Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-11

AUTHORS

Michael C Schatz, Lyza G Maron, Joshua C Stein, Alejandro Hernandez Wences, James Gurtowski, Eric Biggers, Hayan Lee, Melissa Kramer, Eric Antoniou, Elena Ghiban, Mark H Wright, Jer-ming Chia, Doreen Ware, Susan R McCouch, W Richard McCombie

ABSTRACT

The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the ‘pan-genome’ of three divergent rice varieties and document several megabases of each genome absent in the other two. Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species. More... »

PAGES

506

References to SciGraph publications

  • 2010-11. Quake: quality-aware detection and correction of sequencing errors in GENOME BIOLOGY
  • 2005-08. The map-based sequence of the rice genome in NATURE
  • 2013-12. Rayada specialty: the forgotten resource of elite features of rice in RICE
  • 2002-12. The relationship of protein conservation and sequence length in BMC EVOLUTIONARY BIOLOGY
  • 2004-12. Gene finding in novel genomes in BMC BIOINFORMATICS
  • 2011-09. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa in NATURE COMMUNICATIONS
  • 1992-09. Segregation distortion via male gametes in hybrids between Indica and Japonica or wide-compatibility varieties of rice (Oryza sativa L) in THEORETICAL AND APPLIED GENETICS
  • 2009-08. The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water in NATURE
  • 2008-11. Control of a key transition from prostrate to erect growth in rice domestication in NATURE GENETICS
  • 1991. Molecular Markers in Rice Systematics and the Evaluation of Genetic Resources in RICE
  • 2012-01. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes in NATURE BIOTECHNOLOGY
  • 2011-12. Detection of copy number variations in rice using array-based comparative genomic hybridization in BMC GENOMICS
  • 2008-03. Genome assembly forensics: finding the elusive mis-assembly in GENOME BIOLOGY
  • 2008-12. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes in BMC GENOMICS
  • 2011-12. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects in BMC BIOINFORMATICS
  • 2002-11. Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil in THEORETICAL AND APPLIED GENETICS
  • 2014-12. The 3,000 rice genomes project: new opportunities and challenges for future rice research in GIGASCIENCE
  • 2010-11. Genome-wide association studies of 14 agronomic traits in rice landraces in NATURE GENETICS
  • 2006-08. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice in NATURE
  • 1995-02. Molecular analysis of the inheritance of the S-5 locus, conferring wide compatibility in Indica/Japonica hybrids of rice (O. sativa L.) in THEORETICAL AND APPLIED GENETICS
  • 2010-12. Novel genes exhibit distinct patterns of function acquisition and network integration in GENOME BIOLOGY
  • 2012-12. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler in GIGASCIENCE
  • 2013-09. Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions in NATURE GENETICS
  • 2007-11. A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies in PLANT MOLECULAR BIOLOGY
  • 2013-12. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data in RICE
  • 2009-03. Characterization of the effect of a QTL for drought resistance in rice, qtl12.1, over a range of environments in the Philippines and eastern India in EUPHYTICA
  • 2012-10-03. A map of rice genome variation reveals the origin of cultivated rice in NATURE
  • 2008-08. Deletion in a gene associated with grain size increased yields during rice domestication in NATURE GENETICS
  • 2013-06. The advantages of SMRT sequencing in GENOME BIOLOGY
  • 2007-12. Transposable element distribution, abundance and role in genome size variation in the genus Oryza in BMC EVOLUTIONARY BIOLOGY
  • 2004-01. Versatile and open software for comparing large genomes in GENOME BIOLOGY
  • 2013-12. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species in GIGASCIENCE
  • 2012-08. The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency in NATURE
  • 2007-12. Highly asymmetric rice genomes in BMC GENOMICS
  • 1998-10. Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.) in THEORETICAL AND APPLIED GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-014-0506-z

    DOI

    http://dx.doi.org/10.1186/s13059-014-0506-z

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1045336903


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