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Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura

Gong, Li, Jiang, Hui, Zhu, Kehua, Lu, Xinting, Liu, Liqin, Liu, Bingjian, Jiang, Lihua, Ye, Yingying, Lü, Zhenming
Gene 2019 v.695 pp. 75-83
Pagurus, gene order, gene rearrangement, mitochondrial genes, mitochondrial genome, models, phylogeny, ribosomal RNA, taxonomy, transfer RNA
Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (−0.006) and GC-skew (−0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus, which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura.