Assembly and Analysis of the Complete Mitochondrial Genome of <i>Capsella bursa-pastoris</i>

• Main Authors: Denis O. Omelchenko, Maxim S. Makarenko, Artem S. Kasianov, Mikhail I. Schelkunov, Maria D. Logacheva, Aleksey A. Penin
• Format: Article
• Language: English
• Published: MDPI AG 2020-04-01
• Series: Plants
• Subjects: <i>Capsella bursa-pastoris</i>; complete mitochondrial genome; SMRT PacBio; structural variants; RNA editing
• Online Access: https://www.mdpi.com/2223-7747/9/4/469

Shepherd’s purse (<i>Capsella bursa-pastoris</i>) is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of <i>C. rubella</i> is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of <i>C. bursa-pastoris</i> using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of <i>C. bursa-pastoris</i> differs from <i>C. rubella</i>, but not from <i>C. orientalis</i>, by two long inversions, suggesting that <i>C. orientalis</i> could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except <i>cox1</i> and <i>atp8</i> contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in <i>A. thaliana</i>.