Project description:The Korean oily shinner (Sarcocheilichthys nigripinnis morii) is a subspecies belonging to the subfamily Gobioninae in the family Cyprinidae and is endemic to Korea. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of S. nigripinnis morii. The complete mitochondrial genome is 16,679 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitogenomes of 16 species showed that S. nigripinnis morii was clustered with S. nigripinnis and S. variegatus microoculus and grouped with the other Cyprinidae species.
Project description:This study analyzed the complete mitochondrial genome of the short barbeled grunter Hapalogenys nigripinnis (Accession number: MT374064). The complete mitogenome was 16,476 bp long and included 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Nucleotide composition of the genome was A: 28.70%, T:27.46%, G: 15.73%, and C: 28.11%. All genes were encoded on the H-strand, except for the NADH dehydrogenase subunit (ND6) and 8 tRNA genes. When compared this sequence with the mitogenome of Chinese black grunt, Korean short barbeled grunter showed difference of 64 bp of nucleotide sequence in 20 genes. Phylogenetic tree was constructed using the neighbor-joining (NJ) method and showed the phylogenetic position of the short barbeled grunter in Korea.
Project description:Herein, a detailed molecular phylogeny analysis was developed to determine the phylogenetic position of a new freshwater histozoic myxosporean cnidarian, Henneguya markiana sp. nov. from the world's largest tropical wetland area, Pantanal, Brazil. The new species is described using an integrative taxonomy approach including morphology, biological traits and molecular data. Phylogenetic analysis inferred by Maximum Likehood method showed the new Henneguya species in a well-supported clade of myxosporean gill parasites of South American characids fishes. In this same clade, the new Henneguya described appeared in a sub-clade clustering with H. lacustris and H. chydadea. Nevertheless, the sequences of the new species and H. lacustris and H. chydadea have a large genetic divergence of 10.4% (148 nucleotides-nt) and 10.5% (147 nt) respectively. To the best of our knowledge, this is the first report of a cnidarian myxosporean species parasitizing a fish from Stevardiinae from South America. In the light of the differences observed from the integrative taxonomy, we are confident that this isolate is a new species of Henneguya, increasing the knowledge of diversity of this enigmatic group of cnidarians.
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)
Project description:Trithorax group (TrxG) proteins counteract Polycomb silencing by an as yet uncharacterized mechanism. A well-known member of the TrxG is the histone methyltransferase Absent, Small, or Homeotic discs 1 (ASH1). In Drosophila ASH1 is needed for the maintenance of Hox gene expression throughout development, which is tightly coupled to preservation of cell identity. In order to understand the molecular function of ASH1 in this process, we performed affinity purification of tandem-tagged ASH1 followed by mass spectrometry (AP-MS) and identified FSH, another member of the TrxG as interaction partner. Here we provide genome-wide chromatin maps of both proteins based on ChIP-seq. Our Dataset comprises of 4 ChIP-seq samples using chromatin from S2 cells which was immunoprecipitated, using antibodies against Ash1, FSH-L and FSH-SL.
