Mitochondrial Genome Rearrangement And Phylogenetic Analysis Of Three Hermit Crabs

The superfamily Paguroidea belong to Arthropoda,Crustacea,Malacostraca,Decapoda,Anomura.Compared with Brachyura,which belongs to the same order,there are few studies on the complete mitochondrial genome sequence and gene rearrangement of Anomura,especially Paguroidea species.In this study,the characteristics of mitochondrial genome sequence and gene rearrangement of three Paguroidea species,Coenobita brevimanus,Dardanus arrosor and D.aspersus,were determined and analyzed and integrated the mitochondrial genome sequences of another 31 species of Anomura from Gen Bank database to construct the most comprehensive phylogenetic tree of Anomura up to now,and carried out divergence time analysis based on fossil species.The main results are as follows:The mitochondrial genomes of these 3 hermit crabs all contain 37 genes,and a long noncoding region(also known as the control region,CR).In 37 genes,there were 5 proteincoding genes,11 t RNA genes and 2 r RNA genes encoded on the light-strand,the remaining genes are encoded by heavy-strand.In the protein-coding genes,there were 1-17 bp overlap regions and 1-176 bp intervals;There is no uniform start codon for protein-coding genes,but most start with ATG,most stop codon is the standard TAN codon and a few stop codon is the incomplete T;The mitochondrial genome of the three hermit crabs showed obvious AT bias in base composition;The ratio of Non-synonymous mutation rate to synonymous mutation rate(Ka/Ks)of all genes was less than 1,indicating that none of them are subject to positive selection pressure,and ATP8 gene had the highest Ka/Ks,indicating that it was subjected to the least selection pressure of purification.The Ka/Ks of COI was the smallest and the selection pressure of purification was the largest.We downloaded 31 Anomura mitochondrial genomes from Gen Bank database and compared the sequencing of these 34 Anomura mitochondrial genomes with the complete mitochondrial genomes of 3 Paguroidea species newly determined in this study.The results showed that all the 34 mitochondrial genomes underwent gene rearrangement,and we divided them into 16 rearrangement patterns according to their rearrangement characteristics,among which Paguroidea had the largest rearrangement scale and Porcellanidae had the smallest.The types of rearrangement mainly include ranslocation,inversion and shuffling.The gene locations involved in rearrangement mostly exist between trn L and ATP8,gene clusters(trn I-trn Q-trn M),ND2 and gene clusters(trn W-trn C-trn Y)with their adjacent regions.Based on these rearrangement types and mitochondrial genome sequence characteristics,we proposed a possible rearrangement mechanism,suggesting that the duplication-random loss and recombination model is the most likely model for the large-scale rearrangement of mitochondrial genomes of the three hermit crabs in this study.In this study,based on the nucleotide and amino acid sequences of 13 protein-coding genes in the mitochondrial genome,we reconstructed the phylogenetic tree of Anomura by using Bayesian inference(BI)and maximum likelihood(ML)methods,combined with mitochondrial gene rearrangement characteristics.The results support that Galatheoidea and Paguroidea are polygeneic origin;Aegloidea,Chirostyloidea,Lomoidea,Lithodoidea and Hippoidea are monophyletic in origin and also support "Hermit to King" hypothesis of Anomura.According to divergence time analysis that the origin of Anomura originated from the Triassic(～224 MYA).Galatheoidea,Paguroide,Hippoidea,Lithodoidea,Chirostyloidea,Lomoidea and Aegloidea were differentiated in the early Jurassic(～188 MYA).In the Cretaceous,three Paguroide groups were successively divided into ～147 MYA,～119 MYA and ～57 MYA.Coenobitidae was the first to differentiate from ～110 MYA,while Paguridae was the first to differentiate from ～57 MYA.In this study,we first explored the phylogenetic relationship of Anomura from the perspective of mitochondrial genome sequence and gene rearrangement.These results not only enrich Paguroidea mitochondrial genome sequence and mitochondrial genome rearrangement types,but also provide new molecular markers for phylogenetic analysis of Anomura and even Decapoda in the future,which has important theoretical significance and reference value.