences
    217 rdf:type schema:DefinedTerm
    218 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    219 schema:name Genetics
    220 rdf:type schema:DefinedTerm
    221 sg:grant.5540638 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-021-02383-2
    222 rdf:type schema:MonetaryGrant
    223 sg:grant.8194602 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-021-02383-2
    224 rdf:type schema:MonetaryGrant
    225 sg:journal.1023439 schema:issn 1465-6906
    226 1474-760X
    227 schema:name Genome Biology
    228 schema:publisher Springer Nature
    229 rdf:type schema:Periodical
    230 sg:person.01076440533.87 schema:affiliation grid-institutes:grid.464357.7
    231 schema:familyName Wu
    232 schema:givenName Jian
    233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01076440533.87
    234 rdf:type schema:Person
    235 sg:person.01111134275.07 schema:affiliation grid-institutes:grid.464357.7
    236 schema:familyName Wang
    237 schema:givenName Xiaowu
    238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01111134275.07
    239 rdf:type schema:Person
    240 sg:person.011160644607.85 schema:affiliation grid-institutes:grid.464357.7
    241 schema:familyName Cai
    242 schema:givenName Xu
    243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011160644607.85
    244 rdf:type schema:Person
    245 sg:person.01144553733.83 schema:affiliation grid-institutes:grid.464357.7
    246 schema:familyName Liang
    247 schema:givenName Jianli
    248 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01144553733.83
    249 rdf:type schema:Person
    250 sg:person.01243562522.29 schema:affiliation grid-institutes:grid.464357.7
    251 schema:familyName Lin
    252 schema:givenName Runmao
    253 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01243562522.29
    254 rdf:type schema:Person
    255 sg:person.014007700254.13 schema:affiliation grid-institutes:grid.464357.7
    256 schema:familyName Zhang
    257 schema:givenName Lei
    258 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014007700254.13
    259 rdf:type schema:Person
    260 sg:person.014535452473.18 schema:affiliation grid-institutes:grid.464357.7
    261 schema:familyName Chen
    262 schema:givenName Haixu
    263 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014535452473.18
    264 rdf:type schema:Person
    265 sg:person.016547616441.54 schema:affiliation grid-institutes:grid.464357.7
    266 schema:familyName Chang
    267 schema:givenName Lichun
    268 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016547616441.54
    269 rdf:type schema:Person
    270 sg:person.0634660645.76 schema:affiliation grid-institutes:grid.47840.3f
    271 schema:familyName Freeling
    272 schema:givenName Michael
    273 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634660645.76
    274 rdf:type schema:Person
    275 sg:pub.10.1007/s00122-020-03664-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1130003123
    276 https://doi.org/10.1007/s00122-020-03664-3
    277 rdf:type schema:CreativeWork
    278 sg:pub.10.1007/s13580-011-0031-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1022560577
    279 https://doi.org/10.1007/s13580-011-0031-x
    280 rdf:type schema:CreativeWork
    281 sg:pub.10.1038/nature06250 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036876479
    282 https://doi.org/10.1038/nature06250
    283 rdf:type schema:CreativeWork
    284 sg:pub.10.1038/nature11798 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038528047
    285 https://doi.org/10.1038/nature11798
    286 rdf:type schema:CreativeWork
    287 sg:pub.10.1038/nature23264 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090898815
    288 https://doi.org/10.1038/nature23264
    289 rdf:type schema:CreativeWork
    290 sg:pub.10.1038/nbt.1883 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015803168
    291 https://doi.org/10.1038/nbt.1883
    292 rdf:type schema:CreativeWork
    293 sg:pub.10.1038/nbt.2050 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001125924
    294 https://doi.org/10.1038/nbt.2050
    295 rdf:type schema:CreativeWork
    296 sg:pub.10.1038/nbt.4227 schema:sameAs https://app.dimensions.ai/details/publication/pub.1106252579
    297 https://doi.org/10.1038/nbt.4227
    298 rdf:type schema:CreativeWork
    299 sg:pub.10.1038/ncomms13390 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005082733
    300 https://doi.org/10.1038/ncomms13390
    301 rdf:type schema:CreativeWork
    302 sg:pub.10.1038/ncomms4930 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005748112
    303 https://doi.org/10.1038/ncomms4930
    304 rdf:type schema:CreativeWork
    305 sg:pub.10.1038/ng.3634 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050487125
    306 https://doi.org/10.1038/ng.3634
    307 rdf:type schema:CreativeWork
    308 sg:pub.10.1038/ng.3807 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084129147
    309 https://doi.org/10.1038/ng.3807
    310 rdf:type schema:CreativeWork
    311 sg:pub.10.1038/ng.3964 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091911912
    312 https://doi.org/10.1038/ng.3964
    313 rdf:type schema:CreativeWork
    314 sg:pub.10.1038/ng.919 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035519342
    315 https://doi.org/10.1038/ng.919
    316 rdf:type schema:CreativeWork
    317 sg:pub.10.1038/nmeth.3317 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005140994
