Cytoplasmic Genomes of Sunflowers: Assembly, Evolution, Structure, and Function

The mitochondria and chloroplast are responsible for energy metabolism in plants. While the genomes of these organelles are small compared with the nuclear genome, they are important components of a plant’s DNA.  Here we present a de novo assembly and annotation of the mitochondrial genome of sunflower, Helianthus annuus (line HA412), based on the WGS sequencing of a library enriched for mitochondrial DNA on 1/48^th of an Illumina HiSeq 2000 lane. As far as we are aware, this assembly represents the first complete mitochondrial genome sequence from sunflower or from the sunflower family.  This assembly and a previously published plastid genome sequence formed the basis of de novo and reference-guided assemblies of cytoplasmic genomes from several additional sunflower genotypes, including H. annuus (line CMSHA89, a Hopi landrace, and several wild accessions), H. petiolaris, and H. argophyllus. Comparative genomics reveals that, as expected, the plastid genomes are collinear; however, a number of structural rearrangements are apparent in the mitochondrial genomes. A previously reported rearrangement responsible for cytoplasmic male sterility (CMS) in H. annuus was confirmed and fully assembled and several other large rearrangements are mapped in the other Helianthus species.  Some regions of the mitochondrial genome seem more prone to structural rearrangement than others. The genomic sequences reported here represent a rare example of multiple complete organellar genomes from a single genus and, as such, will prove valuable in further investigation of organellar genome evolution in general and genomic evolution in Helianthus in particular.