Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura

Li Gong,Xinting Lu,Zhifu Wang,Kehua Zhu,Liqin Liu,Lihua Jiang,Zhenming Lü,Bingjian Liu

doi:10.1016/j.ygeno.2019.10.012

Abstract

The complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships among organisms, as well as useful information about the process of molecular evolution and gene rearrangement mechanisms. However, knowledge on the complete mitogenome of Coenobitidae (Decapoda: Anomura) is quite scarce. Here, we describe in detail the complete mitogenome of Coenobita brevimanus, which is 16,393 bp in length, and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region. The genome composition shows a moderate A + T bias (65.0%), and exhibited a negative AT-skew (−0.148) and a positive GC-skew (0.183). Five gene clusters (or genes) involving eleven tRNAs and two PCGs were found to have rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination models were determined as most likely to explain the observed large-scale gene rearrangements. Phylogenetic analysis placed all Coenobitidae species into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was inconsistence with previous findings on Anomura. Taken together, our results help to better understand gene rearrangement process and the evolutionary status of C. brevimanus and lay a foundation for further phylogenetic studies of Anomura.

Highlights

Gene arrangement in vertebrate mitochondrial genomes is relatively conserved and fewer gene arrangement is discovered
The newly determined complete mitogenome of C. brevimanus is almost identical with (98.6% similarity) the published one (GenBank accession number KY352233), the authors mainly focused on the phylogenetic analyses, while hardly described the mitogenome features [
It is inverted to the L-strand, which to our best knowledge, is a quite rare phenomenon only occurring in Coenobitidae mitogenomes

Summary

Introduction

Gene arrangement in vertebrate mitochondrial genomes (mitogenomes) is relatively conserved and fewer gene arrangement is discovered. It comprises 13 PCGs, 22 tRNAs, two rRNAs and one CR (Fig. 1, Table 2), which is identical with that in most crabs [

Results

Conclusion