Sequencing and analysis of mitochondrial genomes of fertile and male-sterile lines in perennial ryegrass (Lolium perenne L.)

The mitochondrial genomes of higher plants represent several characteristics that discriminate them from other eukaryotic mitochondrial genomes. Plant mitochondrial genomes are large and variable in size with substantial amounts of non-coding regions. A couple of sequence parts of plant mitochondrial genomes represent “promiscuous” DNA of nuclear and plastid origin, as well as sequence regions that are likely be obtained through horizontal transfer from mitochondria of other species. While angiosperm mitochondrial genomes exhibit extremely slow rates of nucleotide substitutions, they are subjected to a rapid structural evolution due to frequent intra- and intermolecular recombinations among large repeated sequences. Such structural rearrangements within and between circular master molecules usually generate heterogeneous pools of mitochondrial sub-genomes of different sizes and configurations. The complete mitochondrial sequence and a circular molecular map for the fertile ryegrass line F1-30 has been recently published by our group. Here we report on completed mitochondrial genome sequencing projects in further three ryegrass genotypes. Complete genome sequences were generated in two cytoplasmic malesterile (CMS) lines and in a fertile maintainer line by de novo hybrid Next Generation Sequencing approaches using Roche 454 Pyrosequencing and Pacific Biosciences Single Molecule Reads technologies. Genome sequencing reveals the co-existence of mitochondrial sub-genomes with extensive structural rearrangements in all investigated ryegrass genotypes. A proposed general mechanism for building subgenomic molecules as well as the significance of structural changes in the manifestation of male sterility will be discussed in detail.