Genomic insights into the mitochondrial architecture of Sarcandra glabra: structure, evolution, and functional implications
TL;DR
This work offers the first comprehensive analysis of the S. glabra mitochondrial genome, highlighting its structural complexity, dynamic RNA editing, signatures of adaptive evolution, and its phylogenetic position among basal angiosperms.
Abstract
Background Sarcandra glabra, an early-diverging angiosperm of the family Chloranthaceae, is extensively used in traditional medicine and has taxonomic importance. However, the research on the structural information of the complete mitochondrial genome of S. glabra is limited, with no data available for SSR, Ka/Ks ratios, codon analysis, or RNA editing. Results In this study, we present the complete mitochondrial genome of S. glabra, obtained by high-throughput sequencing using Illumina and Nanopore platforms. It enabled the assembly of a multi-branched genome, consisting of a linear chromosome of 1,120,880 bp and a circular chromosome of 192,931 bp. The annotation identified a total of 81 genes, including 39 protein-coding genes, 21 distinct transfer RNAs with multiple gene copies, and 3 ribosomal RNAs, with an overall GC content of 46.03%. The analysis across 9,547 codons revealed a strong preference for A or U ending codons, and serine was found to be the most common amino acid. A total of 524 RNA editing sites were authenticated via RNA-seq, with the nad5 exhibiting the highest frequency of editing events. Ka/Ks analysis showed that the majority of genes were under purifying selection, while increased ratios in nad4, cob, and rpl16 implied instances of adaptive evolution. Extensive potential for chromosomal rearrangement was shown by 399 simple sequence repeats and over 3,585 interspersed repetitions, mostly consisting of short forward or palindromic motifs. Phylogenomic analyses of 21 angiosperm mitochondrial genomes placed S. glabra within Chloranthaceae, clustering with Chloranthus spicatus and forming a well-supported sister relationship with Hedyosmum orientale. Conclusions This work offers the first comprehensive analysis of the S. glabra mitochondrial genome, highlighting its structural complexity, dynamic RNA editing, signatures of adaptive evolution, and its phylogenetic position among basal angiosperms.