Mitochondrial genomes reveal the relationship in Gigartinales

Abstract

Gigartinale is an important class of marine macroalgae in the phylum Rhodophyta, belonging to Florideophyceae, which has important ecological and economic values. In this study, we investigated 11 species of Gigartinales, and systematically analyzed the structural characteristics of the mitochondrial genomes of Gigartinales by using bioinformatics software, such as Geneious, CodonW, MEGA11, TBtools and Origin. We then constructed a phylogenetic tree to explore their evolutionary relationships. The phylogenetic tree was reconstructed to explore their evolutionary relationships. The mitochondrial genome length of Gigartinales is concentrated between 25-26 kb, with a GC content of 27.9%-37.4%. It encodes 48-50 genes, mainly including cytochrome oxidase (cox1-cox3), NADH dehydrogenase (nad1-nad6), ATP synthase (atp4-atp9), and ribosomal protein genes, with the highest number of genes being 57 in Chondrus crispus, and Sarcopeltis skottsbergii had the lowest number of 48. The results of covariance analysis showed that the gene arrangement of the mitochondrial genome of Gigartinales was highly conserved, but there was a small rearrangement of the trnY and trnR genomes among some species. The results of codon usage preference (RSCU) analysis showed that the mitochondrial genomes of Gigartinales prefer codons ending in A/T, among which the leucine codon UUA has the highest RSCU value (2.03-4.43), which fully indicates its obvious preference. 11 species of Gigartinale mitochondrial genomes have a smaller gap in RSCUs. Most of them are larger than 1, which suggests to some extent that the mitochondrial genomes of the Gigartinales are evolutionarily conservative. In addition, the phylogenetic trees constructed by maximum likelihood (ML) and Bayesian inference (BI) methods showed that the species of Gigartinales were divided into two branches and supported the traditional classification framework, while revealing some evolutionary differences among species.