Dataset Open Access

Assembly and comparison of two closely related Brassica napus genomes

Bayer, Philipp Emanuel; Hurgobin, Bhavna; Golicz, Agnieszka A.; Chan, Chon-Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; Zou, Jun; Bancroft, Ian; Chalhoub, Boulos; King, Graham J.; Batley, Jacqueline; Edwards, David


JSON-LD (schema.org) Export

{
  "description": "<p>Here we present the <em>de novo</em> assembly of the <em>B. napus</em> cultivar Tapidor and comparison with an improved assembly of the <em>B. napus</em> cultivar Darmor<em>-bzh</em>. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor<em>-bzh</em> contains a greater number of genes than the genome of Tapidor.</p>", 
  "license": "http://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia", 
      "@type": "Person", 
      "name": "Bayer, Philipp Emanuel"
    }, 
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia, Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia", 
      "@type": "Person", 
      "name": "Hurgobin, Bhavna"
    }, 
    {
      "affiliation": "Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia", 
      "@type": "Person", 
      "name": "Golicz, Agnieszka A."
    }, 
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia", 
      "@type": "Person", 
      "name": "Chan, Chon-Kit Kenneth"
    }, 
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia", 
      "@type": "Person", 
      "name": "Yuan, Yuxuan"
    }, 
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia, Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia", 
      "@type": "Person", 
      "name": "Lee, HueyTyng"
    }, 
    {
      "affiliation": "chool of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia", 
      "@type": "Person", 
      "name": "Renton, Michael"
    }, 
    {
      "affiliation": "National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China", 
      "@type": "Person", 
      "name": "Meng, Jinling"
    }, 
    {
      "affiliation": "National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China", 
      "@type": "Person", 
      "name": "Li, Ruiyuan"
    }, 
    {
      "affiliation": "National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China", 
      "@type": "Person", 
      "name": "Long, Yan"
    }, 
    {
      "affiliation": "National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China", 
      "@type": "Person", 
      "name": "Zou, Jun"
    }, 
    {
      "affiliation": "Department of Biology, University of York, York, UK", 
      "@type": "Person", 
      "name": "Bancroft, Ian"
    }, 
    {
      "affiliation": "Organization and Evolution of Plant Genomes, Unit\u00e9 de Recherche en G\u00e9nomique V\u00e9g\u00e9tale, Unit\u00e9 Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Universit\u00e9 Evry Val d'Essonne), Evry 91057, France", 
      "@type": "Person", 
      "name": "Chalhoub, Boulos"
    }, 
    {
      "affiliation": "National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China, Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia", 
      "@type": "Person", 
      "name": "King, Graham J."
    }, 
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia", 
      "@type": "Person", 
      "name": "Batley, Jacqueline"
    }, 
    {
      "affiliation": "School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia", 
      "@type": "Person", 
      "name": "Edwards, David"
    }
  ], 
  "url": "https://zenodo.org/record/400371", 
  "datePublished": "2017-03-17", 
  "keywords": [
    "genome assembly", 
    "plant genome", 
    "Brassica napus"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Darmor_v81_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Darmor_v81_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Darmor_v81_assembly.augustus_masked_filtered.gff.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Darmor_v81_assembly.fasta.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Darmor_v81_Tapidor_Ningyou_SNPs.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/GO_Arabidopsis_Terms.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/MSTMap_Input.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/MSTMap_Results.txt.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Repetitive_Collapsed_Genes.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Repetitive_Collapsed_Regions.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Tapidor_v63_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Tapidor_v63_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Tapidor_v63_assembly.augustus_masked_filtered.gff.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Tapidor_v63_assembly.fasta.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/47de1504-a316-4001-9a3b-f4aef7c21d23/Tapidor_v63_Tapidor_Ningyou_SNPs.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.400371", 
  "@id": "https://doi.org/10.5281/zenodo.400371", 
  "@type": "Dataset", 
  "name": "Assembly and comparison of two closely related Brassica napus genomes"
}
68
22
views
downloads
All versions This version
Views 6868
Downloads 2222
Data volume 431.9 MB431.9 MB
Unique views 6464
Unique downloads 1818

Share

Cite as