title: Improvement of barley genome annotations by deciphering the Haruna Nijo genome.
abstract: Full-length (FL) cDNA sequences provide the most reliable evidence for the presence of genes in genomes. In this report, detailed gene structures of barley, whole genome shotgun (WGS) and additional transcript data of the cultivar Haruna Nijo were quality controlled and compared with the published Morex genome information. Haruna Nijo scaffolds have longer total sequence length with much higher N50 and fewer sequences than those in Morex WGS contigs. The longer Haruna Nijo scaffolds provided efficient FLcDNA mapping, resulting in high coverage and detection of the transcription start sites. In combination with FLcDNAs and RNA-Seq data from four different tissue samples of Haruna Nijo, we identified 51,249 gene models on 30,606 loci. Overall sequence similarity between Haruna Nijo and Morex genome was 95.99%, while that of exon regions was higher (99.71%). These sequence and annotation data of Haruna Nijo are combined with Morex genome data and released from a genome browser. The genome sequence of Haruna Nijo may provide detailed gene structures in addition to the current Morex barley genome information.
authors.affiliation: Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan kazsato@rib.okayama-u.ac.jp.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Sato
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.affiliation: National Institute for Basic Biology, Okazaki 444-8585, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Shigenobu
authors.affiliation: Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Motoi
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
mesh_terms: D001483:Base Sequence; D018076:DNA, Complementary; D066289:Data Curation; D018745:Genome, Plant; D023281:Genomics; D001467:Hordeum / Q000235:genetics*; D058977:Molecular Sequence Annotation; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018076:DNA, Complementary
keywords: Hordeum; RNA-Seq; full-length cDNA; genome sequencing