    318 https://doi.org/10.1038/nmeth.3317
    319 rdf:type schema:CreativeWork
    320 sg:pub.10.1038/nmeth.3454 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013577548
    321 https://doi.org/10.1038/nmeth.3454
    322 rdf:type schema:CreativeWork
    323 sg:pub.10.1038/nplants.2016.115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032757438
    324 https://doi.org/10.1038/nplants.2016.115
    325 rdf:type schema:CreativeWork
    326 sg:pub.10.1038/nprot.2006.384 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045693921
    327 https://doi.org/10.1038/nprot.2006.384
    328 rdf:type schema:CreativeWork
    329 sg:pub.10.1038/nrg.2017.26 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085409542
    330 https://doi.org/10.1038/nrg.2017.26
    331 rdf:type schema:CreativeWork
    332 sg:pub.10.1038/nrm2020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010209092
    333 https://doi.org/10.1038/nrm2020
    334 rdf:type schema:CreativeWork
    335 sg:pub.10.1038/s41438-018-0071-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1105814076
    336 https://doi.org/10.1038/s41438-018-0071-9
    337 rdf:type schema:CreativeWork
    338 sg:pub.10.1038/s41467-017-02292-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1099705896
    339 https://doi.org/10.1038/s41467-017-02292-8
    340 rdf:type schema:CreativeWork
    341 sg:pub.10.1038/s41467-020-14779-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1125025012
    342 https://doi.org/10.1038/s41467-020-14779-y
    343 rdf:type schema:CreativeWork
    344 sg:pub.10.1038/s41477-018-0136-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103640986
    345 https://doi.org/10.1038/s41477-018-0136-7
    346 rdf:type schema:CreativeWork
    347 sg:pub.10.1038/s41477-018-0289-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107829107
    348 https://doi.org/10.1038/s41477-018-0289-4
    349 rdf:type schema:CreativeWork
    350 sg:pub.10.1038/s41477-018-0329-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110510291
    351 https://doi.org/10.1038/s41477-018-0329-0
    352 rdf:type schema:CreativeWork
    353 sg:pub.10.1038/s41477-019-0577-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1124047707
    354 https://doi.org/10.1038/s41477-019-0577-7
    355 rdf:type schema:CreativeWork
    356 sg:pub.10.1038/s41477-020-0735-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1130021304
    357 https://doi.org/10.1038/s41477-020-0735-y
    358 rdf:type schema:CreativeWork
    359 sg:pub.10.1038/s41588-018-0041-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1100275618
    360 https://doi.org/10.1038/s41588-018-0041-z
    361 rdf:type schema:CreativeWork
    362 sg:pub.10.1038/s41588-018-0182-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1105781352
    363 https://doi.org/10.1038/s41588-018-0182-0
    364 rdf:type schema:CreativeWork
    365 sg:pub.10.1038/s41588-019-0410-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1114164300
    366 https://doi.org/10.1038/s41588-019-0410-2
    367 rdf:type schema:CreativeWork
    368 sg:pub.10.1038/srep42229 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083688654
    369 https://doi.org/10.1038/srep42229
    370 rdf:type schema:CreativeWork
    371 sg:pub.10.1186/1471-2229-12-151 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015231367
    372 https://doi.org/10.1186/1471-2229-12-151
    373 rdf:type schema:CreativeWork
    374 sg:pub.10.1186/gb-2004-5-2-r12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022585853
    375 https://doi.org/10.1186/gb-2004-5-2-r12
    376 rdf:type schema:CreativeWork
    377 sg:pub.10.1186/gb-2008-9-1-r7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029779393
    378 https://doi.org/10.1186/gb-2008-9-1-r7
    379 rdf:type schema:CreativeWork
    380 sg:pub.10.1186/s13059-015-0814-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1030717308
    381 https://doi.org/10.1186/s13059-015-0814-y
    382 rdf:type schema:CreativeWork
    383 sg:pub.10.1186/s13059-019-1717-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1115634496
    384 https://doi.org/10.1186/s13059-019-1717-0
    385 rdf:type schema:CreativeWork
    386 sg:pub.10.1186/s13059-019-1832-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1122590823
    387 https://doi.org/10.1186/s13059-019-1832-y
    388 rdf:type schema:CreativeWork
    389 sg:pub.10.1186/s13059-019-1905-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1123449991
    390 https://doi.org/10.1186/s13059-019-1905-y
    391 rdf:type schema:CreativeWork
    392 sg:pub.10.1186/s13059-019-1910-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123449993
    393 https://doi.org/10.1186/s13059-019-1910-1
    394 rdf:type schema:CreativeWork
    395 sg:pub.10.1186/s13059-019-1911-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123449994
    396 https://doi.org/10.1186/s13059-019-1911-0
    397 rdf:type schema:CreativeWork
    398 grid-institutes:grid.464357.7 schema:alternateName Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China
    399 schema:name Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, 100081, Beijing, China
    400 rdf:type schema:Organization
    401 grid-institutes:grid.47840.3f schema:alternateName Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
    402 schema:name Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
    403 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...