Mitochondrial genome of Paradorippe granulata (Decapoda, Brachyura) and a phylogenetic analysis of the Heterotremata

Abstract The phylogenetic relationships among species of Brachyura, particularly within the subsection Heterotremata, have yet to be fully elucidated. We sequenced the complete mitochondrial genome of Paradorippe granulata to gain further insight into the internal composition and phylogeny of Heterotremata. The results revealed that the complete mitochondrial genome of P. granulata spans 15 084 bp, encoding 37 genes. These genes are composed of 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The nucleotide composition of the genome is as follows: A (36.90%), T (37.92%), C (16.27%) and G (8.91%), demonstrating a pronounced AT bias (74.82%). All tRNA genes, with the exception of trnF (lacking the acceptor arm), trnS 1 (lacking the DHU arm), and trnP , trnY , and trnM (lacking the T ψ C loop), were predicted to form the typical cloverleaf secondary structure. Significant rearrangements were observed in the mitochondrial genome of P. granulata when compared to the ancestral mitochondrial gene arrangement within the Brachyura infraorder. Notably, the relative positions of nad1 , nad2 , nad3 , nad6 and 14 tRNA genes ( , K , D , G , A , R , N , S 1, E , P , , I , W , Y ) were found to differ from those reported in the currently recognized mitochondrial gene orders of Brachyura, indicating a novel gene arrangement. Bayesian Inference and Maximum Likelihood trees of Heterotremata, constructed based on the nucleotide sequences of the 13 PCGs, indicated that P. granulata and Heikeopsis japonica cluster together to form Dorippoidea. This clade was found to share the closest phylogenetic relationship with Leucosioidea. At the family level, most families were determined to be monophyletic, whereas Majidae and Xanthidae were not. With regard to superfamilies, Trapezioidea was identified as non-monophyletic and was divided into two distinct clades. Trapezioidea1 was recovered as the sister group to Pilumnoidea, whereas Trapezioidea2 was positioned more distantly from Trapezioidea1.