Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Per K. I. Wilhelmsson, Jake O. Chandler, Noe Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner-Metzger, Stefan A. Rensing

ABSTRACT

BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds. More... »

PAGES

95

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12864-019-5452-4

DOI

http://dx.doi.org/10.1186/s12864-019-5452-4

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1111769581

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30700268


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Philipp University of Marburg", 
          "id": "https://www.grid.ac/institutes/grid.10253.35", 
          "name": [
            "Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilhelmsson", 
        "givenName": "Per K. I.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Royal Holloway University of London", 
          "id": "https://www.grid.ac/institutes/grid.4970.a", 
          "name": [
            "School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chandler", 
        "givenName": "Jake O.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Philipp University of Marburg", 
          "id": "https://www.grid.ac/institutes/grid.10253.35", 
          "name": [
            "Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fernandez-Pozo", 
        "givenName": "Noe", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Royal Holloway University of London", 
          "id": "https://www.grid.ac/institutes/grid.4970.a", 
          "name": [
            "School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Graeber", 
        "givenName": "Kai", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Philipp University of Marburg", 
          "id": "https://www.grid.ac/institutes/grid.10253.35", 
          "name": [
            "Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany", 
            "Present Address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Stra\u00dfe 2, 24306, Ploen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ullrich", 
        "givenName": "Kristian K.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Royal Holloway University of London", 
          "id": "https://www.grid.ac/institutes/grid.4970.a", 
          "name": [
            "School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Arshad", 
        "givenName": "Waheed", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Royal Holloway University of London", 
          "id": "https://www.grid.ac/institutes/grid.4970.a", 
          "name": [
            "School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Khan", 
        "givenName": "Safina", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wageningen University & Research", 
          "id": "https://www.grid.ac/institutes/grid.4818.5", 
          "name": [
            "Biosystematics Group, Wageningen University, 6708 PB, Wageningen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hofberger", 
        "givenName": "Johannes A.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Philipp University of Marburg", 
          "id": "https://www.grid.ac/institutes/grid.10253.35", 
          "name": [
            "Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Buchta", 
        "givenName": "Karl", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Michigan State University", 
          "id": "https://www.grid.ac/institutes/grid.17088.36", 
          "name": [
            "Department of Horticulture, Michigan State University, 48864, East Lansing, MI, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Edger", 
        "givenName": "Patrick P.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Missouri", 
          "id": "https://www.grid.ac/institutes/grid.134936.a", 
          "name": [
            "Division of Biological Sciences, University of Missouri, 65211, Columbia, MO, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pires", 
        "givenName": "J. Chris", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wageningen University & Research", 
          "id": "https://www.grid.ac/institutes/grid.4818.5", 
          "name": [
            "Biosystematics Group, Wageningen University, 6708 PB, Wageningen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schranz", 
        "givenName": "M. Eric", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Palack\u00fd University, Olomouc", 
          "id": "https://www.grid.ac/institutes/grid.10979.36", 
          "name": [
            "School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK", 
            "Laboratory of Growth Regulators, Centre of the Region Han\u00e1 for Biotechnological and Agricultural Research, Palack\u00fd University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Leubner-Metzger", 
        "givenName": "Gerhard", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Freiburg", 
          "id": "https://www.grid.ac/institutes/grid.5963.9", 
          "name": [
            "Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany", 
            "BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rensing", 
        "givenName": "Stefan A.", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1104/pp.110.171702", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000934969"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0022241", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001929217"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1003530107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004690775"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.000877", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005692655"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti610", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006001436"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkn705", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007096305"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1438-8677.2010.00373.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007991479"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/dvg.22877", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009319297"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11103-010-9603-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009405938", 
          "https://doi.org/10.1007/s11103-010-9603-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11103-010-9603-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009405938", 
          "https://doi.org/10.1007/s11103-010-9603-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/c3np20099j", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010140318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.113.233262", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010152785"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.plipres.2010.01.001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010699252"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.103846.109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010871920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btt688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012587298"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btt688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012587298"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.106.079574", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013386300"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-3040.2012.02542.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013565782"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/b978-0-12-394807-6.00209-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014251859"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1079/ssr2004159", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014892118"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-014-0550-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015222646", 
          "https://doi.org/10.1186/s13059-014-0550-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-014-0550-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015222646", 
          "https://doi.org/10.1186/s13059-014-0550-8"
        ], 
        "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": "https://doi.org/10.1111/tpj.12467", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017550947"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/nph.14355", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017722792"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btr026", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018328066"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ygeno.2006.11.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020849140"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btv351", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021132933"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3389/fpls.2013.00245", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022894769"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp616", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023247882"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0981-9428(01)01350-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023446715"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1117726108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023623551"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/nph.13432", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025182379"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btq057", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025260149"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00299-011-1180-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027690903", 
