Abstract
Mitochondrial genomes of vascular plants are well known for their liability in architecture evolution. However, the evolutionary features of mitogenomes at intra-generic level are seldom studied in vascular plants, especially among gymnosperms. Here we present the complete mitogenome of Cycas debaoensis, an endemic cycad species to the Guangxi region in southern China. In addition to assemblage of draft mitochondrial genome, we test the conservation of gene content and mitogenomic stability by comparing it to the previously published mitogenome of Cycas taitungensis. Furthermore, we explored the factors such as structural rearrangements and nuclear surveillance of double-strand break repair (DSBR) proteins in Cycas in comparison to other vascular plant groups. The C. debaoensis mitogenome is 413,715 bp in size and encodes 69 unique genes, including 40 protein coding genes, 26 tRNAs, and 3 rRNA genes, similar to that of C. taitungensis. Cycas mitogenomes maintained the ancestral intron content of seed plants (26 introns), which is reduced in other lineages of gymnosperms, such as Ginkgo biloba, Taxus cuspidata and Welwitschia mirabilis due to selective pressure or retroprocessing events. C. debaoensis mitogenome holds 1,569 repeated sequences (> 50 bp), which partially account for fairly large intron size (1200 bp in average) of Cycas mitogenome. The comparison of RNA-editing sites revealed 267 shared non-silent editing site among predicted vs. empirically observed editing events. Another 33 silent editing sites from empirical data increase the total number of editing sites in Cycas debaoensis mitochondrial protein coding genes to 300. Our study revealed unexpected conserved evolution between the two Cycas species. Furthermore, we found strict collinearity of the gene order along with the identical set of genomic content in Cycas mt genomes. The stability of Cycas mt genomes is surprising despite the existence of large number of repeats. This structural stability may be related to the relative expansion of three DSBR protein families (i.e., RecA, OSB, and RecG) in Cycas nuclear genome, which inhibit the homologous recombinations, by monitoring the accuracy of mitochondrial chromosome repair.
Highlights
Mitochondrial genomes provide a substantial genetic information for phylogenetic reconstructions and exploration of essential cellular processes
We present the complete mitogenome of C. debaoensis, a cycad species endemic to the Guangxi region in southern China, to test stability of gymnosperm mitogenome at inter-species level by comparing it with the available mitogenome of C. taitungensis
We investigated whether the editing frequencies in gymnosperm species are shaped by selection constraint on genes as suggested by Jobson and Qiu [59]
Summary
Mitochondrial (mt) genomes provide a substantial genetic information for phylogenetic reconstructions and exploration of essential cellular processes. Recent advances in highthroughput sequencing technologies has significantly facilitated the assemblage of plant mt genomes, and analysis of their structural diversity and evolutionary trends [1,2,3]. 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]. Plant mitochondria exhibit extensive inter- or intraspecific variation in genome size and structure, resulting from large sequence duplications and frequent rearrangements in angiosperms [11,12,13]. This phenomenon is less explored in gymnosperms
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