Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura)

Yamauchi, Mitsugu M.; Miya, Masaki; Nishida, Mutsumi

doi:10.1016/s0378-1119(03)00582-1

Cited by 110 publications

(74 citation statements)

References 21 publications

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“…However, tRNA His was between NAD4 and NAD5, which is different to that in Charybdis feriata but the same as that in most arthropods (Table 1). Different gene rearrangements in the mitochondrial genome is relatively common in crustacean species (Shen et al, 2007), and are probably caused by slipped-strand mispair and gene deletions (Yamauchi et al, 2003). Nine 1-to 7-bp overlaps and 13 intergenic spacers that were between 1 and 30 bp in length were found, which in general is similar to that reported in other species' mitochondrial genomes (Ma et al, 2013;Baek et al, 2014;Wang et al, 2014).…”

Section: Genome Organizationsupporting

confidence: 76%

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

Ren

et al. 2016

Genet. Mol. Res.

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ABSTRACT. This study determined the mitochondrial genome structure of the blue swimming crab (Portunus pelagicus), and elucidated its phylogenetic relationships among the species within the order Decapoda. The complete mitochondrial genome was 16,155 bp long, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 DNA control region. The gene order of the genome was the same as that found within the family Portunidae. Twenty-three genes were on the heavy strand and 14 were on the light strand. Almost all of the protein-coding genes were initiated by an ATG codon, except for three genes (ATP6, ND1, and ND3) that started with a rare ATT codon. Of the 13 protein-coding genes, 10 ended with complete TAA or TAG stop codons and three ended with an incomplete T codon. Thirteen non-coding regions were identified that ranged from 1 to 30 bp in length. Nine overlaps were found, which ranged from 1 to 7 bp in length. Phylogenetic analyses based on 12 concatenated protein-coding genes revealed that P. pelagicus formed a monophyletic group with Portunus trituberculatus, which were in a larger group with Callinectes sapidus, while the genera Charybdis and Thalamita formed another group. These two groups clustered together and grouped with the genus Scylla. The phylogenetic analysis supported the inclusion of Charybdis in subfamily Portuninae of the family Portunidae, and revealed a close relationship between Charybdis and Thalamita. We suggest that Thalamita should also be classified into the subfamily Portuninae. The results can be used in the study of phylogenetic, population genetic and conservation genetics of P. pelagicus.

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Section: Genome Organizationsupporting

confidence: 76%

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

Ren

et al. 2016

Genet. Mol. Res.

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“…Such NC regions also show high AT-bias, high length variability and are able to form stem-loop structures as observed even in regions close to COI, COII or tRNALeu(UUR) genes (Smith and Bush, 1997;De La Rua et al, 2000;Shao et al, 2001;Soucy and Danforth, 2002;Dowton et al, 2003;Yamauchi et al, 2003). They might have a role in transcription in addition to that of the mt control region (see Valverde et al, 1994b;Roberti et al, 2003).…”

Section: Nc Regionmentioning

confidence: 99%

“…Relatively short mt NC regions have been observed in crustaceans (eg Valverde et al, 1994a;Hickerson and Cunningham, 2000;Yamauchi et al, 2003) and in other invertebrates. Such NC regions also show high AT-bias, high length variability and are able to form stem-loop structures as observed even in regions close to COI, COII or tRNALeu(UUR) genes (Smith and Bush, 1997;De La Rua et al, 2000;Shao et al, 2001;Soucy and Danforth, 2002;Dowton et al, 2003;Yamauchi et al, 2003).…”

Section: Nc Regionmentioning

confidence: 99%

Mitochondrial COI-NC-COII sequences in talitrid amphipods (Crustacea)

Davolos

Maclean

2004

Heredity

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Mitochondrial (mt) sequences from cytochrome oxidase subunit I to the subunit II gene (COI, COII) were analysed in crustacean talitrid amphipods. Species of the genera Orchestia, Talitrus and Talorchestia from the MediterraneanEast Atlantic area were examined. The expected tRNALeu-UUR gene was not revealed between COI and COII. Instead, a short (35-48 bp) noncoding (NC) AT-rich (ca. 90%) region with putative stem loops was found. Here, we discuss briefly the NC region and explore its potential involvement in generating this novel rearrangement. The COI-NC-COII organization, as well as preliminary phylogenetic results, based on both COI-COII nucleotide and amino-acid sequence indicate monophyly of these talitrid taxa. Heredity (2005) 94, 81-86.

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“…PCR primers were designed based on the published complete mitochondrial genome sequences of the crab species Charybdis feriata (Ma et al, 2015a), Scylla paramamosain (Ma et al, 2013), and Portunus trituberculatus (Yamauchi et al, 2003). PCR amplification was conducted in a 25-µL volume that contained 0.4 µM each primer, 0.2 mM each dNTP, 1X PCR buffer, 1.5 mM MgCl 2 , 0.75 U Taq polymerase, and approximately 50 ng DNA under the following conditions: one cycle of denaturation at 94°C for 4 min; 35 cycles of 30 s at 94°C, 50 s at a primer-specific annealing temperature, and 50 s at 72°C.…”

Section: Polymerase Chain Reaction (Pcr) Amplificationmentioning

confidence: 99%

“…Gene rearrangements in the mitochondrial genome are relatively common events in crustacean species (Shen et al, 2007). The tandem duplication of gene regions is the most probable mechanism of mitochondrial gene rearrangement; in this case, a slipped-strand mispairing occurred first and was followed by gene deletions (Yamauchi et al, 2003).…”

Section: Mitochondrial Genome Structurementioning

confidence: 99%

Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus)

Zhu

et al. 2016

Genet. Mol. Res.

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ABSTRACT. In this study, we determined the whole mitochondrial genome profile of the three-spot swimming crab (Portunus sanguinolentus) and elucidated phylogenetic relationships between representative species in the order Decapoda. The mitochondrial genome was 16,024 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Of the 37 genes, 23 were encoded by the heavy strand while 14 were encoded by the light strand. Four types of start codons were identified; ATG initiated nine genes, ATT initiated two genes, and ATC and GTG each started one gene. Nine protein-coding genes ended with a complete TAA or TAG stop codon, and four genes ended with an incomplete T or TA codon. Fourteen non-coding regions were found, which ranged from 1 to 34 bp in length. Nine overlaps were observed, with lengths between 1 and 7 bp. Phylogenetic analysis suggested that P. sanguinolentus is genetically closest to P. trituberculatus and P. pelagicus. Charybdis feriata, C. japonica, and Thalamita crenata formed a single cluster, and were close to the genera Callinectes and Portunus. Therefore, the genera Charybdis and Thalamita should be classified into the subfamily Portuninae.

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Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura)

Cited by 110 publications

References 21 publications

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

Mitochondrial COI-NC-COII sequences in talitrid amphipods (Crustacea)

Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus)

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