          "https://doi.org/10.1007/s00299-011-1180-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00299-011-1180-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027690903", 
          "https://doi.org/10.1007/s00299-011-1180-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0103207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027745843"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-014-0553-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027805047", 
          "https://doi.org/10.1186/s13059-014-0553-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-014-0553-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027805047", 
          "https://doi.org/10.1186/s13059-014-0553-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2005.02337.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027900238"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0000718", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028213885"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2009.04096.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029315031"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2009.04096.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029315031"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/pcp/pcn185", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032227879"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.plantsci.2016.08.012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034657869"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-12-s14-s2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034796819", 
          "https://doi.org/10.1186/1471-2105-12-s14-s2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks865", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036199832"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3389/fpls.2015.00284", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037431322"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.111.084103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037893627"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.13.3.495", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038125788"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/tpj.12735", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038972425"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2009.04011.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040197421"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2009.04011.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040197421"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-016-0881-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041902478", 
          "https://doi.org/10.1186/s13059-016-0881-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btu170", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042720804"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature07002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044718936", 
          "https://doi.org/10.1038/nature07002"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/tpj.12542", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045325195"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.112.096313", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045528404"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2014.06.006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045544701"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.2684", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045626706", 
          "https://doi.org/10.1038/ng.2684"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.124321.111", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046681345"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/25.17.3389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047265454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-9-118", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047291046", 
          "https://doi.org/10.1186/1471-2164-9-118"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.106.049221", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048584675"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msp188", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052429020"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msp188", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052429020"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btu638", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053282140"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/jxb/erw363", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059858738"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/pcp/pcv186", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059972002"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.15.01040", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060841608"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.16.00838", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060841747"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4161/psb.3.7.5577", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1072308652"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.16.00735", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084199412"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-017-1228-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085382661", 
          "https://doi.org/10.1186/s13059-017-1228-9"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-017-1228-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085382661", 
          "https://doi.org/10.1186/s13059-017-1228-9"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3732/ajb.1700091", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1090897782"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/tpj.13710", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091493596"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/tpj.13758", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1092457424"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/gbe/evx258", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1093159285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/tpj.13940", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1103518816"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/nph.15490", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1107082718"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.2517-6161.1995.tb02031.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1110458929"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.2517-6161.1995.tb02031.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1110458929"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019-12", 
    "datePublishedReg": "2019-12-01", 
    "description": "BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs).\nRESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms.\nCONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/s12864-019-5452-4", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.4124756", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3861488", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3864034", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "20"
      }
    ], 
    "name": "Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds", 
    "pagination": "95", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "05cdacb49f85ad7631ddaf2c66d959e3045baf3bb204e4a18caab5361e05de6d"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30700268"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s12864-019-5452-4"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1111769581"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s12864-019-5452-4", 
      "https://app.dimensions.ai/details/publication/pub.1111769581"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T09:01", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000330_0000000330/records_116375_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2Fs12864-019-5452-4"
  }
]
 

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/s12864-019-5452-4'

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/s12864-019-5452-4'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12864-019-5452-4'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12864-019-5452-4'


