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Acheilognathus longipinnis

ABSTRACT: Phylogenomics of the endangered bitterling Acheilognathus longipinnis

PROVIDER: PRJDB15958 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR480451_1.fastq.gz	Fastqsanger.gz
	DRR480451_2.fastq.gz	Fastqsanger.gz
	DRR480452_1.fastq.gz	Fastqsanger.gz
	DRR480452_2.fastq.gz	Fastqsanger.gz
	DRR480453_1.fastq.gz	Fastqsanger.gz

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Mutation Mapping of 40 Streptococcus suis strains

Project description:Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. In this study,we evaluated the genetic difference of 40 Streptococcus suis strains belonging to various sequence types by comparative genomic hybridization to identify genes associated with the variation in pathogenicity using NimbleGen’s tilling microarray platform. Application of Comparative Phylogenomics to Identify Genetic Differences Relating to Pathogenicity of Streptococcus suis

2014-05-20 | GSE40035 | GEO

Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae).

Project description:Genotyping of endangered species is helpful for establishing and evaluating conservation strategies. Mitochondrial sequence data was analyzed from 541 individuals of a critically endangered fish, Acheilognathus typus from present-day range-wide localities to re-evaluate an in-progress restoration program around Lake Izunuma-Uchinuma, Miyagi, Japan. Acheilognathus typus showed low sequence diversity with only eight haplotypes and π and ĥ values of 0.59129 and 0.00118 respectively. Genetic data suggests Acheilognathus typus is adapted to pulsed environments and prone to population flush and crash. Genotyping of populations in introduced localities revealed that their source is not from nearby localities.

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Molecular Cloning and Characterization of the Estrogen Receptor from the Striped Bitterling (Acheilognathus yamatsutae).

Project description:ObjectivesIn order to identify the possibility of striped bitterling (SB) (Acheilognathus yamatsutae) being used as a test species for estrogenic endocrine disrupting chemicals (EEDCs), we carried out the cloning and sequence characterization of the estrogen receptor (ER).MethodsThe ER from a striped bitterling was obtained by reverse transcriptase-polymerase chain reaction (RT-PCR), 5'- and 3'-rapid amplification of cDNA ends (5'-RACE and 3'-RACE) and T-vector cloning. The expression of ER mRNA was also analyzed in six tissues (brain, liver, kidney, gill, gonad, and intestines) by real-time PCR.ResultsWe obtained an ER from the striped bitterling. The SB ER cDNA was 2189 base pairs (bp) in length and contained a 1707 bp open reading frame that encoded 568 amino acid residues. The SB ER amino acid sequence clustered in a monophyletic group with the ERα of other fish, and was more closely related to zebrafish ERα (88% identity) than to the ERα of other fish. The SB ER cDNA was divided into A/B, C, D, E and F domains. The SB ER has conserved important sequences for ER functions, such as the DNA binding domain (D domain), which are consistent with those of other teleosts.ConclusionsThe ER of the striped bitterling could provide basic information in toxicological studies of EEDCs in the striped bitterling.

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Identification and analysis of the complete mitochondrial genome of Acheilognathus omeiensis (Cypriniformes, Cyprinidae).

Project description:Acheilognathus omeiensis is a small-size freshwater ornamental fish. In this study, the complete mitochondrial genome sequence of A. omeiensis was first determined. This mitogenome was 16,774 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 2 main noncoding regions. Most mitochondrial genes were encoded on the H-strand, except for ND6 and eight tRNA genes. The base composition was 28.97% A, 27.72% T, 26.02% C, and 17.29% G, with 56.69% AT, respectively. Phylogenetic tree was constructed based on the nucleotide sequence of 13 PCGs of A. omeiensis and closely related 12 species ticks to assess their phylogenic relationship and evolution. These data should be helpful for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.

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Complete mitochondrial genome and phylogenetic implications of the rainbow bitterling Acheilognathus tonkinensis (Cypriniformes: Cyprinidae).

Project description:Acheilognathus tonkinensis is a magnificent bitterling fish of genus Acheilognathus belonging to the sub-family Acheilognathinae of the family Cyprinidae. In this study, we first determined and described the 16,767 bp mitochondrial DNA sequence of A. tonkinensis. The mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, 12S, and 16S rRNA genes, and a D-loop region. The overall nucleotide composition was 29.4% A, 27.1% T, 17.0% G, and 26.5% C, with a slight AT bias (56.5%). Phylogenetic analysis suggested that A. tonkinensis had the closest evolutionary relationship with A. macropterus. The availability of mitogenome sequence of A. tonkinensis would facilitate species identification of the Acheilognathinae, as well as genetic evaluations for resource conservation and management of this species.

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