Mitochondrial genomes reveal the differential mechanism between Saccharina and Laminaria

Abstract

In this study, the genera Saccharina and Laminaria, which are economically important in the Phaeophyceae phylum, were used to obtain the mitochondrial genome data of a total of 10 species of the two genera from the NCBI database, and bioinformatic analysis software such as OGDRAW, Mauve, and CodonW were utilized to execute the genome mapping, covariate analysis, and codon preference analysis, and to reconstruct the phylogenetic tree using the ML (maximum likelihood method) to reconstruct the phylogenetic tree. The results of the study showed that the genome length of the genus Saccharina (37,500-37,657 bp) was shorter than that of the genus Laminaria (37,862-38,047 bp), the GC content of the genus Saccharina (35.20- 35.30%) was more stable than that of Laminaria (34.20-35.20%); five species in Laminaria encoded 36-39 protein-coding genes, whereas the number of protein-coding genes in Saccharina was highly conserved with 38 genes in all of them; covariance analysis showed that there was a difference in the gene arrangement of the two genera, with gene duplications occurring in the trnC to trnS regions. Covariance analysis showed that there were differences in gene arrangement between the two genera, with gene duplications and deletions in the trnC to trnS regions: duplications of the trnM gene in Laminaria ephemera, deletions of the trnK and trnS genes in five species of the genus Saccharina, and in Laminaria solidungula; and codon preferences were found to be weaker in the two genera. The codon preference study revealed that the genomic codon preferences of both genera were weak, and the rps10 termination codon was TAG in Saccharina and TAA in Laminaria, which could be used as molecular characters for intergeneric classification; the evolutionary tree supported the independent classification of Saccharina and Laminaria, and the species within the genera were closely related, and the intergeneric differentiation was significant, which verified the revision of the traditional classification by molecular phylogeny. This study is the first to systematically compare the characteristics of the mitochondrial genomes of the genera Saccharina and Laminaria. By comparing the structural features, covariance and phylogenetic relationships of the mitochondrial genomes, the structural differences between the two genera and their evolutionary history are revealed, which provides theoretical basis for the taxonomy of Phaeophyceae, the development of germplasm resources, and molecular-assisted breeding.