 

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

402 TRIPLES      21 PREDICATES      102 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s12864-019-5452-4 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N0019872c847c41b7b53af38c1cc6c7f2
4 schema:citation sg:pub.10.1007/s00299-011-1180-1
5 sg:pub.10.1007/s11103-010-9603-x
6 sg:pub.10.1038/nature07002
7 sg:pub.10.1038/nbt.1883
8 sg:pub.10.1038/ng.2684
9 sg:pub.10.1186/1471-2105-12-s14-s2
10 sg:pub.10.1186/1471-2164-9-118
11 sg:pub.10.1186/s13059-014-0550-8
12 sg:pub.10.1186/s13059-014-0553-5
13 sg:pub.10.1186/s13059-016-0881-8
14 sg:pub.10.1186/s13059-017-1228-9
15 https://doi.org/10.1002/dvg.22877
16 https://doi.org/10.1016/b978-0-12-394807-6.00209-4
17 https://doi.org/10.1016/j.cell.2014.06.006
18 https://doi.org/10.1016/j.plantsci.2016.08.012
19 https://doi.org/10.1016/j.plipres.2010.01.001
20 https://doi.org/10.1016/j.ygeno.2006.11.008
21 https://doi.org/10.1016/s0981-9428(01)01350-x
22 https://doi.org/10.1039/c3np20099j
23 https://doi.org/10.1073/pnas.1003530107
24 https://doi.org/10.1073/pnas.1117726108
25 https://doi.org/10.1079/ssr2004159
26 https://doi.org/10.1093/bioinformatics/bti610
27 https://doi.org/10.1093/bioinformatics/btp616
28 https://doi.org/10.1093/bioinformatics/btq057
29 https://doi.org/10.1093/bioinformatics/btr026
30 https://doi.org/10.1093/bioinformatics/btt688
31 https://doi.org/10.1093/bioinformatics/btu170
32 https://doi.org/10.1093/bioinformatics/btu638
33 https://doi.org/10.1093/bioinformatics/btv351
34 https://doi.org/10.1093/gbe/evx258
35 https://doi.org/10.1093/jxb/erw363
36 https://doi.org/10.1093/molbev/msp188
37 https://doi.org/10.1093/nar/25.17.3389
38 https://doi.org/10.1093/nar/gkn705
39 https://doi.org/10.1093/nar/gks865
40 https://doi.org/10.1093/pcp/pcn185
41 https://doi.org/10.1093/pcp/pcv186
42 https://doi.org/10.1101/gr.103846.109
43 https://doi.org/10.1101/gr.124321.111
44 https://doi.org/10.1104/pp.106.079574
45 https://doi.org/10.1104/pp.110.171702
46 https://doi.org/10.1104/pp.113.233262
47 https://doi.org/10.1104/pp.15.01040
48 https://doi.org/10.1104/pp.16.00838
49 https://doi.org/10.1105/tpc.000877
50 https://doi.org/10.1105/tpc.106.049221
51 https://doi.org/10.1105/tpc.111.084103
52 https://doi.org/10.1105/tpc.112.096313
53 https://doi.org/10.1105/tpc.13.3.495
54 https://doi.org/10.1105/tpc.16.00735
55 https://doi.org/10.1111/j.1365-3040.2012.02542.x
56 https://doi.org/10.1111/j.1365-313x.2005.02337.x
57 https://doi.org/10.1111/j.1365-313x.2009.04011.x
58 https://doi.org/10.1111/j.1365-313x.2009.04096.x
59 https://doi.org/10.1111/j.1438-8677.2010.00373.x
60 https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
61 https://doi.org/10.1111/nph.13432
62 https://doi.org/10.1111/nph.14355
63 https://doi.org/10.1111/nph.15490
64 https://doi.org/10.1111/tpj.12467
65 https://doi.org/10.1111/tpj.12542
66 https://doi.org/10.1111/tpj.12735
67 https://doi.org/10.1111/tpj.13710
68 https://doi.org/10.1111/tpj.13758
69 https://doi.org/10.1111/tpj.13940
70 https://doi.org/10.1371/journal.pone.0000718
71 https://doi.org/10.1371/journal.pone.0022241
72 https://doi.org/10.1371/journal.pone.0103207
73 https://doi.org/10.3389/fpls.2013.00245
74 https://doi.org/10.3389/fpls.2015.00284
75 https://doi.org/10.3732/ajb.1700091
76 https://doi.org/10.4161/psb.3.7.5577
77 schema:datePublished 2019-12
78 schema:datePublishedReg 2019-12-01
79 schema:description BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.
80 schema:genre research_article
81 schema:inLanguage en
82 schema:isAccessibleForFree true
83 schema:isPartOf N1666b3a3f2f34a01b292bd7850c20ab2
84 N956e1ff1fc2e4552a9bb6ca4e877f560
85 sg:journal.1023790
86 schema:name Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds
87 schema:pagination 95
88 schema:productId N2dd9ceaf8e1b4311a4a9454f092e611d
