Chloroplast genome sequencing and evolutionary analysis of Ecklonia maxima and its comparison and phylogenetic analysis with its close relatives
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Background Ecklonia maxima , a key brown algae in marine ecosystems, possesses significant economic, social, and ecological value. It is increasingly gaining attention in aquaculture and blue carbon sequestration, yet its genomic characteristics remain poorly understood, particularly regarding its chloroplast (cp) genome structure, genetic variation, and adaptive mechanisms. Therefore, this study sequenced, assembled, and analyzed its cp genome, investigated its phylogenetic relationships, and compared it with related species within the Ecklonia genus. Results In this study, we sequenced and assembled the cp genome of the E. maxima . The cp genome of E. maxima is 130,900 bp in length and has a typical circular double-stranded structure, consisting of a pair of inverted repeats (IRs) regions (each 5,484 bp), a large single-copy (LSC) region (76,991 bp), and a small single-copy (SSC) region (42,941 bp). This genome encodes 169 genes, including 137 protein-coding genes (PCGs), 29 tRNAs, and 3 rRNAs, with non-coding sequences accounting for 25.27% of the genome. Simple sequence repeat (SSR) analysis revealed 47 SSRs, primarily composed of short tandem repeat units (1–2 bp in length), with a distinct AT preference. The phylogenetic tree indicates a close relationship between E. maxima and E. radiata , with 100% bootstrap support. Comparative analysis with five other species of the genus Ecklonia showed high homology in the cp genome, with the IR region exhibiting higher conservation than the LSC/SSC regions. Ka/Ks (nonsynonymous/synonymous substitution rate) calculations indicated that the petF , rpl24 , and syfB genes were under positive selection, while most other genes were under purifying selection. Conclusions The sequencing and analysis of the cp genome of E. maxima in this study is important for species identification, evolutionary and phylogenetic relationships among species in the genus Ecklonia .
