The complete mitochondrial genome of the Japanese mud shrimp<i>Upogebia major</i>(Crustacea, Decapoda)

Kim, Sanghee; Kim, Sang Woo; Choi, Han Gu; Park, Joong Ki; Ahn, Dong Ha; Min, Gi–Sik

doi:10.3109/19401736.2011.624609

Cited by 10 publications

(5 citation statements)

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“…There is no clear consensus on their phylogeny. To determine decapod phylogeny, especially for the major reptant lineage relationships, we used four more reptant sequences: two from northern hemisphere crayfish species, which were determined in this study, and two published sequences of Upogebia major (the first representative of the infraorder Thalassinidea) (Kim et al. 2011a) and H. americanus (Kim et al.…”

Section: Resultsmentioning

confidence: 99%

The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia

Kim¹,

Park²,

Jung³

et al. 2012

Zoologica Scripta

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S. (2012). The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. -Zoologica Scripta, 41, 281-292. We determined the complete mitochondrial (mt) genome sequences of two northern hemisphere freshwater crayfish species, Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae). These species have an identical gene order with typical metazoan mt genome compositions. However, their gene arrangement was very distinctive compared with the pan-crustacean ground pattern because of the presence of a long inverted block, which included 19 coding genes and a control region (CR). Because the CR was inverted, their nucleotide frequencies showed a reversed strand-specific bias compared with the other decapods. Based on a comparative analysis of mt genome arrangements between southern and northern hemisphere crayfish and their putative close marine relative (Homarus americanus, a true clawed lobster), we postulated that the ancestor of freshwater crayfish had a typical pan-crustacean mtDNA gene order, similar to its marine relatives. Based on this assumption, we traced the most parsimonious gene rearrangement scenario of the northern hemisphere crayfish. In a phylogenetic study on the infraordinal relationships in reptan decapods, the lineage Lineata [Thalassinidea (Brachyura, Anomura)] was well supported, while the infraorder positions of Achelata and Astacidea remained unidentified.Complete mitochondrial genomes of northern hemisphere crayfish d S. Kim et al.

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Section: Resultsmentioning

confidence: 99%

The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia

Kim¹,

Park²,

Jung³

et al. 2012

Zoologica Scripta

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“…However, the U . major mtDNA annotated by Kim et al [53] has an extra tRNA Leu ( CUN ) between nad1 and lrRNA . The different annotation is due to amphibolous beginning of lrRNA and identification of tRNA Leu ( CUN ) .…”

Section: Discussionmentioning

confidence: 99%

“…No anticodon and tRNA-like secondary structure of tRNA Leu ( CUN ) is identified between nad1 and lrRNA in the U . major mtDNA we sequenced, as in the one sequenced by Kim et al [53]. …”

Section: Discussionmentioning

confidence: 99%

“…Most variations in size in mitochondrial genomes are caused by sequences in non-coding regions [53,58]. N .…”

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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Comparison of the novel dipstick DNA extraction technique with two established techniques for use in biological barcoding

Martello

Lambert

Johnston³

et al. 2019

Mol Biol Rep

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The complete mitochondrial genome of the Japanese mud shrimpUpogebia major(Crustacea, Decapoda)

Cited by 10 publications

References 5 publications

The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia

The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia

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

Comparison of the novel dipstick DNA extraction technique with two established techniques for use in biological barcoding

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