Comparative Chloroplast Genomics and Codon Usage Bias Analysis in Genus.

OBJECTIVES

This study investigates the cpDNA sequences from six species, aiming to explore their genomic characteristics, gene content, and genetic relationships. The objectives include understanding the structure of these genomes, identifying potential gene rearrangements, and providing insights into genetic improvement and conservation strategies for the genus.

METHODS

cpDNA sequences from six species were sequenced and analyzed. Genome sizes, GC content, gene encoding potential, and structural integrity were assessed. Simple sequence repeats (SSRs) and codon usage were analyzed, with a focus on optimal codons and their frequency. Phylogenetic analysis was conducted to determine the genetic relationships within the genus.

RESULTS

The cpDNAs from the six species exhibited genome sizes ranging from 161,093 bp to 161,254 bp, with GC content between 35.72% and 35.75%. Each genome contained 91 to 92 protein-coding genes, with the infA gene consistently present. No significant gene rearrangements were detected, and SSR analysis revealed mono-repeats primarily composed of A/T bases. Codon usage analysis indicated that leucine is predominantly encoded by the UUA codon, and 31 optimal codons were identified, mainly ending in A or U. Phylogenetic analysis clarified the genetic relationships among the species.

CONCLUSIONS

The study provides detailed insights into the cpDNA characteristics of species, highlighting stable genome structures, conserved genes, and specific patterns of codon usage. These findings are valuable for conservation efforts, genetic improvement strategies, and the sustainable use of germplasm.