Comparative Analysis and Characterization of Plastid Genomes of Mycetia (Rubiaceae)

Mycetia, a subshrub genus within the subfamily Rubioideae (Rubiaceae), is predominantly distributed in tropical Asia, lacking comprehensive plastid genomic resources. This study aimed to characterize the complete plastid genomes of two Mycetia species and explore their structural features and evolutionary relationships.

The plastid genomes of Mycetia hirta and Mycetia sinensis were sequenced and assembled. We analyzed genome structure, simple sequence repeats (SSRs), long repeats, codon usage, nucleotide diversity (π), and Ka/Ks and conducted phylogenetic analysis.

Both genomes exhibited a typical quadripartite structure (153,989-154,588 bp; GC content 37.7-37.8%), encoding 126 genes (86 protein-coding, 8 rRNA, and 32 tRNA). Both chloroplast genomes contained 52-60 SSRs and three repeat types with minor interspecific differences. Junction regions and codon usage were highly conserved, with slight variations in RSCU values. The average π was 0.0096, and the non-coding trnE-trnT (π = 0.0817) emerged as a potential DNA barcode. The average Ka/Ks was 0.2900, indicating purifying selection. Phylogenetic analysis confirmed the monophyly of Mycetia within Argostemmateae.

This study provides the first comparative plastid genomic analysis for Mycetia, enhancing our understanding of its genetic diversity and supporting future phylogenetic and taxonomic research on the genus.