Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes

Abstract

Background: The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders.Results: We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Conclusions: Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

The complete mitochondrial genomes of Umalia orientalis and Lyreidus brevifrons: The phylogenetic position of the family Raninidae within Brachyuran crabs

“…In U. orientalis, genome overlaps are observed at 17 gene junctions with a total of 40 bp, while in L. brevifrons, gene overlaps are observed at 11 gene junctions with a total of 28 bp. Both atp8/atp6 and nad4/nad4L share seven nucleotides, as observed in other crustaceans (Lin et al, 2012;Hui et al, 2014). The U. orientalis mitogenome harbors a total of 677 bp intergenetic spacer sequences, whereas in L. brevifrons, there are 1323 bp spacer sequences.…”

Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences

“…Decapod mitochondrial genome is observed to be A+T biased with the highest A+T content in the putative control regions (Lin et al, 2012). Regions rich in A+T nucleotides are indicators of reduced selective constraints (Nigro et al, 1991).…”

A molecular phylogeny of Bopyroidea and Cryptoniscoidea (Crustacea: Isopoda)

“…Unfortunately, coevolutionary analyses are limited by the fact that there is little consensus on the phylogeny of the hosts, especially within Malacostraca (Jenner et al, 2009;Koenemann et al, 2010). Because of this, we used several current molecular phylogenies on crustacean hosts (Jenner et al, 2009;Koenemann et al, 2010;Regier et al, 2010;Lin et al, 2012;Shen et al, 2012), and 500 C. B. Boyko et al…”