89 N74f04bf0ceb7439f8e70f3d7d38d17fc
90 N8b6da774b6944db6b5b9e78720863b35
91 N919707703c454ae68bda251a00b36dff
92 N9f625bbc27fd4438baa7d3c41f451059
93 schema:sameAs https://app.dimensions.ai/details/publication/pub.1111769581
94 https://doi.org/10.1186/s12864-019-5452-4
95 schema:sdDatePublished 2019-04-11T09:01
96 schema:sdLicense https://scigraph.springernature.com/explorer/license/
97 schema:sdPublisher Nbb3315c65c734f5a9bb370f535dde2d1
98 schema:url https://link.springer.com/10.1186%2Fs12864-019-5452-4
99 sgo:license sg:explorer/license/
100 sgo:sdDataset articles
101 rdf:type schema:ScholarlyArticle
102 N0019872c847c41b7b53af38c1cc6c7f2 rdf:first N207bf81bf0e44eb29bf49c2f2283c375
103 rdf:rest N62bdbb03d70342ddb01cbbb24731e57f
104 N12fde20a580d4a598fcc73b8afae7162 schema:affiliation https://www.grid.ac/institutes/grid.10253.35
105 schema:familyName Buchta
106 schema:givenName Karl
107 rdf:type schema:Person
108 N1666b3a3f2f34a01b292bd7850c20ab2 schema:volumeNumber 20
109 rdf:type schema:PublicationVolume
110 N16695acbd63e455cbd38d094f8306a37 rdf:first N478afe3c9e2d4f1e8863afb1697955e6
111 rdf:rest rdf:nil
112 N1a6a8f858f0d40039542e67596d2eb7d schema:affiliation https://www.grid.ac/institutes/grid.10253.35
113 schema:familyName Ullrich
114 schema:givenName Kristian K.
115 rdf:type schema:Person
116 N1ba17f7e7017434f92cba55398b90ded schema:affiliation https://www.grid.ac/institutes/grid.10253.35
117 schema:familyName Fernandez-Pozo
118 schema:givenName Noe
119 rdf:type schema:Person
120 N20439ab3881947e7be3094b235475898 schema:affiliation https://www.grid.ac/institutes/grid.10979.36
121 schema:familyName Leubner-Metzger
122 schema:givenName Gerhard
123 rdf:type schema:Person
124 N207bf81bf0e44eb29bf49c2f2283c375 schema:affiliation https://www.grid.ac/institutes/grid.10253.35
125 schema:familyName Wilhelmsson
126 schema:givenName Per K. I.
127 rdf:type schema:Person
128 N27240658fe294528bc9b968bfa51952e rdf:first N73578e3222bb4c3d9801cb370c708cc6
129 rdf:rest N55837cf3402646f9a2f5506226cfe644
130 N2dd9ceaf8e1b4311a4a9454f092e611d schema:name readcube_id
131 schema:value 05cdacb49f85ad7631ddaf2c66d959e3045baf3bb204e4a18caab5361e05de6d
132 rdf:type schema:PropertyValue
133 N478afe3c9e2d4f1e8863afb1697955e6 schema:affiliation https://www.grid.ac/institutes/grid.5963.9
134 schema:familyName Rensing
135 schema:givenName Stefan A.
136 rdf:type schema:Person
137 N506839083a1c49368c3d2f49a4568e28 rdf:first N921a81d16d014aeda8d2e48aea5881c5
138 rdf:rest Ndeb13bb9de944f9ba04a6a597f255741
139 N55837cf3402646f9a2f5506226cfe644 rdf:first N12fde20a580d4a598fcc73b8afae7162
140 rdf:rest N7addecebe7984caaab48bf9a56907807
141 N5b3b6738ea52462b86c823a8c7d50436 schema:affiliation https://www.grid.ac/institutes/grid.4970.a
142 schema:familyName Chandler
143 schema:givenName Jake O.
144 rdf:type schema:Person
145 N5b3b892b15b947ddb1fa8a40b42566d0 rdf:first N1ba17f7e7017434f92cba55398b90ded
146 rdf:rest N9d0a31e5b8ab4aba857fafc4e1284e4d
147 N5de29833562f4b5686db7cb1d0f61604 schema:affiliation https://www.grid.ac/institutes/grid.17088.36
148 schema:familyName Edger
149 schema:givenName Patrick P.
150 rdf:type schema:Person
151 N62bdbb03d70342ddb01cbbb24731e57f rdf:first N5b3b6738ea52462b86c823a8c7d50436
152 rdf:rest N5b3b892b15b947ddb1fa8a40b42566d0
153 N7199fbe1567546dca993dd73bfa59d35 rdf:first N20439ab3881947e7be3094b235475898
154 rdf:rest N16695acbd63e455cbd38d094f8306a37
155 N73578e3222bb4c3d9801cb370c708cc6 schema:affiliation https://www.grid.ac/institutes/grid.4818.5
156 schema:familyName Hofberger
157 schema:givenName Johannes A.
158 rdf:type schema:Person
159 N74f04bf0ceb7439f8e70f3d7d38d17fc schema:name dimensions_id
160 schema:value pub.1111769581
161 rdf:type schema:PropertyValue
162 N7770fd26088d44de9b151ef01e000dfc schema:affiliation https://www.grid.ac/institutes/grid.4970.a
