Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure

Abstract

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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.…”

Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

“…Additional assemblies have suggested the existence of multiple mitome configurations, a hypothesis supported by long reads that span alternate assembly graph paths. This builds on a body of work that increasingly refutes the existence of a single, static circular mitochondrial genome (Sloan 2013; Kozik et al 2019; Wu et al 2020; Jackman et al 2020).…”

“…Although the mitome has traditionally been represented as a single circular structure, there is physical evidence of multiple shapes (Bendich 1996) . Long sequencing reads indicate several linear, branched, or smaller circular structures (Kozik et al 2019;Jackman et al 2020) that may recombine at repeat regions (Z. Chen et al 2017) .…”

“…Long reads provide strong evidence that the plastome exists in two structural haplotypes in equal proportions across land plants (Wang and Lanfear 2019) which supports certain theories of recombination. Gymnosperm mitome assemblies based on long reads reveal significant complexity in mitome structure, and branching may be related to recombination processes (Jackman et al 2020) .…”

Heteroplasmy and repeat expansion in the plant-like mitochondrial genome of a bivalve mollusc

“…The size of these expanded genomes are remarkable amongst the animals, however they are frequently dwarfed by those of plants. The Sitka spruce, for example, has a mitogenome size of 5.4 Mb and encodes 41 protein-coding genes (Jackman et al 2020) . Although DUI is restricted to a subset of bivalve lineages, mitochondria-based sex determination mechanisms have also evolved in plants through gynodioecy, in which females are derived from the hermaphroditic condition through cytoplasmic male sterility (CMS, Chase 2007) .…”