Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris.

Denis O Omelchenko,Maria D Logacheva,Artem S Kasianov,Aleksey A Penin,Maxim S Makarenko,Mikhail I Schelkunov

doi:10.3390/plants9040469

Abstract

Shepherd’s purse (Capsella bursa-pastoris) 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 C. rubella is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of C. bursa-pastoris 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 C. bursa-pastoris differs from C. rubella, but not from C. orientalis, by two long inversions, suggesting that C. orientalis could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except cox1 and atp8 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 A. thaliana.

Highlights

Shepherd’s purse (Capsella bursa-pastoris) is a small herbaceous plant of the mustard family (Brassicaceae) and one of the most common weeds growing in diverse habitats on almost every continent
C. rubella and A. thaliana We have investigated RNA editing sites using RNAseq data obtained from rRNA depleted total RNA of C. bursa-pastoris, and have identified several long open reading frames (ORFs), the expression of which is supported by the RNAseq data
It is 287,799 bp long, contains 32 protein-coding genes, 3 rRNAs, and 25 tRNAs, which coincides with the average length and gene profile of the other known complete mitogenomes of the Brassicaceae species

Summary

Introduction

Shepherd’s purse (Capsella bursa-pastoris) is a small herbaceous plant of the mustard family (Brassicaceae) and one of the most common weeds growing in diverse habitats on almost every continent. Being a recent allotetraploid and a close relative of the well-known model plant Arabidopsis thaliana, it is a promising model plant for studying polyploidization and its role in the adaptation and evolution of the flowering plants [1,2]. Mitochondrial genomes (mitogenomes) are a valuable source of genetic information for phylogenetic studies and the investigation of essential cellular processes. Plant mitogenomes are highly variable molecules in both size and structure, in contrast to chloroplast genomes that have highly conserved quadripartite structure among land plants [3]. Mitochondrial genomes vary greatly between species but sometimes even within the same species [4,5]. The size of known angiosperm mitogenomes varies

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