163 schema:familyName Khan
164 schema:givenName Safina
165 rdf:type schema:Person
166 N7addecebe7984caaab48bf9a56907807 rdf:first N5de29833562f4b5686db7cb1d0f61604
167 rdf:rest N506839083a1c49368c3d2f49a4568e28
168 N8b6da774b6944db6b5b9e78720863b35 schema:name pubmed_id
169 schema:value 30700268
170 rdf:type schema:PropertyValue
171 N919707703c454ae68bda251a00b36dff schema:name doi
172 schema:value 10.1186/s12864-019-5452-4
173 rdf:type schema:PropertyValue
174 N921a81d16d014aeda8d2e48aea5881c5 schema:affiliation https://www.grid.ac/institutes/grid.134936.a
175 schema:familyName Pires
176 schema:givenName J. Chris
177 rdf:type schema:Person
178 N956e1ff1fc2e4552a9bb6ca4e877f560 schema:issueNumber 1
179 rdf:type schema:PublicationIssue
180 N9d0a31e5b8ab4aba857fafc4e1284e4d rdf:first Na1e542a556c54ea3bccc464e6b2c46fc
181 rdf:rest Ndb32f0cf44f54ae08fbcbaaffc167fcd
182 N9df32bdbf0db481a8d5702f491cc502f schema:affiliation https://www.grid.ac/institutes/grid.4970.a
183 schema:familyName Arshad
184 schema:givenName Waheed
185 rdf:type schema:Person
186 N9f625bbc27fd4438baa7d3c41f451059 schema:name nlm_unique_id
187 schema:value 100965258
188 rdf:type schema:PropertyValue
189 Na1e542a556c54ea3bccc464e6b2c46fc schema:affiliation https://www.grid.ac/institutes/grid.4970.a
190 schema:familyName Graeber
191 schema:givenName Kai
192 rdf:type schema:Person
193 Nb48e99fef0e246adb17176ce6bcb4e92 rdf:first N7770fd26088d44de9b151ef01e000dfc
194 rdf:rest N27240658fe294528bc9b968bfa51952e
195 Nbb3315c65c734f5a9bb370f535dde2d1 schema:name Springer Nature - SN SciGraph project
196 rdf:type schema:Organization
197 Ndb32f0cf44f54ae08fbcbaaffc167fcd rdf:first N1a6a8f858f0d40039542e67596d2eb7d
198 rdf:rest Nfcc813625cc041b795e3876841e7f355
199 Ndeb13bb9de944f9ba04a6a597f255741 rdf:first Nf737a525b15d49efbd0e7dcedda6b416
200 rdf:rest N7199fbe1567546dca993dd73bfa59d35
201 Nf737a525b15d49efbd0e7dcedda6b416 schema:affiliation https://www.grid.ac/institutes/grid.4818.5
202 schema:familyName Schranz
203 schema:givenName M. Eric
204 rdf:type schema:Person
205 Nfcc813625cc041b795e3876841e7f355 rdf:first N9df32bdbf0db481a8d5702f491cc502f
206 rdf:rest Nb48e99fef0e246adb17176ce6bcb4e92
207 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
208 schema:name Biological Sciences
209 rdf:type schema:DefinedTerm
210 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
211 schema:name Genetics
212 rdf:type schema:DefinedTerm
213 sg:grant.3861488 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-019-5452-4
214 rdf:type schema:MonetaryGrant
215 sg:grant.3864034 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-019-5452-4
216 rdf:type schema:MonetaryGrant
217 sg:grant.4124756 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-019-5452-4
218 rdf:type schema:MonetaryGrant
219 sg:journal.1023790 schema:issn 1471-2164
220 schema:name BMC Genomics
221 rdf:type schema:Periodical
222 sg:pub.10.1007/s00299-011-1180-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027690903
223 https://doi.org/10.1007/s00299-011-1180-1
224 rdf:type schema:CreativeWork
225 sg:pub.10.1007/s11103-010-9603-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1009405938
226 https://doi.org/10.1007/s11103-010-9603-x
227 rdf:type schema:CreativeWork
228 sg:pub.10.1038/nature07002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044718936
229 https://doi.org/10.1038/nature07002
230 rdf:type schema:CreativeWork
231 sg:pub.10.1038/nbt.1883 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015803168
232 https://doi.org/10.1038/nbt.1883
233 rdf:type schema:CreativeWork
234 sg:pub.10.1038/ng.2684 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045626706
235 https://doi.org/10.1038/ng.2684
236 rdf:type schema:CreativeWork
