Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

Abstract

Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

“…Plant mitochondrial genomes (mitogenomes) are well known for their highly variable and expanded size, which can be as large as free-living bacteria [14,15]. The hitherto largest known mitogenome (11.7 mega base pairs) was found from Larix sibirica (Pinaceae) [16]. However, their size expansion usually does not reflect an increase in mitochondrial (mt) protein-coding genes (PCGs).…”

The complete mitochondrial genome of Cycas debaoensis revealed unexpected static evolution in gymnosperm species

“…Among major land plant groups, mitochondrial genomes of the earliest land plant groups are relatively conserved due to narrow size variation and similar gene content [4,5]. Conversely, mitogenomes of vascular plants exhibit highly dynamic characters: from 66 Kb in Viscum scurruloideum [2] to 11 Mb in Larix sibirica [6], with known genes ranging from 19 to 64 excluding duplicate genes and ORFs (Open reading frames), and intron content ranging from 5 in Viscum [2] to 26 in ferns and early diverging gymnosperms [7,8]. Additionally, plant mitogenomes vary significantly in their nucleotide substitution rates, RNA editing site abundance, and the occurrence of repeat-mediated recombinations [1,2,9,10].…”

“…Among the main lineages gymnosperms, mitogenome has representative for each of the five major groups, i.e., cycads: Cycas taitungensis [8], ginkgo: Ginkgo biloba [9], gnetophytes: Welwitschia mirabilis [9], Pinaceae (Pinus taeda, [direct submission at NCBI, MF991879.1] Picea abies [16], Picea glauca [17], Picea sitchensis [18], Pinus lambertiana [19], Pinus sylvestris [https://www.ncbi.nlm.nih.gov/assembly/GCA_900143225. 1/], Larix sibirica [6]) and Conifers II: Taxus cuspidata [20].…”

“…Gymnosperm mitogenomes are featured by structural dynamics with 40 [9] to 69 [8] genes, 10 to 26 introns [21] and highly variable intergenic spacer regions [20]. Despite having significant variation among genes and non-coding regions (repeated sequences, introns, and plastid and nucleus derived sequences) in gymnosperms, the range of draft mitogenome size divergence of 346 Kb in G. biloba to 11 Mb in L. sibirica is primarily due to the unidentified DNA [6] and mechanism of mitogenome expansion is differed among gymnosperms [20]. The phenomenon of inter-or intra-specific variation is less studied among gymnosperms.…”

“…The phenomenon of inter-or intra-specific variation is less studied among gymnosperms. Mitogenomes of P. abies, P. glauca, and L. sibirica are revealed to be extensively rearranged but with exact gene order is unknown due to their highly fragmented mt-genomes [6,22]. Among gymnosperms, study of interspecific variations in earliest diverging group would improve the entire view on the evolutionary pattern of its mechanism in gymnosperms.…”