Limits...
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.


Features present in the putative control region of C. globiceps mitogenome.The conserved motifs ATGTA and its complement TACAT which may form thermostable hairpin structure are shaded. The conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 are underlined and labeled by name. The arrows above the nucleotides indicate the tandem repeats.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4836748&req=5

pone.0153666.g007: Features present in the putative control region of C. globiceps mitogenome.The conserved motifs ATGTA and its complement TACAT which may form thermostable hairpin structure are shaded. The conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 are underlined and labeled by name. The arrows above the nucleotides indicate the tandem repeats.

Mentions: Similar to that in most vertebrates, the control region of C. globiceps was adjacent to the 5’ portion of tRNAPhe [33, 46,54]. The control regions of teleost fish contain a number of conserved sequence blocks (CSBs), which may play important roles in mitochondrial metabolism [14]. CSB-D, -E and–F are found typically present in central conserved domain of control region of teleost fish and CSB-1, CSB-2 and CSB-3 present in the conserved sequence block domain [14]. By comparing with the recognition sites in teleost species, several conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 have been identified (Fig 7) [45]. These sequence elements are thought to function as proper regulatory sites as well as recognition sites for transcription primer strand synthesis and for replication priming [34]. Further study into the mechanism of mtDNA transcription and replication is thus warranted. Consistent with other Gadiformes, the GTGGG-box, which is the typical characteristic of CSB-E, was absent in C. globiceps, while this motif is commonly found in teleosts [33, 54]. Notably, tandem repeats are indicated in the 3' portion of CR, and it harbors two types of tandem repeats comprising a 13 bp repeat (ATTAAACCAAATA) and 8 bp repeat (CAGTGTTA) unit, named Repeat 1 and Repeat 2 respectively and shown in Fig 7. No similar repetitive motif is present in other gadiform species, except V. garmani, suggesting that the duplication events occurred after family diversification. Nevertheless, more information is needed to provide a useful model system to study how these repeat clusters evolved.


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)

Features present in the putative control region of C. globiceps mitogenome.The conserved motifs ATGTA and its complement TACAT which may form thermostable hairpin structure are shaded. The conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 are underlined and labeled by name. The arrows above the nucleotides indicate the tandem repeats.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153666.g007: Features present in the putative control region of C. globiceps mitogenome.The conserved motifs ATGTA and its complement TACAT which may form thermostable hairpin structure are shaded. The conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 are underlined and labeled by name. The arrows above the nucleotides indicate the tandem repeats.
Mentions: Similar to that in most vertebrates, the control region of C. globiceps was adjacent to the 5’ portion of tRNAPhe [33, 46,54]. The control regions of teleost fish contain a number of conserved sequence blocks (CSBs), which may play important roles in mitochondrial metabolism [14]. CSB-D, -E and–F are found typically present in central conserved domain of control region of teleost fish and CSB-1, CSB-2 and CSB-3 present in the conserved sequence block domain [14]. By comparing with the recognition sites in teleost species, several conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 have been identified (Fig 7) [45]. These sequence elements are thought to function as proper regulatory sites as well as recognition sites for transcription primer strand synthesis and for replication priming [34]. Further study into the mechanism of mtDNA transcription and replication is thus warranted. Consistent with other Gadiformes, the GTGGG-box, which is the typical characteristic of CSB-E, was absent in C. globiceps, while this motif is commonly found in teleosts [33, 54]. Notably, tandem repeats are indicated in the 3' portion of CR, and it harbors two types of tandem repeats comprising a 13 bp repeat (ATTAAACCAAATA) and 8 bp repeat (CAGTGTTA) unit, named Repeat 1 and Repeat 2 respectively and shown in Fig 7. No similar repetitive motif is present in other gadiform species, except V. garmani, suggesting that the duplication events occurred after family diversification. Nevertheless, more information is needed to provide a useful model system to study how these repeat clusters evolved.

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.