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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.


Intergenic T-P spacer sequence of five Gadiform species.Gm: Gadus morhua, Tc: Theragra chalcogramma, Bs: Boreogadus saida, Cg: Cetonurus globiceps, Vg: Ventrifossa garmani. Dots indicate identical positions and dashes indicate deletions. Conserved regions and tRNAs are marked by boxes.
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pone.0153666.g005: Intergenic T-P spacer sequence of five Gadiform species.Gm: Gadus morhua, Tc: Theragra chalcogramma, Bs: Boreogadus saida, Cg: Cetonurus globiceps, Vg: Ventrifossa garmani. Dots indicate identical positions and dashes indicate deletions. Conserved regions and tRNAs are marked by boxes.

Mentions: A codfish-unique T-P spacer, 70bp in size, was also observed in C. Globiceps [20, 40]. After sequence alignment with the published corresponding sequences of Gadus morhua (Gm), Theragra chalcogramma (Tc) and Boreogadus saida (Bs), the spacer was revealed to be similar to that in other codfishes thus the sequence was divided into five regions (regions I-V, Fig 5), following the findings of Bakke and colleagues [40]. As previously observed, region II of the T-P spacer in C. globiceps was found to be the most conserved region in terms of the sequence as well as the placement, while other regions showed great variability (Fig 5). The T-P intergenic spacer being found in all species of the family Gadidae is indicative of its evolution before the family began to diversify and of its evolutionary stability over time [20, 40]. It has become clear, regarding the evolution of mtDNA genomes, that genomic size is usually minimized under strong purifying selection [53]. Thus, the presence of conserved non-coding motifs in C. globiceps as well as in other codfish suggests that they are evolutionarily homologous and supports a conservation of universal important functions, such as mitochondrial replication and/or transcription [20]. Notably, it was interesting that the highest sequence similarities of regionII appeared in C. globiceps and V. garmani, which belong to different subfamilies of Macrouridae. Considering that it is unlikely for different species to acquire the same element by chance, we propose that different species of Macrouridae might share similar molecular characteristics of the ancestral T-P spacer. These similarities may reflect the phylogenetic relationship between the species.


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)

Intergenic T-P spacer sequence of five Gadiform species.Gm: Gadus morhua, Tc: Theragra chalcogramma, Bs: Boreogadus saida, Cg: Cetonurus globiceps, Vg: Ventrifossa garmani. Dots indicate identical positions and dashes indicate deletions. Conserved regions and tRNAs are marked by boxes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153666.g005: Intergenic T-P spacer sequence of five Gadiform species.Gm: Gadus morhua, Tc: Theragra chalcogramma, Bs: Boreogadus saida, Cg: Cetonurus globiceps, Vg: Ventrifossa garmani. Dots indicate identical positions and dashes indicate deletions. Conserved regions and tRNAs are marked by boxes.
Mentions: A codfish-unique T-P spacer, 70bp in size, was also observed in C. Globiceps [20, 40]. After sequence alignment with the published corresponding sequences of Gadus morhua (Gm), Theragra chalcogramma (Tc) and Boreogadus saida (Bs), the spacer was revealed to be similar to that in other codfishes thus the sequence was divided into five regions (regions I-V, Fig 5), following the findings of Bakke and colleagues [40]. As previously observed, region II of the T-P spacer in C. globiceps was found to be the most conserved region in terms of the sequence as well as the placement, while other regions showed great variability (Fig 5). The T-P intergenic spacer being found in all species of the family Gadidae is indicative of its evolution before the family began to diversify and of its evolutionary stability over time [20, 40]. It has become clear, regarding the evolution of mtDNA genomes, that genomic size is usually minimized under strong purifying selection [53]. Thus, the presence of conserved non-coding motifs in C. globiceps as well as in other codfish suggests that they are evolutionarily homologous and supports a conservation of universal important functions, such as mitochondrial replication and/or transcription [20]. Notably, it was interesting that the highest sequence similarities of regionII appeared in C. globiceps and V. garmani, which belong to different subfamilies of Macrouridae. Considering that it is unlikely for different species to acquire the same element by chance, we propose that different species of Macrouridae might share similar molecular characteristics of the ancestral T-P spacer. These similarities may reflect the phylogenetic relationship between the species.

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.