Mitochondrial genomes reveal the differential mechanism between Gracilariopsis and Gracilaria

Abstract

Studies have shown that all five species of the Gracilaria genus have 25 protein-coding genes. The number of proteins encoded by the mitochondrial genomes of different species in the genus Gracilariopsis is 23 to 27. The differences among them lie in the quantity or type of orf. Regarding the number of coding genes, species of the Gracilaria genus are more conserved compared to those of the Gracilariopsis genus. The mitochondrial genomes of the 10 species selected in this study contain most of the two rRNA genes (LSU, SSU). The mitochondrial genome of only Gp. lemaneiformis in the genus Gracilariopsis contains three rRNA genes, and an additional rrn5 gene is encoded. The collinearity analysis performed using Mauve indicates that tRNA deletions, duplexes, or rearrangements often occur in the trnN-trnA rich region. The trnH gene in the mitochondrial genome of the genus Gracilariopsis has undergone rearrangement, which can serve as evidence to distinguish Gracilaria from the genus Gracilariopsis. There are differences in the relevant parameters of mitochondrial genomic codons between the two. The ENC range and average value of the mitochondrial genomes of Gracilaria and Gracilariopsis are different. The average values of CBI and Fop are different, and there are also differences in the RSCU values. The preference for the use of mitochondrial genome codons in both is relatively weak, and compared with the genus Gracilariopsis, the preference for codons in the mitochondrial genome of the genus Gracilaria is even weaker. The phylogenetic trees of Gracilaria and Gracilariopsis were reconstructed using two methods: Bayesian Inference (BI) and maximum likelihood (ML). The research shows that Gracilaria and Gracilariopsis are divided into two subbranches, with Gracilariopsis being the first to separate. Gracilaria has a higher evolutionary status, supporting Gracilariopsis to become an independent genus.