ena-PROJECT-xxx-04-12-2012-12:34:50:115-14
Whole Genome Shotgun Sequencing and Assembly of Barley cv. Barke
Barley (Hordeum vulgare L.) is amongst the oldest domesticated crop plants and remains one of the world’s most important crop species. It is diploid with a haploid genome of 5.1 gigabases (Gb), twice the size of those of human and maize, and closely related to the most widely grown crop, hexaploid wheat. To meet global demand for food, feed and fibre, it is commonly agreed that reference genome sequences of our crop plants are urgently required to enable genome-assisted crop improvement. Here we present the gene-ome of the barley cultivar (cv.) Morex. Despite its genome comprising >84% repetitive sequence, we provide an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physicalmap with a cumulative length of 4.98 Gb, 4.56 Gb assigned to individual chromosome arms and more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole genome shotgun (WGS) assembly, cDNA and RNA-seq data onto this framework provides support for 79,379 transcript clusters, with 75,258 anchored to the WGS. A ‘high confidence’ (HC) set of 26,159 genes has homology support from other plant genomes. These HC genes exhibit dynamic patterns of gene expression with extensive developmental and tissue specific post-transcriptional regulation. We observe abundant alternative splicing (AS), premature stop codons (PTCs) and novel transcriptionally active regions (nTARs) that suggest post-transcriptional processing in barley forms an important regulatory layer. WGS survey sequences from additional cultivars and a wild barley accession reveal a landscape of extensive single nucleotide variation (SNV) and evidence for islands of reduced diversity likely a product of recent breeding history. The barley gene-ome represents a new paradigm for genomeassisted research in a very large crop genome and paves the way for genomics-based crop improvement.
Barley (Hordeum vulgare L.) is amongst the oldest domesticated crop plants and remains one of the world’s most important crop species. It is diploid with a haploid genome of 5.1 gigabases (Gb), twice the size of those of human and maize, and closely related to the most widely grown crop, hexaploid wheat. To meet global demand for food, feed and fibre, it is commonly agreed that reference genome sequences of our crop plants are urgently required to enable genome-assisted crop improvement. Here we present the gene-ome of the barley cultivar (cv.) Morex. Despite its genome comprising >84% repetitive sequence, we provide an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physicalmap with a cumulative length of 4.98 Gb, 4.56 Gb assigned to individual chromosome arms and more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole genome shotgun (WGS) assembly, cDNA and RNA-seq data onto this framework provides support for 79,379 transcript clusters, with 75,258 anchored to the WGS. A ‘high confidence’ (HC) set of 26,159 genes has homology support from other plant genomes. These HC genes exhibit dynamic patterns of gene expression with extensive developmental and tissue specific post-transcriptional regulation. We observe abundant alternative splicing (AS), premature stop codons (PTCs) and novel transcriptionally active regions (nTARs) that suggest post-transcriptional processing in barley forms an important regulatory layer. WGS survey sequences from additional cultivars and a wild barley accession reveal a landscape of extensive single nucleotide variation (SNV) and evidence for islands of reduced diversity likely a product of recent breeding history. The barley gene-ome represents a new paradigm for genomeassisted research in a very large crop genome and paves the way for genomics-based crop improvement.