The Chironomus tentans draft genome annotation
type: Dataset
description: If you use this data, please cite: Kutsenko, A., Svensson, T., Nystedt, B. et al. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 15, 819 (2014). https://doi.org/10.1186/1471-2164-15-819 The dipteran Chironomus tentans (C. tentans) and its Balbiani ring (BR) genes serve as a model system for eukaryotic gene expression studies. Kutsenko, A. et al. (2014), reports the first draft genome of C. tentans, characterizing its gene expression machinery and the genomic architecture of its BR genes. In brief, genomic DNA was extracted and sequenced, resulting in an assembly size of 213 Mb, which was likely an overestimate due to allelic variants. The estimated genome size is around 200 Mb, with low GC content (31%) and repeat fraction (15%) compared to other dipterans. Phylogenetic analysis places it as a sister clade to mosquitoes, diverging 150-250 million years ago. The assembled genome was relatively fragmented (scaffold NG50=65 Kbp), but was still found to be reasonably complete regarding gene content, with 97% of 248 highly conserved core eukaryotic genes being represented. For transcriptome sequencing and genome annotation, poly (A)+ RNA was extracted from various tissues and developmental stages. This data was used as evidence for ab initio predictions of gene models and alternative splice variants, resulting in a draft annotation of 15,120 predicted genes. The C. tentans draft genome assembly can be downloaded here or from NCBI: GenBank accession number: CBTT000000000.1 https://www.ncbi.nlm.nih.gov/assembly/GCA_000786525.1/ The draft genome annotation and the corresponding longest predicted proteins for each gene locus is provided here for download. Note that these preliminary annotations are provided as is, and incomplete, missing, or incorrect gene models are to be expected to some extent. Acknowledgements We acknowledge the Science for Life Laboratory and the National Genomics Infrastructure (NGI) for sequencing …
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Alexey Kutsenko
  type: Person
  family name: Kutsenko
  given name: Alexey
creator: Thomas Svensson
  type: Person
  affiliation: Science for Life Laboratory
  family name: Svensson
  given name: Thomas
creator: Björn Nystedt
creator: Joakim Lundeberg
  type: Person
  family name: Lundeberg
  given name: Joakim
creator: Petra Björk
  type: Person
  family name: Björk
  given name: Petra
creator: Erik Sonnhammer
  type: Person
  family name: Sonnhammer
  given name: Erik
creator: Stefania Giacomello
  type: Person
  family name: Giacomello
  given name: Stefania
creator: Neus Visa
  type: Person
  family name: Visa
  given name: Neus
creator: Lars Wieslander
  type: Person
  family name: Wieslander
  given name: Lars
date modified: 2023-08-03
date published: 2023-08-03
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Genetics and Genomics
  type: DefinedTerm
  term code: 10609
keywords: Genomics
license: https://creativecommons.org/licenses/by/4.0/
publisher: Stockholm University
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.23532288

Science for Life Laboratory
type: Organization

Björn Nystedt
type: Person
affiliation: Science for Life Laboratory
family name: Nystedt
given name: Björn

Stockholm University
type: Organization