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Background  Cytoplasmic male sterility (CMS) is a common phenotype in higher plants, that is often associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce hybrid seeds in a variety of valuable crop species. Investigation of the CMS phenomenon promotes understanding of fundamental issues of nuclear-cytoplasmic interactions in the ontogeny of higher plants. In the present study, we analyzed the structural changes in mitochondrial genomes of three alloplasmic lines of sunflower ( Helianthus annuus  L.). The investigation was focused on CMS line PET2, as there are very few reports about its mtDNA organization.    Methods  The NGS sequencing,  de novo  assembly, and annotation of sunflower mitochondrial genomes were performed. The comparative analysis of mtDNA of HA89 fertile line and two HA89 CMS lines (PET1, PET2) occurred.    Results  The mtDNA of the HA89 fertile line was almost identical to the HA412 line ( NC_023337 ). The comparative analysis of HA89 fertile and CMS (PET1) analog mitochondrial genomes revealed 11,852 bp inversion, 4,732 bp insertion, 451 bp deletion and 18 variant sites. In the mtDNA of HA89 (PET2) CMS line we determined 27.5 kb and 106.5 kb translocations, 711 bp and 3,780 bp deletions, as well as, 5,050 bp and 15,885 bp insertions. There are also 83 polymorphic sites in the PET2 mitochondrial genome, as compared with the fertile line.    Discussion  The observed mitochondrial reorganizations in PET1 resulted in only one new open reading frame formation ( orfH522 ), and PET2 mtDNA rearrangements led to the elimination of  orf777 , duplication of  atp6  gene and appearance of four new ORFs with transcription activity specific for the HA89 (PET2) CMS line— orf645 ,  orf2565 ,  orf228  and  orf285 .  Orf228  and  orf285  are the  atp9  chimeric ORFs, containing transmembrane domains and possibly may impact on mitochondrial membrane potential. So  orf228  and  orf285  may be the cause for the appearance of the PET2 CMS phenotype, while the contribution of other mtDNA reorganizations in CMS formation is negligible.

Mitochondrial genomes organization in alloplasmic lines of sunflower (Helianthus annuusL.) with various types of cytoplasmic male sterility