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- Title
De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales.
- Authors
Yu, Runxian; Chen, Xudong; Long, Lingjie; Jost, Matthias; Zhao, Ran; Liu, Lumei; Mower, Jeffrey P; dePamphilis, Claude W; Wanke, Stefan; Jiao, Yuannian
- Abstract
The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea , Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus , a member of the perianth-less Piperales. The average number of short repeats (50–99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis - to trans -splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox 1 and atp 8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.
- Subjects
MITOCHONDRIAL DNA; TRANSFER RNA; PIPERALES; GENOMES; MITOCHONDRIA; HORIZONTAL gene transfer; ARISTOLOCHIA; COMPARATIVE studies
- Publication
Genome Biology & Evolution, 2023, Vol 15, Issue 3, p1
- ISSN
1759-6653
- Publication type
Article
- DOI
10.1093/gbe/evad041