Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes. (6th January 2014)

• Record Type: Journal Article
• Authors: Hirsch, Cory D.; Evans, Joseph; Buell, C. Robin; Hirsch, Candice N.
• Is Part Of: Briefings in functional genomics. Volume 13:Number 4(2014:Jul.)
• Page Start: 257
• Page End: 267
• Publication Date: 2014-01-06
• Subjects: exome capture -- re-sequencing -- genome diversity -- RNA-Seq; Genomics -- Methodology -- Periodicals; Genomics -- Technological innovations -- Periodicals; 572.86072
• DOI: 10.1093/bfgp/elt051
• Languages: English
• ISSNs: 2041-2649

Abstract

Abstract : Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security.