237 sg:pub.10.1186/1471-2105-12-s14-s2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034796819
238 https://doi.org/10.1186/1471-2105-12-s14-s2
239 rdf:type schema:CreativeWork
240 sg:pub.10.1186/1471-2164-9-118 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047291046
241 https://doi.org/10.1186/1471-2164-9-118
242 rdf:type schema:CreativeWork
243 sg:pub.10.1186/s13059-014-0550-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015222646
244 https://doi.org/10.1186/s13059-014-0550-8
245 rdf:type schema:CreativeWork
246 sg:pub.10.1186/s13059-014-0553-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027805047
247 https://doi.org/10.1186/s13059-014-0553-5
248 rdf:type schema:CreativeWork
249 sg:pub.10.1186/s13059-016-0881-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041902478
250 https://doi.org/10.1186/s13059-016-0881-8
251 rdf:type schema:CreativeWork
252 sg:pub.10.1186/s13059-017-1228-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085382661
253 https://doi.org/10.1186/s13059-017-1228-9
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1002/dvg.22877 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009319297
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1016/b978-0-12-394807-6.00209-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014251859
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1016/j.cell.2014.06.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045544701
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1016/j.plantsci.2016.08.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034657869
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1016/j.plipres.2010.01.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010699252
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1016/j.ygeno.2006.11.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020849140
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1016/s0981-9428(01)01350-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1023446715
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1039/c3np20099j schema:sameAs https://app.dimensions.ai/details/publication/pub.1010140318
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1073/pnas.1003530107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004690775
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1073/pnas.1117726108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023623551
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1079/ssr2004159 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014892118
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1093/bioinformatics/bti610 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006001436
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1093/bioinformatics/btp616 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023247882
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1093/bioinformatics/btq057 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025260149
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1093/bioinformatics/btr026 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018328066
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1093/bioinformatics/btt688 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012587298
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1093/bioinformatics/btu170 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042720804
288 rdf:type schema:CreativeWork
289 https://doi.org/10.1093/bioinformatics/btu638 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053282140
290 rdf:type schema:CreativeWork
291 https://doi.org/10.1093/bioinformatics/btv351 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021132933
292 rdf:type schema:CreativeWork
293 https://doi.org/10.1093/gbe/evx258 schema:sameAs https://app.dimensions.ai/details/publication/pub.1093159285
