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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.


Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of C. globiceps.
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pone.0153666.g002: Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of C. globiceps.

Mentions: To further evaluate the degree of base bias, the base-skew was measured. The AT-skew and GC-skew values of the protein-coding genes of C. globiceps mtDNA are shown in Fig 2. All GC-skew and AT-skew values were negative, except for the L-strand gene ND6, which had a positive GC skew. This finding indicated that more Cs and Ts were present in most protein-coding genes. In the whole genome of C. globiceps, the AT-skew and GC-skew values were 0 and -0.2877, respectively (Table 1), revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was strongly C skewed. The GC-skew and AT-skew values of protein-coding genes across 11 Gadiform species as shown in Table 1 were all negative, and it was apparent that, besides C. globiceps, the amount of Cs and Ts were more prevalent in the protein-coding genes of Gadiform species, similar to most previous observations of a bias against the use of G [46]. Notably, the two species, C. globiceps and V. garmani, which had the same rearranged gene order, were not T skewed in whole mitogenome, while most of other complete mitogenomes of gadiform species in Table 1 had a negative AT-skew value.


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)

Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of C. globiceps.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153666.g002: Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of C. globiceps.
Mentions: To further evaluate the degree of base bias, the base-skew was measured. The AT-skew and GC-skew values of the protein-coding genes of C. globiceps mtDNA are shown in Fig 2. All GC-skew and AT-skew values were negative, except for the L-strand gene ND6, which had a positive GC skew. This finding indicated that more Cs and Ts were present in most protein-coding genes. In the whole genome of C. globiceps, the AT-skew and GC-skew values were 0 and -0.2877, respectively (Table 1), revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was strongly C skewed. The GC-skew and AT-skew values of protein-coding genes across 11 Gadiform species as shown in Table 1 were all negative, and it was apparent that, besides C. globiceps, the amount of Cs and Ts were more prevalent in the protein-coding genes of Gadiform species, similar to most previous observations of a bias against the use of G [46]. Notably, the two species, C. globiceps and V. garmani, which had the same rearranged gene order, were not T skewed in whole mitogenome, while most of other complete mitogenomes of gadiform species in Table 1 had a negative AT-skew value.

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.