Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster

Shi, Huafeng; Liu, Ruiyu; Sha, Zhongli; Ma, Jiping

doi:10.1016/j.margen.2011.11.002

Cited by 14 publications

(13 citation statements)

References 57 publications

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“…thermophilus is higher than any two other randomly chosen tRNA s. It seems to be more possible that two tRNA Leu arose from duplication followed by anticodon mutation. The similar duplication/anticodon mutation events have also been reported in other crustaceans, for example in amphipods Caprella scaura [69] and Gammarus duebeni [70], and decapods Geothelphusa dehaani [71] and Stenopus hispidus [52]. …”

Section: Discussionsupporting

confidence: 63%

“…Secondly, an independent duplication/random loss events occurred to account for the translocation of tRNA Gln ( Q ) (Figure 3B). Thirdly, a duplication/anticodon mutation/non-random loss event [52,68] is expected to account for translocation of tRNA Leu ( CUN ) ( L 1 ) (Figure 3C). A duplication of tRNA Leu ( UUR ) ( L 2 ) on H-strand might have happened.…”

Section: Discussionmentioning

confidence: 99%

“…This was followed by transposition of tRNA Asp (D) and tRNA Val ( V ) and a recombination event (Figure 4C). Finally, a duplication/anticodon mutation/non-random loss event [52,68] occurred to account for the translocation of tRNA Leu ( CUN ) ( L 1 ) (Figure 4D). …”

Section: Discussionmentioning

confidence: 99%

“…This interpretation seems less likely given that there is a long distance between tRNA Leu ( UUR ) ( L 2 ) and tRNA Leu ( CUN ) ( L 1 ) in the ancient arrangement, as well as the presence of inversion in tRNA Leu ( CUN ) ( L 1 ) [52]. Moreover, the sequence homology between tRNA Leu ( UUR ) ( L 2 ) and tRNA Leu ( CUN ) ( L 1 ) in A .…”

Section: Discussionmentioning

confidence: 99%

“…However, the latest phylogenetic reconstruction of decapod crustaceans using complete mitochondrial genome sequences [51,52] still has low resolution in most of the deep branches, notably with the status of Stenopodidea, lobsters and mud shrimps unresolved. Moreover, only a single species of mud shrimp collected from Korea, namely Upogebia major (De Haan, 1841) belonged to Gebiidea, has been sequenced for mitochondrial genome [53].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2012

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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.

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