Mitochondrial Genome Characteristics of Rhodobryum laxelimbatum and Comparative Analysis of RNA Editing and Codon Usage Bias With the Chloroplast Genome.

Abstract

Rhodobryum laxelimbatum is a traditional medicinal plant belonging to the genus Rhodobryum. To date, studies on this genus have focused primarily on its geographical distribution, chemical constituents, and biological activities, whereas genomic data within the genus are limited. The mitochondrial genome of R. laxelimbatum was sequenced, assembled, and annotated. Genomic structural features and simple sequence repeats (SSRs) were comprehensively characterized. Comparative analyses of RNA editing patterns and codon usage bias were performed using the mitochondrial and chloroplast genomes of R. laxelimbatum. The results revealed that the complete mitochondrial genome of R. laxelimbatum was 103,071 bp in length. It comprises 40 protein-coding genes (Nad7 is a pseudogene), 24 transfer RNA genes, and 3 ribosomal RNA genes. In total, 76 SSRs were detected. The mitochondrial and chloroplast genomes contained 189 and 608 RNA editing sites, respectively, with the conversion of hydrophilic amino acids to hydrophobic amino acids being dominant. Both organellar genomes exhibited the highest GC content at the first codon position. GC12 was significantly associated with GC3 only in chloroplasts with steeper regression trends. Mitochondrial genes exhibited greater variation in the effective number of codons (ENC), and most genes in both genomes clustered near the expected ENC curve. Parity Rule 2 plot revealed a distinct base-composition imbalance at synonymous third codon positions-mitochondria exhibited T3s > A3s with comparable G3s and C3s, whereas chloroplasts exhibited T3s > A3s and G3s > C3s. Five optimal codons were identified in the mitochondrial genome, predominantly ending in G/A/C, whereas nine were identified in the chloroplast genome, ending in A/U. Correspondence analysis demonstrated that codon usage bias was shaped by multiple interacting factors rather than a single determinant. This study provides crucial evidence for clarifying the evolutionary patterns of organelle genomes in Rhodobryum, and for understanding its genetic characteristics and molecular basis.