294 rdf:type schema:CreativeWork
295 https://doi.org/10.1093/jxb/erw363 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059858738
296 rdf:type schema:CreativeWork
297 https://doi.org/10.1093/molbev/msp188 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052429020
298 rdf:type schema:CreativeWork
299 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
300 rdf:type schema:CreativeWork
301 https://doi.org/10.1093/nar/gkn705 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007096305
302 rdf:type schema:CreativeWork
303 https://doi.org/10.1093/nar/gks865 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036199832
304 rdf:type schema:CreativeWork
305 https://doi.org/10.1093/pcp/pcn185 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032227879
306 rdf:type schema:CreativeWork
307 https://doi.org/10.1093/pcp/pcv186 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059972002
308 rdf:type schema:CreativeWork
309 https://doi.org/10.1101/gr.103846.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010871920
310 rdf:type schema:CreativeWork
311 https://doi.org/10.1101/gr.124321.111 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046681345
312 rdf:type schema:CreativeWork
313 https://doi.org/10.1104/pp.106.079574 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013386300
314 rdf:type schema:CreativeWork
315 https://doi.org/10.1104/pp.110.171702 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000934969
316 rdf:type schema:CreativeWork
317 https://doi.org/10.1104/pp.113.233262 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010152785
318 rdf:type schema:CreativeWork
319 https://doi.org/10.1104/pp.15.01040 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060841608
320 rdf:type schema:CreativeWork
321 https://doi.org/10.1104/pp.16.00838 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060841747
322 rdf:type schema:CreativeWork
323 https://doi.org/10.1105/tpc.000877 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005692655
324 rdf:type schema:CreativeWork
325 https://doi.org/10.1105/tpc.106.049221 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048584675
326 rdf:type schema:CreativeWork
327 https://doi.org/10.1105/tpc.111.084103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037893627
328 rdf:type schema:CreativeWork
329 https://doi.org/10.1105/tpc.112.096313 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045528404
330 rdf:type schema:CreativeWork
331 https://doi.org/10.1105/tpc.13.3.495 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038125788
332 rdf:type schema:CreativeWork
333 https://doi.org/10.1105/tpc.16.00735 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084199412
334 rdf:type schema:CreativeWork
335 https://doi.org/10.1111/j.1365-3040.2012.02542.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1013565782
336 rdf:type schema:CreativeWork
337 https://doi.org/10.1111/j.1365-313x.2005.02337.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1027900238
338 rdf:type schema:CreativeWork
339 https://doi.org/10.1111/j.1365-313x.2009.04011.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1040197421
340 rdf:type schema:CreativeWork
341 https://doi.org/10.1111/j.1365-313x.2009.04096.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1029315031
342 rdf:type schema:CreativeWork
343 https://doi.org/10.1111/j.1438-8677.2010.00373.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1007991479
344 rdf:type schema:CreativeWork
345 https://doi.org/10.1111/j.2517-6161.1995.tb02031.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1110458929
346 rdf:type schema:CreativeWork
347 https://doi.org/10.1111/nph.13432 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025182379
348 rdf:type schema:CreativeWork
349 https://doi.org/10.1111/nph.14355 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017722792
