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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.


Evolutionary rates of C. globiceps mitogenome.The rate of non-synonymous substitutions (Ka), the rate of synonymous substitutions (Ks) and the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions (Ka/Ks) for each protein-coding gene.
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pone.0153666.g003: Evolutionary rates of C. globiceps mitogenome.The rate of non-synonymous substitutions (Ka), the rate of synonymous substitutions (Ks) and the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions (Ka/Ks) for each protein-coding gene.

Mentions: Methionine (ATG) is the start codon for most of the protein-coding genes, while COI utilizes GTG, which is also an accepted canonical mitochondrial start codon for vertebrate mitogenomes [19]. Interestingly, ND4L of C. globiceps begins with GTG as well, which is different than most of gadiform species, except for V. garmani. With regard to stop codons, four genes terminated with TAA, two genes end with AGA, and ND6 ends in AGG. The other six genes had incomplete stop codons, either TA (ATP6 and COIII) or T (COI, COII, ND4 and ND3), which would be presumably completed as entire stop codon (TAA) via post-transcriptional polyadenylation. In all 13 protein-coding genes, the average Ka/Ks ratio varied from 0.0177 (COI) to 0.2462 (ATP8) and was lower than 0.5 for all other genes (Fig 3). As is reported, two nonadaptive forces, random genetic drift and mutation pressure define the fundamental features of genome evolution. However, functional constraint imposes burden on mutation [47]. Therefore, the mutation-associated disadvantages are difficult to establish under purifying selection. The selection processes maintain long-term stability of the biological structure. Our result of the Ka/Ks ratio indicated that the various functional genes evolved under strong purifying selection which means natural selection against deleterious mutations with negative selective coefficients [48]. The selection pressures differed among genes [47], and they are likely to evolve in different ways. Additionally, ATP8 and ND6 had the highest ratios, indicating that the selection pressures were independent of which strand the gene was located.


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)

Evolutionary rates of C. globiceps mitogenome.The rate of non-synonymous substitutions (Ka), the rate of synonymous substitutions (Ks) and the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions (Ka/Ks) for each protein-coding gene.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153666.g003: Evolutionary rates of C. globiceps mitogenome.The rate of non-synonymous substitutions (Ka), the rate of synonymous substitutions (Ks) and the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions (Ka/Ks) for each protein-coding gene.
Mentions: Methionine (ATG) is the start codon for most of the protein-coding genes, while COI utilizes GTG, which is also an accepted canonical mitochondrial start codon for vertebrate mitogenomes [19]. Interestingly, ND4L of C. globiceps begins with GTG as well, which is different than most of gadiform species, except for V. garmani. With regard to stop codons, four genes terminated with TAA, two genes end with AGA, and ND6 ends in AGG. The other six genes had incomplete stop codons, either TA (ATP6 and COIII) or T (COI, COII, ND4 and ND3), which would be presumably completed as entire stop codon (TAA) via post-transcriptional polyadenylation. In all 13 protein-coding genes, the average Ka/Ks ratio varied from 0.0177 (COI) to 0.2462 (ATP8) and was lower than 0.5 for all other genes (Fig 3). As is reported, two nonadaptive forces, random genetic drift and mutation pressure define the fundamental features of genome evolution. However, functional constraint imposes burden on mutation [47]. Therefore, the mutation-associated disadvantages are difficult to establish under purifying selection. The selection processes maintain long-term stability of the biological structure. Our result of the Ka/Ks ratio indicated that the various functional genes evolved under strong purifying selection which means natural selection against deleterious mutations with negative selective coefficients [48]. The selection pressures differed among genes [47], and they are likely to evolve in different ways. Additionally, ATP8 and ND6 had the highest ratios, indicating that the selection pressures were independent of which strand the gene was located.

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.