title: Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare).
abstract: Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. vulgare ssp. vulgare) have cross compatibility and closely related genomes, although a significant number of nucleotide polymorphisms have been reported between their genomes.
  
  
  
  We determined the complete nucleotide sequences of the mitochondrial genomes of wild and cultivated barley. Two independent circular maps of the 525,599 bp barley mitochondrial genome were constructed by de novo assembly of high-throughput sequencing reads of barley lines H602 and Haruna Nijo, with only three SNPs detected between haplotypes. These mitochondrial genomes contained 33 protein-coding genes, three ribosomal RNAs, 16 transfer RNAs, 188 new ORFs, six major repeat sequences and several types of transposable elements. Of the barley mitochondrial genome-encoded proteins, NAD6, NAD9 and RPS4 had unique structures among grass species.
  
  
  
  The mitochondrial genome of barley was similar to those of other grass species in terms of gene content, but the configuration of the genes was highly differentiated from that of other grass species. Mitochondrial genome sequencing is essential for annotating the barley nuclear genome; our mitochondrial sequencing identified a significant number of fragmented mitochondrial sequences in the reported nuclear genome sequences. Little polymorphism was detected in the barley mitochondrial genome sequences, which should be explored further to elucidate the evolution of barley.
authors: Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
authors: Hiroshi
authors: H
authors: Hisano
authors: Plant Organelle Genomics Research Center and Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan.
authors: Mai
authors: M
authors: Tsujimura
authors: Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
authors: Hideya
authors: H
authors: Yoshida
authors: Plant Organelle Genomics Research Center and Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan.
authors: Toru
authors: T
authors: Terachi
authors: Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan. kazsato@rib.okayama-u.ac.jp.
authors: Kazuhiro
authors: 0000-0001-8818-5203
authors: K
authors: Sato
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000235:genetics*; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements
keywords: Comparative genomics; De novo assembly; Hordeum vulgare; Mitochondrial genome