TY - JOUR
T1 - Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)
AU - Hisano, Hiroshi
AU - Tsujimura, Mai
AU - Yoshida, Hideya
AU - Terachi, Toru
AU - Sato, Kazuhiro
N1 - Funding Information:
KS is supported by the scientific technique research promotion program for agriculture, forestry fisheries and food industry of Japan (grant Number 25013A) and JSPS KAKENHI (grant Number JP15K07257). TT is supported by JSPS KAKENHI (grant Number JP26292007). We thank Dr. Tsuyoshi Tanaka for repeat sequence analysis and Ms. Yuka Motoi, Ms. Hiromi Ando and Ms. Nami Yamaji for technical assistance. Barley seeds were provided by the National Bioresource Project of Barley, MEXT of Japan.
Publisher Copyright:
© 2016 The Author(s).
PY - 2016/10/24
Y1 - 2016/10/24
N2 - Background: 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. Results: 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. Conclusions: 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.
AB - Background: 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. Results: 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. Conclusions: 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.
KW - Comparative genomics
KW - De novo assembly
KW - Hordeum vulgare
KW - Mitochondrial genome
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U2 - 10.1186/s12864-016-3159-3
DO - 10.1186/s12864-016-3159-3
M3 - Article
C2 - 27776481
AN - SCOPUS:84992432073
VL - 17
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 1
M1 - 824
ER -