Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda)

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

doi:10.1016/s0378-1119(02)00824-7

Cited by 93 publications

(62 citation statements)

References 24 publications

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“…The bootstrap support of the dendrogram was tested using WinBoot program (Yap & Nelson, 1996). mtDNA sequencing and data analysis Partial sequences of mitochondrial genes were generated using PCR employing following primer pairs: Jerry/Pat (Simon et al, 1994) for the hypervariable region of COI (800 bp) and L10061-CYB (Yamauchi et al, 2002) ? H10699-CYB (Machida et al, 2002) for the CYB (650 bp).…”

Section: Rapd Electrophoresis and Profile Analysismentioning

confidence: 99%

Population genetic structure of the shovel-nosed lobster Thenus unimaculatus (Decapoda, Scyllaridae) in Indian waters based on RAPD and mitochondrial gene sequences

et al. 2015

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Thenus unimaculatus is one of the most important commercially exploited lobster species in India. The declining trend in catches as well as collapse of fishery in some localities necessitated assessment of the stock structure to manage this resource sustainably. We ascertained the genetic stock structure of T. unimaculatus along the Indian coast, using molecular markers. RAPD and concatenated dataset of mitochondrial DNA genes (partial sequences of Cytochrome Oxidase I and Cytochrome b) were used to detect population differentiation. RAPD markers showed moderate genetic variability with an overall G ST value of 0.0442, which indicated low genetic differentiation among subpopulations. The mtDNA dataset revealed high haplotype diversity coupled with very low nucleotide diversity that suggested recent population expansion after a period of low effective population size. The median-joining haplotype network showed no geographical clustering of haplotypes. The low levels of genetic differentiation with non-significant P values (F ST =0.0593) may be due high connectivity among shovel-nosed lobster populations and resultant panmixia. This may be due to the planktonic phyllosoma larval phase that extends for[1 month in wild and their transport and dispersal by monsoon currents of Northern Indian Ocean. The results of this study will aid in better management of this dwindling resource.

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Section: Rapd Electrophoresis and Profile Analysismentioning

confidence: 99%

Population genetic structure of the shovel-nosed lobster Thenus unimaculatus (Decapoda, Scyllaridae) in Indian waters based on RAPD and mitochondrial gene sequences

et al. 2015

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“…Partial sequences of the cox1 and cob genes from the A. japonicus DNA were amplified by polymerase chain reaction (PCR) using the following primer pairs: LCO1490 + HCO2198 [5] for the cox1 gene; and L10061-CYB + H10699-CYB [6,7] for the cob gene. The PCR products were purified using the Montage PCR Cleanup Kit (Millipore) and directly sequenced on a 3730×1 DNA Analyzer (ABI).…”

Section: Long Pcr Amplificationmentioning

confidence: 99%

Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea

Shen

Xiao

Sha

et al. 2012

Sci. China Life Sci.

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The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers (Crustacea: Decapoda: Caridea) is presented here. A comparative analysis based on the currently available mitochondrial genomic data revealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mitochondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mitochondrial genomes of four previously studied carideans (Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra) were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rearrangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving inversion was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mitochondrial genome that has been studied so far; however, the translocation of one transfer RNA gene (trnP or trnT) was reported in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous substitutions rates (Ka/Ks) for the 13 protein coding genes from two Alpheus species (A. japonicus and A. distinguendus) and three Macrobrachium species (M. rosenbergii, M. nipponense, M. lanchesteri) were calculated, the Ka/Ks values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 (between 0.0048 and 0.2057), indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, (Palaemonidae+Alpheidae)+Atyidae, at the family level. With few exceptions, the mitochondrial DNA of Metazoa is circular, 11-20 kb in length, and encodes 37 genes: 13 protein coding genes cob, nad4L, atp6 and atp8), two ribosomal RNAs (rRNAs: srRNA and lrRNA), and 22 transfer RNAs (tRNAs) [1]. Complete mitochondrial genomes are potentially powerful tools that have been used to study the evolutionary history and phylogenetic relationships among metazoans [2]. Mitochondrial genomes also can provide important background information for molecular ecology and population genetics of related species. Caridea Dana, 1852 is one of the largest infraorders in the order Decapoda and is very common in marine and fresh waters. It contains many species of commercial interest. Alpheidae, which currently contains 46

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“…For example, some unusual oligonucleotides, such as the TTA in Panulirus japonicus (Yamauchi et al, 2002), TCG in Bactrocera oleae (Nardi et al, 2003), ACG in Vargula hilgendorfii (Ogoh and Ohmiya, 2004), TATCTA in Penaeis monodon (Wilson et al, 2000), TTTTAG in Bombyx mandarina (Yukuhiro et al, 2002), and TATTAG in Ostrinia nubilalis and O. furnicalis (Coates et al, 2005), have been proposed as the cox1 start codons. As for the start codons for the lepidopteran cox1 genes, they are also controversial.…”

Section: Protein-coding Genesmentioning

confidence: 99%

Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae)

Sun¹,

Sun²,

Wang³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. We sequenced the complete mitochondrial genome of Phalera flavescens. The mitogenome is 15,659 bp in length, including 13 protein-coding genes (atp6, atp8, cox1-3, nad1-6, nad4L, cob), two ribosomal RNAs (rrnS and rrnL), 22 transfer RNAs and an AT-rich region, a putative control region (D-loop). Gene order and orientation were found to be identical to those of other completely sequenced lepidopteran mitogenomes. All 13 protein-coding genes start with the common codon ATN, except for the cox1 gene, which uses CGA as the initial codon. Nine of the 13 protein-coding genes stop with codon TAA, while the cox1, cox2, nad5, and nad4 genes stop with the single nucleotide T. All tRNA genes can be folded into canonical cloverleaf secondary structure, except for trnS1, which loses the ''DHU'' arm. Six overlapping sequences totaling 20 bp (1-8 bp for each sequence) and 16 intergenic spacer sequences, totaling 276 bp (1-58 bp for each sequence) are scattered throughout the genome; the largest intergenic spacer is located between the trnQ and nad2 genes. A microsatellitelike structure (AT) 6 ACC(AT) 6 and 16-bp poly-T elements preceded by the ATTTA motif are present in the D-loop region. Additionally, unexpectedly, an extra 190-bp insertion, with unknown function, was found in the small subunit rRNA gene (rrnS); this gene is the longest known (1020 bp) among all of the Lepidoptera.

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Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda)

Cited by 93 publications

References 24 publications

Population genetic structure of the shovel-nosed lobster Thenus unimaculatus (Decapoda, Scyllaridae) in Indian waters based on RAPD and mitochondrial gene sequences

Population genetic structure of the shovel-nosed lobster Thenus unimaculatus (Decapoda, Scyllaridae) in Indian waters based on RAPD and mitochondrial gene sequences

Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea

Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae)

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