Complete genome sequence of mulberry dwarf phytoplasma strain MDAK-01: comparative genomics and evolutionary analyses

Abstract

Phytoplasmas are phloem-limited plant pathogens that cause substantial economic losses in global agriculture. Complete genome sequences are essential for clarifying their taxonomic status, evolutionary relationships, and pathogenic mechanisms. In this study, we generated a high-quality, complete circular genome of Mulberry dwarf phytoplasma (MDP) strain MDAK-01—the first formally described species in the genus Candidatus Phytoplasma—using a hybrid sequencing strategy combining Illumina and Oxford Nanopore Technology. Furthermore, we performed a comprehensive comparative analysis between the MDAK-01 genome and 36 publicly available phytoplasma genomes. The MDAK-01 genome is 782,702 bp in length, with 755 coding sequences (CDSs), 2 rRNA operons and 32 tRNA genes. Functional annotation based on homology searches identified 753 CDSs. In addition, 10 types of Potential Mobile Units with a total of 61 copies were detected, and 12 secreted proteins were predicted. Phylogenetic analyses based on 151 single-copy homologous proteins and 16 S rRNA gene sequences from 37 phytoplasma strains bothassigned MDAK-01 to the 16SrI group. Average amino acid identity values within 16Sr groups were consistently higher than those between groups. However, inter-group ANI between 16SrI and 16SrXII (97.65%) surpassed the intra-group ANI of the 16SrXII group (96.77%). For the 16SrI group, Relative Synonymous Codon Usage analysis revealed a preference for AT-ending codons. Further analyses of Parity Rule 2-bias, GC12-GC3, and Effective Number of Codons-GC3s indicated that codon usage patterns were mainly shaped by natural selection. All 37 phytoplasma strains possessed the dnaA gene (a potential replication origin), located near the trough of typical or atypical V-shaped cumulative GC-skew plot. This study presents the complete genome of the MDP strain MDAK-01, analyzes the codon usage bias of the 16SrI group, clarifies the phylogenetic relationships and replication characteristics of 37 phytoplasma strains, and provides valuable genomic resources for the taxonomic revision and evolutionary research of phytoplasmas.