Decoding the chloroplast genome of the Amazonian fruit Myrciaria dubia (camu-camu): molecular evolution and comparative genomics across the order Myrtales

Abstract

Myrciaria dubia (camu-camu) is an economically important Amazonian fruit species with severely limited genomic resources despite growing commercial interest and conservation needs. This study sequenced, assembled, and comprehensively analyzed the complete chloroplast (cp) genome of M. dubia and performed comparative genomic analyses across the order Myrtales, including codon usage, codon decoding mechanisms, repetitive elements, nucleotide diversity, and phylogenetic reconstruction. The cp genome spanned 158,664 bp with a typical quadripartite organization: a large single-copy region (LSC = 87,640 bp), a small single-copy region (SSC = 18,324 bp), and paired inverted repeats (IRA/IRB = 26,350 bp each). Functional annotation identified 135 genomic features, comprising 84 protein-coding genes, 37 tRNA genes, eight rRNA genes, and five pseudogenes. Codon usage analysis revealed a strong AT bias (62.50%), with 30 preferred codons (RSCU >1.0) predominantly ending with A/T nucleotides. Codon decoding analysis assigned all 61 sense codons to five mechanistic categories, collectively achieving complete codon coverage across all 23 Myrtales accessions. Repetitive element analysis identified 69 simple sequence repeats in M. dubia (91.3% mononucleotide, predominantly adenine motifs in LSC intergenic spacers) and 439 long dispersed repeat pairs (97.5% palindromic, concentrated in the inverted repeat regions). Nucleotide diversity varied significantly across structural regions (SSC, mean π = 0.173; LSC, mean π = 0.084; IRA/IRB, mean π = 0.010–0.015), with the highest diversity window (π = 0.240) located in the SSC at approximately 117.7 kb. SWAN analysis of 78 protein-coding genes identified rpl22, ycf1, matK, ndhF, and ndhD as the most variable loci, with no gene exceeding ω = 1.0, indicating a pervasive purifying selection. Comparative analysis across 19 Myrtaceae accessions demonstrated complete gene collinearity and conserved IR boundary arrangement, with divergence concentrated in the SSC intergenic regions. Phylogenetic analysis positioned M. dubia as a sister species to Plinia trunciflora within the Myrteae tribe, nested in a well-supported monophyletic Myrtaceae clade (bootstrap = 100%).