Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

Abstract

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.

Keywords: Comparative genomics; De novo assembly; Hordeum vulgare; Mitochondrial genome.

Fig. 1

Positions of genes on the barley mitochondrial genome map (Hordeum vulgare ssp. spontaneum acc. H602). Genes encoding proteins (red), rRNA (orange) and tRNA (blue) are shown outside (forward direction) and inside (reverse complementary direction) the circle. Arrowhead indicates gene or exon, p indicates pseudogene, a, b, c, d and e indicate cis- and trans-spliced genic exon and underscores followed by numbers indicate gene copies

Fig. 2

Repeat sequences and integrated chloroplast genome in the map of the barley mitochondrial genome of accession H602. Repeat sequences in different colors are mapped onto the barley mitochondrial genome (outside). Detailed information about these repeats is shown in Additional file 6: Table S6. The predicted sequences integrated from the chloroplast genome are shown inside the circle

Fig. 3

Structures of the encoded protein sequences in various grass species. The structures of a NAD6, b NAD9 and c RPS4 in the barley mitochondrial genome were compared with those of seven other grass species and subspecies (T. timopheevii, Ae. speltoides, L. perenne, S. bicolor, Z. mays, O. sativa ssp. japonica and O. sativa ssp. indica). Light blue bars show the primary structures of proteins, and orange lines indicate the start codon. The numbers above the light blue bars indicate the position from the start codons of barley proteins. a Green box I indicates the non-conserved amino acid sequences in NAD6 among grass species. b NAD9 of T. aestivum, Ae. speltoides and T. timopheevii have an additional 97 aa on their N-terminal side compared with those of other grass species including barley. c Red bars indicate 13 aa repeats. Green boxes II and III indicate species-specific amino acid sequences in RPS4

Fig. 4

Phylogenetic tree constructed using the DNA sequences of 24 protein-coding genes comprising a total of 23,875 bp in the mitochondrial genomes of eight grass species and subspecies by the maximum likelihood method. The protein-coding genes include all electron transport chain genes, ccmB, ccmC, ccmFN, matR and mttB. The sequences of these genes can be found under the following accession numbers: AP013106 (T. timopheevii), AP013107 (Ae. speltoides), JX999996 (L. perenne), DQ984518 (S. bicolor), AY506529 (Z. mays), BA000029 (O. sativa ssp. japonica) and DQ167399 (O. sativa ssp. indica). The percentage of trees in which the associated taxa clustered together in 1000 replicates of the bootstrap test is shown next to the branches. Scale bar indicates the number of base substitutions per site