Comparative analysis of the complete chloroplast genome sequences of a normal male-fertile cytoplasm and two different cytoplasms conferring cytoplasmic male sterility in onion (Allium cepa L.)

The complete chloroplast genome sequences of a normal male-fertile (N) and two male-sterile (CMS) cytoplasms of onion (Allium cepa L.) were produced by next-generation sequencing (Illumina HiSeq2000). The sizes of the normal (N), CMS-S, and CMS-T chloroplast genomes were 153,529 bp, 153,440 bp, and 153,568 bp, respectively. All chloroplast genome structures consisted of a pair of large inverted repeats (26,450 - 26,468 bp) plus large and small single-copy regions. The content and order of genes in the three chloroplast genomes were identical. Each contained 74 protein-coding, four rRNA, and 30 tRNA genes. Many polymorphisms [352 single nucleotide polymorphisms (SNPs) and 141 insertions or deletions of bases (indels)] were observed between the N and CMS-S cytotypes, but only four SNPs and two indels were found between the N and CMS-T cytotypes, supporting the alloplasmic and autoplasmic origins of CMS-S and CMS-T male-sterility, respectively. A 7.6-fold reduction in mutation rate was observed in the large inverted repeats, while an elevated mutation rate was found in the intergenic region between the ndhF and rpl32 genes. Increased mutation rates were also observed in the ycf1, accD, and ndhF coding regions. A simple PCR marker was developed to distinguish the three cytotypes on the basis of the different lengths of the indels positioned between the petN and psbM genes. A total of 247 domestic breeding lines and 130 exotic accessions of onion, originating from diverse countries, were analysed using this and other previously developed markers to identify variant cytotypes. Two variants of each N and CMS-T cytotype were identified. In addition, two novel cytotypes showing different stoichiometries of the mitochondrial orf725 and cox1 genes were identified in the diverse germplasm.