De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales. (10th March 2023)

• Record Type: Journal Article
• Authors: Yu, Runxian; Chen, Xudong; Long, Lingjie; Jost, Matthias; Zhao, Ran; Liu, Lumei; Mower, Jeffrey P; dePamphilis, Claude W; Wanke, Stefan; Jiao, Yuannian
• Editors: Milani, Liliana
• Is Part Of: Genome biology and evolution. Volume 15:Number 3(2023)
• Publication Date: 2023-03-10
• Subjects: Piperales -- Aristolochiaceae -- mitochondrial genome -- mutation spectrum -- HGT; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evad041
• Languages: English
• ISSNs: 1759-6653

Abstract

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.