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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.


Phylogenetic tree of Gadiform species reconstructed from concatenated DNA sequences of mitochondrial protein-coding genes.Twelve mitochondrial protein-coding genes (with the exception of ND6) were used for the phylogenetic tree, which was produced by Bayesian inferences (BI). Sardinops melanostictus was used as the outgroup. Bayesian posterior probability are shown orderly on the nodes. The asterisk indicates the sequence generated in this study.
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pone.0153666.g008: Phylogenetic tree of Gadiform species reconstructed from concatenated DNA sequences of mitochondrial protein-coding genes.Twelve mitochondrial protein-coding genes (with the exception of ND6) were used for the phylogenetic tree, which was produced by Bayesian inferences (BI). Sardinops melanostictus was used as the outgroup. Bayesian posterior probability are shown orderly on the nodes. The asterisk indicates the sequence generated in this study.

Mentions: Gadiformes have been typically positioned in the center of Paracanthopterygii [10]. However, the systematic organization within this order represents a problematic issue. Endo, in 2002, reported a comprehensive classification of Gadiformes and formed the basis for the current Gadiformes classification system [10]. However, the results still reflected several unresolved relationships [41]. Following a number of molecular studies conducted to resolve the phylogenetic relationships at the genus level [55, 56], the most recent work, carried out by Roa-Varon and colleague, made great progress in confirming the monophyly of most of the proposed families for Gadiformes. However, taxon samples remained limited [41]. In this study, the phylogenetic position of C. globiceps, based on the 12 concatenated protein-coding genes of mitochondria, was first analyzed. The accession numbers for the mitochondrial genome sequences of the 19 species utilized in this study were shown in Fig 8. Different methods (BI, ML and NJ) generated similar tree topologies, and most of the nodes were statistically supported by high bootstrap and posterior probability values. Only the Bayesian tree is shown in Fig 8. The phylogenetic trees included 19 Gadiform species, representing 7 families and 16 genera, and revealed two main clades, namely the suborders Macrouroidei and Gadoidei, following the taxonomic system proposed by Roa-Varon and colleague [41]. Four Macrouridae species including C. globiceps, Bathygadus antrodes, Coelorinchus kishinouyei and Ventrifossa garmani formed a monophyletic group. Our findings suggests that the genetically closest relationship exists between C. globiceps and V. garmani. The two species were shown to be in the most evolved clade (Fig 8.). Combined with the previously mentioned, unexpected motifs in the control regions of C. globiceps and V. garmani, which were absent in other gadiform fish, it is reasonable to assume that these two species might have separated recently. Furthermore, the hydraulic pressure of the marine environments plays a pivotal role in the speciation process of fish that geographically evolve from shallow environments to the deep sea [57, 58]. V. garmani was distributed at a depth ranging from 200–720 m, which is much shallower than that of C. globiceps. These clues may indicate that the control region evolved before C. globiceps had adapted to the deep-water environment. However, further investigation such as heterologous assays in vitro or hybridization experiments is needed to determine whether the structure of the non-coding region was important in adaptation and acclimation to the deep sea environment.


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)

Phylogenetic tree of Gadiform species reconstructed from concatenated DNA sequences of mitochondrial protein-coding genes.Twelve mitochondrial protein-coding genes (with the exception of ND6) were used for the phylogenetic tree, which was produced by Bayesian inferences (BI). Sardinops melanostictus was used as the outgroup. Bayesian posterior probability are shown orderly on the nodes. The asterisk indicates the sequence generated in this study.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153666.g008: Phylogenetic tree of Gadiform species reconstructed from concatenated DNA sequences of mitochondrial protein-coding genes.Twelve mitochondrial protein-coding genes (with the exception of ND6) were used for the phylogenetic tree, which was produced by Bayesian inferences (BI). Sardinops melanostictus was used as the outgroup. Bayesian posterior probability are shown orderly on the nodes. The asterisk indicates the sequence generated in this study.
Mentions: Gadiformes have been typically positioned in the center of Paracanthopterygii [10]. However, the systematic organization within this order represents a problematic issue. Endo, in 2002, reported a comprehensive classification of Gadiformes and formed the basis for the current Gadiformes classification system [10]. However, the results still reflected several unresolved relationships [41]. Following a number of molecular studies conducted to resolve the phylogenetic relationships at the genus level [55, 56], the most recent work, carried out by Roa-Varon and colleague, made great progress in confirming the monophyly of most of the proposed families for Gadiformes. However, taxon samples remained limited [41]. In this study, the phylogenetic position of C. globiceps, based on the 12 concatenated protein-coding genes of mitochondria, was first analyzed. The accession numbers for the mitochondrial genome sequences of the 19 species utilized in this study were shown in Fig 8. Different methods (BI, ML and NJ) generated similar tree topologies, and most of the nodes were statistically supported by high bootstrap and posterior probability values. Only the Bayesian tree is shown in Fig 8. The phylogenetic trees included 19 Gadiform species, representing 7 families and 16 genera, and revealed two main clades, namely the suborders Macrouroidei and Gadoidei, following the taxonomic system proposed by Roa-Varon and colleague [41]. Four Macrouridae species including C. globiceps, Bathygadus antrodes, Coelorinchus kishinouyei and Ventrifossa garmani formed a monophyletic group. Our findings suggests that the genetically closest relationship exists between C. globiceps and V. garmani. The two species were shown to be in the most evolved clade (Fig 8.). Combined with the previously mentioned, unexpected motifs in the control regions of C. globiceps and V. garmani, which were absent in other gadiform fish, it is reasonable to assume that these two species might have separated recently. Furthermore, the hydraulic pressure of the marine environments plays a pivotal role in the speciation process of fish that geographically evolve from shallow environments to the deep sea [57, 58]. V. garmani was distributed at a depth ranging from 200–720 m, which is much shallower than that of C. globiceps. These clues may indicate that the control region evolved before C. globiceps had adapted to the deep-water environment. However, further investigation such as heterologous assays in vitro or hybridization experiments is needed to determine whether the structure of the non-coding region was important in adaptation and acclimation to the deep sea environment.

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.