Dataset Information

The complete mitochondrial genome of Hypomesus olidus (Osmeriformes: Osmeridae).

ABSTRACT: Pond smelt Hypomesus olidus is a small-sized economic species of freshwater fish with delicious meat and high output. In this study, the complete mitochondrial genome of H. olidus sequenced to be 16,786?bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The overall base composition of H. olidus is 24.3% for A, 27.3% for T, 29.2% for C and 19.2% for G, with a slight A?+?T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of H. olidus and the elucidation of evolutionary mechanisms in Hypomesus fish.

SUBMITTER: Bai X

PROVIDER: S-EPMC7799710 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of Hypomesus olidus (Osmeriformes: Osmeridae).

Bai Xiaohui X Luo Zhang Z Feng Shouming S Sun Zhijing Z Wu Hui-Min HM Li Chun-Yan CY Jiang Ju-Feng JF Liu Xiaolian X Wang Na N

Mitochondrial DNA. Part B, Resources 20171019 2

Pond smelt Hypomesus olidus is a small-sized economic species of freshwater fish with delicious meat and high output. In this study, the complete mitochondrial genome of H. olidus sequenced to be 16,786 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The overall base composition of H. olidus is 24.3% for A, 27.3% for T, 29.2% for C and 19.2% for G, with a slight A + T bias. The mitogenome sequence data may provide use ...[more]

PMID: 33473948

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Project description:BACKGROUND: The delta smelt (Hypomesus transpacificus) is a pelagic fish species listed as endangered under both the USA Federal and Californian State Endangered Species Acts and considered an indicator of ecosystem health in its habitat range, which is limited to the Sacramento-San Joaquin estuary in California, USA. Anthropogenic contaminants are one of multiple stressors affecting this system, and among them, current-use insecticides are of major concern. Interrogative tools are required to successfully monitor effects of contaminants on the delta smelt, and to research potential causes of population decline in this species. We have created a microarray to investigate genome-wide effects of potentially causative stressors, and applied this tool to assess effects of the pyrethroid insecticide esfenvalerate on larval delta smelt. Selected genes were further investigated as molecular biomarkers using quantitative PCR analyses. RESULTS: Exposure to esfenvalerate affected swimming behavior of larval delta smelt at concentrations as low as 0.0625 mug.L-1, and significant differences in expression were measured in genes involved in neuromuscular activity. Alterations in the expression of genes associated with immune responses, along with apoptosis, redox, osmotic stress, detoxification, and growth and development appear to have been invoked by esfenvalerate exposure. Swimming impairment correlated significantly with expression of aspartoacylase (ASPA), an enzyme involved in brain cell function and associated with numerous human diseases. Selected genes were investigated for their use as molecular biomarkers, and strong links were determined between measured downregulation in ASPA and observed behavioral responses in fish exposed to environmentally relevant pyrethroid concentrations. CONCLUSIONS: The results of this study show that microarray technology is a useful approach in screening for, and generation of molecular biomarkers in endangered, non-model organisms, identifying specific genes that can be directly linked with sublethal toxicological endpoints; such as changes in expression levels of neuromuscular genes resulting in measurable swimming impairments. The developed microarrays were successfully applied on larval fish exposed to esfenvalerate, a known contaminant of the Sacramento-San Joaquin estuary, and has permitted the identification of specific biomarkers which could provide insight into the factors contributing to delta smelt population decline.

Project description:The complete sequence of honeybee (Apis mellifera) mitochondrial DNA is reported being 16,343 bp long in the strain sequenced. Relative to their positions in the Drosophila map, 11 of the tRNA genes are in altered positions, but the other genes and regions are in the same relative positions. Comparisons of the predicted protein sequences indicate that the honeybee mitochondrial genetic code is the same as that for Drosophila; but the anticodons of two tRNAs differ between these two insects. The base composition shows extreme bias, being 84.9% AT (cf. 78.6% in Drosophila yakuba). In protein-encoding genes, the AT bias is strongest at the third codon positions (which in some cases lack guanines altogether), and least in second codon positions. Multiple stepwise regression analysis of the predicted products of the protein-encoding genes shows a significant association between the numbers of occurrences of amino acids and %T in codon family, but not with the number of codons per codon family or other parameters associated with codon family base composition. Differences in amino acid abundances are apparent between the predicted Apis and Drosophila proteins, with a relative abundance in the Apis proteins of lysine and a relative deficiency of alanine. Drosophila alanine residues are as often replaced by serine as conserved in Apis. The differences in abundances between Drosophila and Apis are associated with %AT in the codon families, and the degree of divergence in amino acid composition between proteins correlates with the divergence in %AT at the second codon positions. Overall, transversions are about twice as abundant as transitions when comparing Drosophila and Apis protein-encoding genes, but this ratio varies between codon positions. Marked excesses of transitions over chance expectation are seen for the third positions of protein-coding genes and for the gene for the small subunit of ribosomal RNA. For the third codon positions the excess of transitions is adequately explained as due to the restriction of observable substitutions to transitions for conserved amino acids with two-codon families; the excess of transitions over expectation for the small ribosomal subunit suggests that the conservation of nucleotide size is favored by selection.

Dataset Information

The complete mitochondrial genome of Hypomesus olidus (Osmeriformes: Osmeridae).

Publications

The complete mitochondrial genome of <i>Hypomesus olidus</i> (Osmeriformes: Osmeridae).

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