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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.


Gene map and organization of the complete mitochondrial genome of C. globiceps.Genes encoded on the heavy and light strand are shown outside and inside the circle, respectively. The inner grey ring indicates the GC content.
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pone.0153666.g001: Gene map and organization of the complete mitochondrial genome of C. globiceps.Genes encoded on the heavy and light strand are shown outside and inside the circle, respectively. The inner grey ring indicates the GC content.

Mentions: The complete mitochondrial DNA sequence (17,137bp in length) consists of 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes (12S rRNA and 16S rRNA) and two major non-coding regions (the origin of light strand replication (OL) and control region (CR)) (GenBank accession NO. KF751382) (Fig 1). Additionally, a tRNAThr-tRNAPro (T-P) intergenic spacer (70 bp in length) unique to Gadiformes was observed [20, 40]. The C. globiceps mitogenome is shorter than those of Ventrifossa garmani and Bathygadus antrodes but considerably longer than those of other Gadiform species (Table 1). Most of the genes were encoded on the heavy strand (H-strand), except for ND6 and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Glu, and Pro).


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)

Gene map and organization of the complete mitochondrial genome of C. globiceps.Genes encoded on the heavy and light strand are shown outside and inside the circle, respectively. The inner grey ring indicates the GC content.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153666.g001: Gene map and organization of the complete mitochondrial genome of C. globiceps.Genes encoded on the heavy and light strand are shown outside and inside the circle, respectively. The inner grey ring indicates the GC content.
Mentions: The complete mitochondrial DNA sequence (17,137bp in length) consists of 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes (12S rRNA and 16S rRNA) and two major non-coding regions (the origin of light strand replication (OL) and control region (CR)) (GenBank accession NO. KF751382) (Fig 1). Additionally, a tRNAThr-tRNAPro (T-P) intergenic spacer (70 bp in length) unique to Gadiformes was observed [20, 40]. The C. globiceps mitogenome is shorter than those of Ventrifossa garmani and Bathygadus antrodes but considerably longer than those of other Gadiform species (Table 1). Most of the genes were encoded on the heavy strand (H-strand), except for ND6 and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Glu, and Pro).

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.