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Mabuchi, Kohji; Miya, Masaki; Azuma, Yoichiro; Nishida, Mutsumi

doi:10.1186/1471-2148-7-10

Cited by 129 publications

(65 citation statements)

References 38 publications

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“…1, Table 1) including the two other published surfperch genomes (Iwasaki et al, 2013;Mabuchi et al, 2007). As commonly found in other vertebrates, most genes were encoded on the heavy strand except for eight tRNAs (Gln, Ala, Asn, Cys, Tyr, Ser, Glu, and Pro) and NADH dehydrogenase subunit 6 (ND6) (Fig.…”

Section: Genome Organizationmentioning

confidence: 99%

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The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

et al. 2016

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The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae) The complete 16,515 bp nucleotide sequence of the mitochondrial genome was determined for the black surfperch, Embiotoca jacksoni (Perciformes: Embiotocidae). The black surfperch mitochondrial genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (Dloop), the gene order of which is identical to that observed in most vertebrates. The protein-coding gene sequences of E. jacksoni mitochondrial DNA were compared with two other embiotocid surfperches with available complete mitochondrial genomes, Cymatogaster aggregata and Ditrema temminckii. Across all mitochondrial protein-coding genes in surfperches the weighted average substitution rate was 2.079% per My and average dN/dS ratios for each protein-coding gene ranged from 0.016 in CytB to 0.608 in ND3. Substitution rates and dN/dS ratios were relatively high for ATP8 compared to other protein-coding genes. Although most protein-coding genes showed signals of purifying selection, we found evidence for positive selection in ND3 in E. jacksoni.

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Section: Genome Organizationmentioning

confidence: 99%

“…The mitogenomes of C. aggregata (NC_009059) and D. temminckii (NC_009060) were downloaded from NCBI (Mabuchi et al, 2007). We Marine Genomics xxx (2016) xxx-xxx generated a de novo mitochondrial genome of E. jacksoni using gill and liver tissue from a single individual freshly collected in Monterey, California (Fig.…”

Section: Sample Collection and Dna Extractionmentioning

confidence: 99%

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

et al. 2016

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“…Micromesis australis (AB44464), Tja. Trachurus japonicus (AP003091) [14], real-time PCR procedures. The present study is a part of our attempt to develop a procedure to authenticate agonoyaki products and to properly authorize the labeling of the E-mark on commercial fishery products in Japan.…”

Section: Resultsmentioning

confidence: 99%

“…The analyzed fish species are those that are usually used in ago-noyaki production. Besides flying fishes, these are [13], Japanese jack mackerel (T. japonicus, AP003091) [14], tropical twowing flying fish (Exocoetus volitans, AP002933) [15], and Alaska pollock (T. chalcogramma, AB182300) [16]] were designed from the conserved regions of the nucleotide sequence. PCR was conducted in 100-ll reaction volumes.…”

Section: Fish Sample and Dna Extractionmentioning

confidence: 99%

Authentication of flying-fish-meal content of processed food using PCR-RFLP

Nagase

Maeta²,

Aimi

et al. 2009

Fish Sci

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Nucleotide sequence and polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the 3 0 -portion of the mitochondrial 16S RNA gene (rDNA) coding sequence were used to differentiate between flying fishes and other fishes that are frequently used in ago-noyaki production. In this study, we successfully distinguished between flying fishes and the other fishes by combining amplified DNA fragments with universally designed primers and digesting the PCR products with AfaI and MfeI restriction endonucleases. PCR-RFLP of 15 ago-noyaki, 2 noyaki, and 8 other processed flying-fish products were analyzed to authenticate flyingfish content among processed seafood products. After digestion of the PCR products with both enzymes, we found that all ago-noyaki and processed flying fish products contained either two or three DNA fragments of *200, 300, and 530 bp, and noyaki samples (which do not contain flying fish) contained only one fragment of *530 bp. Here, we present a new procedure to confirm the content of flying-fish meal in ago-noyaki.

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“…brasiliensis species group and another included genus were performed using PAUP4 by most parsimonious reconstruction method (Swofford 1993). The relative numeric position was determined for each transformation through sequence alignment with the complete mitochondrial genome of Astronotus ocellatus (Agassiz, 1831) (Mabuchi et al 2007). Plesiomorphic state for each species was presented before arrow and apomorphic state after the arrow.…”

Section: Species Delimitationmentioning

confidence: 99%

Three new species of the ‘ Geophagus’ brasiliensis species group from the northeast Brazil (Cichlidae, Geophagini)

Mattos¹,

Costa²

2018

ZSE

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Morphological characters and phylogenetic trees generated by analyses of segments of two mitochondrial genes cytochrome b and cytochrome c oxidase I support recognition of three new species of the 'Geophagus' brasiliensis species group from coastal basins of northeast Brazil. All new species were diagnosed by exclusive morphological characters and exclusive nucleotide transformations. Geophagus rufomarginatus sp. n., from the Rio Buranhém Basin, is distinguished from all other species of the group by dorsal-fin lappets with red edges, the presence of longitudinal series of small light blue spots between the anal-fin spines and rays, and non-denticulated gill-rakers; it is closely related to G. brasiliensis and G. iporangensis. Geophagus multiocellus sp. n., from the Rio de Contas Basin, is distinguished from all other species of the group by having small pale blue spots with minute bright blue dots at their centres, that are often vertically coalesced to form short bars on the caudal fin. Geophagus santosi sp. n., from the Rio Mariana Basin, is distinguished from all other species of the group by having blue stripes parallel to the dorsal and anal fin rays on their longest portions. Geophagus multiocellus and G. santosi belong to the same clade of G. itapicuruensis. The clade composed by the Rio Paraguaçu Basin species was recovered as the sister group of the other species of the 'G.' brasiliensis species group.

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Cited by 129 publications

References 38 publications

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

Authentication of flying-fish-meal content of processed food using PCR-RFLP

Three new species of the ‘ Geophagus’ brasiliensis species group from the northeast Brazil (Cichlidae, Geophagini)

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