Characterization and comparison of the mitochondrial genomes from two Alpheidae species and insights into the phylogeny of Caridea

The mitochondrial genome (mitogenome) has been widely used in phylogenetics and molecular evolution as a parameter, due to its simple genetic structure, high evolutionary rate, and compositional heterogeneity properties. Alpheidae is a large and highly diverse family of the Caridea infraorder, currently containing about 600 species dispersed all over the world. However, only a few shrimps in Alpheidae have their complete mitogenome annotated in GenBank. In our study, the entire mitogenomes of two shrimps from Alpheidae were determined, Alpheus randalli and Alpheus bellulus. The mitogenomes of both shrimps share the complete set of 37 mitochondrial genes found in other Alpheidae species. In A. randalli the AT-skew is slightly positive and GC-skew is negative, whereas in A. bellulus the AT-skew is negative and GC-skew is slightly positive. Furthermore, the secondary structures of trnS1 in the two shrimps are partially missing, and another three tRNAs formed the typical cloverleaf shaped secondary structures. Also, the trnS1 of A. randalli has an unusual anticodon stem with some unpaired nucleotides. Comparative genomic analysis suggests that the mitochondrial gene order of Alpheus genus exhibits a different gene rearrangement compared with that of Caridea. Most species in Alpheus share the same gene order, except for A. lobidens, which has an additional pseudogenomic trnQ (trnQ*). Compared with the mitochondrial gene order of Caridea the Alpheus trnE underwent both translocation and inversion, which were caused by a recombination event. Bayesian inferences (BI) and Maximum Likelihood (ML) phylogenetic analyses of 105 species amino acid datasets resulted in a well-supported topology, whereas four families in Caridea are monophyletic and can be divided into two major clades. Moreover, we demonstrated the phylogenetic relationships of six infraorders in Decapoda (Dendrobranchiata, (Caridea, (Stenopodidea, (Achelata, (Polychelida, Astacidea))))). This study used the large taxon sampling available to date for phylomitogenomic analysis. The results provide a theoretical basis for further research on the evolution of the Decapoda order, specifically Caridea infraorder.