The complete mitochondrial genome sequence of Brassica oleracea and analysis of coexisting mitotypes

Abstract

The complete mitochondrial genome sequences of Brassica species have provided insight into inter- and intraspecific variation of plant mitochondrial genomes. However, the size of mitochondrial genome sequenced for Brassica oleracea hitherto does not match to its physical mapping data. This fact led us to investigate B. oleracea mitochondrial genome in detail. Here we report novel B. oleracea mitochondrial genome, derived from var. capitata, a cabbage cultivar ''Fujiwase''. The genome was assembled into a 219,952-bp circular sequence that is comparable to the mitochondrial genomes of other Brassica species (ca. 220-232 kb). This genome contained 34 protein-coding genes, 3 rRNA genes and 17 tRNA genes. Due to absence of a large repeat (140 kb), the mitochondrial genome of ''Fujiwase'' is clearly smaller than the previously reported mitochondrial genome of B. oleracea accession ''08C717'' (360 kb). In both mitotypes, all genes were identical, except cox2-2, which was present only in the Fujiwase type. At least two rearrangement events via large and small repeat sequences have contributed to the structural differences between the two mitotypes. PCR-based marker analysis revealed that the Fujiwase type is predominant, whereas the 08C717 type coexists at low frequency in all B. oleracea cultivars examined. Intraspecific variations in the mitochondrial genome in B. oleracea may occur because of heteroplasmy, coexistence of different mitotypes within an individual, and substoichiometric shifting. Our data indicate that the Fujiwase-type genome should be used as the representative genome of B. oleracea.

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica

“…), and this heteroplasmic phenomenon was also observed in B. oleracea , of which sub‐stoichiometrical mitotypes coexist in the 08C717‐ and Fujiwase‐type B. oleracea mitochondrial genome (Tanaka et al . ).…”

“…The processes driving the rapid evolution of plant mitochondrial genomes are directly linked to the intrinsic heteroplasmy of the mtDNA (Kmiec et al 2006). Sub-stoichiometric mitotypes coexist in napus-and polima-type B. napus mitochondrial genomes , and this heteroplasmic phenomenon was also observed in B. oleracea, of which sub-stoichiometrical mitotypes coexist in the 08C717-and Fujiwase-type B. oleracea mitochondrial genome (Tanaka et al 2014).…”

“…; Sloan ; Tanaka et al . ). This dynamic organisation of the angiosperm mitochondrial genome provides an appropriate framework for studying genome structure and evolution.…”

“…In terms of structure, angiosperm mitochondrial genomes are typically mapped as circular molecules with one or more larger (>1 kb) repetitive sequences, which promote active homologous inter-and intra-genomic recombination. This can lead to dynamic structural diversity, consisting of multiple, coexisting mitochondrial genomic forms (Palmer & Shields 1984;Marechal & Brisson 2010;Chang et al 2011;Chen et al 2011;Mower et al 2012a;Sloan 2013;Tanaka et al 2014). This dynamic organisation of the angiosperm mitochondrial genome provides an appropriate framework for studying genome structure and evolution.…”

“…This is U's triangle theory of evolution in Brassica (Nagaharu 1935). Mitochondrial genome sequencing was completed in B. napus (Handa 2003;Chang et al 2011), B. rapa (Chang et al 2011), B. oleracea (Chang et al 2011Grewe et al 2014;Tanaka et al 2014), B. juncea ) and B. carinata ). Because of their small sizes (200-300 kb), the mitochondrial genome sequences of these five Brassica species served as an early model for understanding genomic structure and evolution in Brassica species.…”