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

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.

Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae)

“…This argues for a hybrid origin of C. bursa‐pastoris between the two lineages, which has been confirmed by other genomic studies that show two subgenomes in C. bursa‐pastoris , one originating from the western and one from the eastern lineage (Douglas et al., 2015 ; Han et al., 2015 ; Kryvokhyzha, Salcedo et al., 2019 ). Furthermore, subsequent evidence argues that the maternal parent came from the eastern lineage represented by Capsella orientalis (Douglas et al., 2015 ; Hurka et al., 2012 ; Omelchenko et al., 2020 ). To interpret the polyploidization event in a phylogeographic framework, we have to postulate firstly, a split of the continuous MRCA distribution area of Capsella dividing it into two separated areas, and secondly, subsequent expansion out of the two part areas leading to a contact zone where the tetraploid ancestor of C. bursa‐pastoris arose through allopolyploidy.…”

“…Capsella bursa‐pastoris and C. thracica emerged from hybridization between the western and eastern lineages. Meanwhile, Capsella has become a model system for genomic studies of plant mating systems (e.g., Bachmann et al., 2019 , 2021 ; Brandvain et al, 2013 ; Mattila et al., 2020 ; Woźniak et al., 2020 ) and polyploidization (Douglas et al., 2015 ; Han et al., 2015 ; Kryvokhyzha, Salcedo et al., 2019 ; Omelchenko et al., 2020 ). In contrast to the increasing knowledge about Capsella at the genomic level, a detailed phylogeographical aspect of its evolution, especially of the eastern lineage consisting of C. orientalis , is currently missing.…”

Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing

“…Since the emergence of Illumina sequencing technology, the mitogenomes of many species (e.g., rice) have been assembled as circular contigs [5]. Long-read sequencers released by PacBio or Oxford Nanopore Technology have accelerated this process [6][7][8][9][10][11][12][13][14][15]. Consequently, many studies have determined the nucleotide sequences of plant mitogenomes, compared the resulting assemblies, and proposed evolutionary scenarios for current patterns [11], [16].…”

The Insights into Mitochondrial Genomes of Sunflowers

“…However, there is still little information about the biological roles of mitochondrial plasmids and their appearance in the mitochondrion [ 41 , 42 ]. Though the number of mitochondrial genome investigations using NGS techniques has significantly increased [ 43 , 44 , 45 ], we could not find reports about mitochondrial plasmids in such studies to the best of our knowledge. In case of similarity between mitochondrial plasmids and master chromosomes and short-read sequencing (<300 bp), the plasmid sequences could be integrated into the mtDNA during assembly.…”