350 rdf:type schema:CreativeWork
351 https://doi.org/10.1111/nph.15490 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107082718
352 rdf:type schema:CreativeWork
353 https://doi.org/10.1111/tpj.12467 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017550947
354 rdf:type schema:CreativeWork
355 https://doi.org/10.1111/tpj.12542 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045325195
356 rdf:type schema:CreativeWork
357 https://doi.org/10.1111/tpj.12735 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038972425
358 rdf:type schema:CreativeWork
359 https://doi.org/10.1111/tpj.13710 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091493596
360 rdf:type schema:CreativeWork
361 https://doi.org/10.1111/tpj.13758 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092457424
362 rdf:type schema:CreativeWork
363 https://doi.org/10.1111/tpj.13940 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103518816
364 rdf:type schema:CreativeWork
365 https://doi.org/10.1371/journal.pone.0000718 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028213885
366 rdf:type schema:CreativeWork
367 https://doi.org/10.1371/journal.pone.0022241 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001929217
368 rdf:type schema:CreativeWork
369 https://doi.org/10.1371/journal.pone.0103207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027745843
370 rdf:type schema:CreativeWork
371 https://doi.org/10.3389/fpls.2013.00245 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022894769
372 rdf:type schema:CreativeWork
373 https://doi.org/10.3389/fpls.2015.00284 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037431322
374 rdf:type schema:CreativeWork
375 https://doi.org/10.3732/ajb.1700091 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090897782
376 rdf:type schema:CreativeWork
377 https://doi.org/10.4161/psb.3.7.5577 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072308652
378 rdf:type schema:CreativeWork
379 https://www.grid.ac/institutes/grid.10253.35 schema:alternateName Philipp University of Marburg
380 schema:name Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
381 Present Address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Ploen, Germany
382 rdf:type schema:Organization
383 https://www.grid.ac/institutes/grid.10979.36 schema:alternateName Palacký University, Olomouc
384 schema:name Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic
385 School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK
386 rdf:type schema:Organization
387 https://www.grid.ac/institutes/grid.134936.a schema:alternateName University of Missouri
388 schema:name Division of Biological Sciences, University of Missouri, 65211, Columbia, MO, USA
389 rdf:type schema:Organization
390 https://www.grid.ac/institutes/grid.17088.36 schema:alternateName Michigan State University
391 schema:name Department of Horticulture, Michigan State University, 48864, East Lansing, MI, USA
392 rdf:type schema:Organization
393 https://www.grid.ac/institutes/grid.4818.5 schema:alternateName Wageningen University & Research
394 schema:name Biosystematics Group, Wageningen University, 6708 PB, Wageningen, The Netherlands
395 rdf:type schema:Organization
396 https://www.grid.ac/institutes/grid.4970.a schema:alternateName Royal Holloway University of London
397 schema:name School of Biological Sciences, Royal Holloway University of London, TW20 0EX, Egham, Surrey, UK
398 rdf:type schema:Organization
399 https://www.grid.ac/institutes/grid.5963.9 schema:alternateName University of Freiburg
400 schema:name BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
401 Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
402 rdf:type schema:Organization
 




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


...