Plotosus fisadoha
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ABSTRACT:
PROVIDER: PRJNA837957 | ENA |
REPOSITORIES: ENA
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Project description:The complete mitochondrial genome of stripped eel catfish, Plotosus lineatus, is sequenced in this study. The mitochondrial genome sequence is 16?480?bp in length, with the base composition of 24.7% A, 31.8% T, 27.8% G and 15.7% C. The G?+?C content is 43.5%. The mitochondria includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one D-loop region. Except for NAD6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. Plotosus lineatus was confirmed to be closely related to P. japonicus (GenBank: KR270437.1), based on our phylogenetic analysis on complete mitochondrial genome sequences of 13 species. Our complete mitogenome data are going to provide the basis for taxonomic and phylogenetic research of catfishes.
| S-EPMC7871829 | biostudies-literature
Project description:Unique amongst the teleost, Plotosidae catfish possess a dendritic organ (DO) as a purported salt secreting organ, whereas other marine teleosts rely on their gill ionocytes for active NaCl excretion. To address the role of the DO in ionregulation, ligation experiments were conducted in brackish water (BW) 3‰ and seawater (SW) 34‰ acclimated Plotosus lineatus and compared to sham operated fish. Ligation in SW resulted in an osmoregulatory impairment in blood (elevated ions and hematocrit) and muscle (dehydration). However, SW ligation did not elicit compensatory changes in gill or kidney Na+/K+-ATPase (NKA) activity and/or protein expression while a decrease in anterior intestine and increased in posterior intestine were observed but this was not reflected at the protein level. Following ligation in SW, protein levels of carbonic anhydrase (CA) and V-ATPase B subunit (VHAB) were higher in kidney but either lower (CA) or unchanged (VHAB) in other tissues. Taken together, the osmotic disturbance in ligated SW fish indicates the central role of the DO in salt secretion and the absence of a compensatory response from the gill.
| S-EPMC6198982 | biostudies-literature
Project description:Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395-0.771 and 0.033-0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho ) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.
| S-EPMC4878373 | biostudies-literature
Project description:modENCODE_submission_5986 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population; EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody NURF-1 SDQ3525 (target is NURF-1)
2013-08-28 | E-GEOD-50296 | biostudies-arrayexpress