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Characterization of the complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus (Spariformes, Nemipteridae) and phylogenetic analysis.

ABSTRACT: The complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus, which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,882 bp in size and encoded of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Nemipterus furcosus has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that N. furcosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for addressing taxonomic issues.

SUBMITTER: Song HY

PROVIDER: S-EPMC7783152 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome and phylogenetic relationship of ornate threadfin bream, Nemipterus hexodon (Perciformes, Nemipteridae).

Project description:The complete mitochondrial genome of the ornate threadfin bream, Nemipterus hexodon, was first determined by the pairs-walking sequencing in this study. The circular mtDNA molecule was 17,115 bp in size and the overall nucleotide composition of H-stand was A (29.55%), T (27.36%), G (16.08%), and C (27.01%), with a slight bias towards A + T. The complete mitogenome encoded 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (an origin of L-strand replication and a control region). The Bayesian tree supported the phylogenetic position of N. hexodon, which provided useful information for phylogenetic relationship in genus Nemipterus.

| S-EPMC7687645 | biostudies-literature

Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand.

Project description:Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F ST , and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

| S-EPMC8054670 | biostudies-literature

Population genetic structure of Randall's threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences.

Project description:Nemipterus randalli, commonly known as Randall's threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.

| S-EPMC10981751 | biostudies-literature

Characterization of the complete mitochondrial genome of the Butterfly whiptail, Pentapodus setosus (Spariformes, Nemipteridae) and phylogenetic analysis.

Project description:The complete mitochondrial genome of Pentapodus setosus which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,836 bp in length with 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that P. setosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for resolving the taxonomic issues.

| S-EPMC7782546 | biostudies-literature

Morphological and Molecular Characteristics of Anisakis typica Larvae in Two Species of Threadfin Bream, Nemipterus hexodon and N. japonicus, from the Gulf of Thailand.

Project description:The third stage larvae (L3) of Anisakis typica were detected in 2 species of threadfin bream, Nemipterus hexodon and N. japonicus, from the Gulf of Thailand, and were morphologically and molecularly characterized. Total 100 threadfin breams, 50 Nemipterus hexodon and 50 N. japonicus, were examined with naked eyes after the opening of abdominal cavity with scissors. Almost all infected larvae remained alive and active even the fish were transported for 1-2 days. Anisakid larvae were exclusively distributed in the body cavity and rarely in the liver. The prevalence of A. typica L3 were 68.0% and 60.0% in N. hexodon and N. japonicus and their infection intensities were 3.5 and 4.2 per fish infected each. Morphological and morphometric analysis were performed by viewing specimens under both a light microscope and a scanning electron microscope. Interestingly, the protruded mucron of Anisakis typica under SEM showed a distinct cylindrical shape that differed from the cone shape of A. simplex. The protruded mucron could be used to identify A. typica L3 larvae in the future. A comparison of the ITS1-5.8S-ITS2 rDNA nucleotide sequences of these species revealed high blast scores with A. typica. Conclusively, it was confirmed that A. typica L3 are prevalent in threadfin breams from the Gulf of Thailand, and their morphological and molecular characters are something different from those of other anisakid larvae, including A. simplex and A. pegreffii.

| S-EPMC7066448 | biostudies-literature

Textural, Sensory, and Chemical Characteristic of Threadfin Bream (Nemipterus sp.) Surimi Gel Fortified with Bio-Calcium from Bone of Asian Sea Bass (Lates calcarifer).

Project description:The effects of Asian sea bass (Lates calcarifer) bio-calcium (ASBB) at different levels (0, 2, 4, 6, 8, and 10%) (w/w) on properties of threadfin bream (Nemipterus sp.) surimi gel were investigated. ASBB addition increased breaking force and deformation, while reduced expressible moisture content (p < 0.05) of surimi gel. L* (lightness), a* (redness), and b* (yellowness) values were increased with augmenting ASBB levels; however, whiteness slightly decreased in surimi gel incorporated with ASBB (p < 0.05). Higher likeness scores were noticed in surimi gel containing ASBB, compared to that of the control. However, a slight decrease in the likeness score was noticed in surimi gel with 10% (w/w) ASBB (p < 0.05). Surimi gel added with 8% (w/w) ASBB possessed the increase in breaking force by 80% from the control and had the highest likeness score. Texture profile analysis of surimi gel added with ASBB showed the improved texture characteristics with coincidentally higher storage modulus of surimi paste. Surimi gel with 8% (w/w) ASBB had a denser and finer microstructure with higher ash, calcium, and phosphorous contents, compared to the control. Thus, incorporation of bio-calcium up to 8% (w/w) not only increased mineral content, but also improved textural, sensory, and microstructural properties of surimi gel.

| S-EPMC8146884 | biostudies-literature

The complete mitochondrial genome of threadfin butterflyfish, Chaetodon auriga (Chaetodontiformes: Chaetodontidae) and phylogenetic analysis.

Project description:Chaetodon auriga (Forsskal, 1775) belongs to the family Chaetodontidae and the order Chaetodontiformes. Here, we report the complete mitochondrial genome of C. auriga assembled using the Illumina MiSeq platform. The circular mitochondrial genome of C. auriga is 16,527 bp long, has an A + T content of 54.53%, and contains 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes), and a non-coding region. The overall nucleotide composition was A: 28.19%, T: 26.34%, G: 16.27%, and C: 29.20%. The mitochondrial genome of C. auriga contributes to revealing the phylogenetic relationships among species of the Chaetodontidae family.

| S-EPMC9639548 | biostudies-literature

Fork tailed flycatchers

Project description:Speciation in fork tailed flycatchers (GBS data)

| PRJNA600207 | ENA

Scolopsislacrima, a new species of monocle bream (Teleostei, Perciformes, Nemipteridae) from New Caledonia.

Project description:The new monocle bream Scolopsislacrima sp. nov. is described from a single specimen (213.6 mm standard length) collected from Grande-Terre Island, New Caledonia. The new species closely resembles S.meridiana, both species having the upper part of the pectoral-fin base with reddish blotch when fresh, two bands across the top of the snout, a dorsal scaled area on the head reaching anteriorly to between the anterior margin of the eye and anterior nostril, a similar number of lateral-line scales, and absence of a small antrorse spine below the eye. However, S.lacrima sp. nov. is distinguished from S.meridiana by having diagonal lines on the body absent (vs. 18-20 diagonal lines in the latter), a dark longitudinal band below the lateral line (vs. longitudinal lines absent), the caudal fin central area not patterned (vs. with several dark horizontal lines), a narrower body and shallower caudal peduncle.

| S-EPMC6629716 | biostudies-literature

Characterization of the complete mitochondrial genome of short-tailed field vole, Microtus agrestis.

Project description:In this study, the complete mitochondrial genome of short-tailed field vole, Microtus agrestis, was determined through sequencing of PCR fragments. The complete mitochondrial genome of M. agrestis was 16,538?bp in length and encoded 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes. The overall nucleotide composition is: 15.7% A, 27.5% T, 25.5% C, and 31.4% G, with a total G?+?C content of 56.9%. By phylogenetic analysis using Bayesian method, M. agrestisa showed the closest relationship with the southern vole (Microtus rossiaemeridionalis).

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