Improvement of barley genome annotations by deciphering the Haruna Nijo genome

Kazuhiro Sato, Tsuyoshi Tanaka, Shuji Shigenobu, Yuka Motoi, Jianzhong Wu, Takeshi Itoh

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)21-28
Number of pages8
JournalDNA Research
Volume23
Issue number1
DOIs
Publication statusPublished - Aug 2 2015

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Hordeum
Genome
Firearms
Genes
Transcription Initiation Site
Exons
Complementary DNA
RNA

Keywords

  • full-length cDNA
  • genome sequencing
  • Hordeum
  • RNA-Seq

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Improvement of barley genome annotations by deciphering the Haruna Nijo genome. / Sato, Kazuhiro; Tanaka, Tsuyoshi; Shigenobu, Shuji; Motoi, Yuka; Wu, Jianzhong; Itoh, Takeshi.

In: DNA Research, Vol. 23, No. 1, 02.08.2015, p. 21-28.

Research output: Contribution to journalArticle

Sato, K, Tanaka, T, Shigenobu, S, Motoi, Y, Wu, J & Itoh, T 2015, 'Improvement of barley genome annotations by deciphering the Haruna Nijo genome', DNA Research, vol. 23, no. 1, pp. 21-28. https://doi.org/10.1093/dnares/dsv033
Sato, Kazuhiro ; Tanaka, Tsuyoshi ; Shigenobu, Shuji ; Motoi, Yuka ; Wu, Jianzhong ; Itoh, Takeshi. / Improvement of barley genome annotations by deciphering the Haruna Nijo genome. In: DNA Research. 2015 ; Vol. 23, No. 1. pp. 21-28.
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