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Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis.

Shi X, Tian P, Lin R, Huang D, Wang J - PLoS ONE (2016)

Bottom Line: Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade.Some relationships however, are in contrast with those presented in previous studies.This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China.

ABSTRACT
The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr)-tRNA(Pro) intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY)) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

No MeSH data available.


Overall mean p-genetic distance of six Macrouridae species for each of 13 protein genes.They were calculated based on the first and second nucleotide positions and on the third nucleotide position of amino acid codons, and on the full sequence among six Macrouridae species, respectively.
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pone.0153666.g004: Overall mean p-genetic distance of six Macrouridae species for each of 13 protein genes.They were calculated based on the first and second nucleotide positions and on the third nucleotide position of amino acid codons, and on the full sequence among six Macrouridae species, respectively.

Mentions: The conservation of mtDNA genes was evaluated based on the overall p-genetic distance among six Macrouridae species, including C. globiceps, V. garmani, Trachyrincus murrayi, Squalogadus modificatus, C. kishinouyei, and Arctogadus glacialis [49]. Of the 13 protein-coding genes, the COI gene has the lowest overall p-genetic distance (0.051) among species, and the ATP8 gene has the highest value (0.321) based on data of the first and second nucleotides of codons. According to full-length sequence comparisons for each gene, ATP8 also has the highest value (0.374), and COI has the lowest value (0.193). Base on these results, it can be found that ATP8 likely has the fastest evolutionary rate among Macrouridae species, while COI has the lowest rate. For the third nucleotide, all genes have a high overall p-genetic distance value. As is the case for other fish, most of the differences in the mtDNA protein-coding genes occurred at the third codon position [34] (Fig 4).


Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis.

Shi X, Tian P, Lin R, Huang D, Wang J - PLoS ONE (2016)

Overall mean p-genetic distance of six Macrouridae species for each of 13 protein genes.They were calculated based on the first and second nucleotide positions and on the third nucleotide position of amino acid codons, and on the full sequence among six Macrouridae species, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836748&req=5

pone.0153666.g004: Overall mean p-genetic distance of six Macrouridae species for each of 13 protein genes.They were calculated based on the first and second nucleotide positions and on the third nucleotide position of amino acid codons, and on the full sequence among six Macrouridae species, respectively.
Mentions: The conservation of mtDNA genes was evaluated based on the overall p-genetic distance among six Macrouridae species, including C. globiceps, V. garmani, Trachyrincus murrayi, Squalogadus modificatus, C. kishinouyei, and Arctogadus glacialis [49]. Of the 13 protein-coding genes, the COI gene has the lowest overall p-genetic distance (0.051) among species, and the ATP8 gene has the highest value (0.321) based on data of the first and second nucleotides of codons. According to full-length sequence comparisons for each gene, ATP8 also has the highest value (0.374), and COI has the lowest value (0.193). Base on these results, it can be found that ATP8 likely has the fastest evolutionary rate among Macrouridae species, while COI has the lowest rate. For the third nucleotide, all genes have a high overall p-genetic distance value. As is the case for other fish, most of the differences in the mtDNA protein-coding genes occurred at the third codon position [34] (Fig 4).

Bottom Line: Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade.Some relationships however, are in contrast with those presented in previous studies.This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China.

ABSTRACT
The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr)-tRNA(Pro) intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY)) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

No MeSH data available.