Complete chloroplast genome of Ecklonia maxima and comparative analysis with related species

Ecklonia maxima, an ecologically and economically critical brown alga, holds substantial value in social, economic, and ecological contexts. While it is garnering growing interest for its applications in aquaculture and blue carbon sequestration, its genomic characteristics remain poorly characterized, particularly those of its chloroplast (cp.) genome, including its structure, genetic variation, and adaptive mechanisms. To address this knowledge gap, we sequenced, assembled, and annotated the complete cp. genome of E. maxima to investigate its phylogenetic relationships and conduct a comparative analysis with related species within the Ecklonia genus. We sequenced and assembled the complete cp. genome of E. maxima. The assembled genome is 130,900 bp in length and exhibits the typical quadripartite structure, consisting of a large single-copy (LSC) region of 76,991 bp, a small single-copy (SSC) region of 42,941 bp, and a pair of inverted repeat (IR) regions (each 5,484 bp). Genome annotation identified 169 genes, comprising 137 protein-coding genes (PCGs), 29 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Non-coding sequences accounted for 25.27% of the genome. Simple sequence repeat (SSR) analysis revealed 47 SSRs, which were predominantly mononucleotide and tetranucleotide repeats with a distinct AT bias. Phylogenetic analysis revealed that E. maxima forms a well-supported sister group (96% bootstrap) to a clade containing its congeners E. radiata, E. cava, E. cava subsp. stolonifera and E. radicosa, indicating their close evolutionary relationship. Comparative genomic analysis among the six Ecklonia species (including E. maxima) showed high sequence conservation, with the IR regions being more conserved than the LSC and SSC regions. The Ka/Ks (nonsynonymous/synonymous substitution rate) analysis indicated that petF, rpl24, and syfB were under positive selection, while the majority of genes were under purifying selection. The signatures of positive selection and the high nucleotide diversity (e.g., petF, PI = 0.038) observed in these genes provide direct evidence supporting adaptive evolution to environmental fluctuations. The sequencing and analysis of the complete cp. genome of E. maxima in this study provide a valuable genomic resource for future studies on species identification and for elucidating the evolutionary and phylogenetic relationships among species within the genus Ecklonia.