Chlamydomonas reinhardtii Assembly and Gene Annotation
About Chlamydomonas reinhardtii
Chlamydomonas reinhardtii is a unicellular green alga from the phylum Chlorophyta, which diverged from land plants over a billion years ago. C. reinhardtii is a model species for studying a broad range of fundamental biological processes including the evolution of chloroplast-based photosynthesis and the structure of eukaryotic flagella. It is haploid, and has a nuclear genome comprising 17 chromosomes with a total size of ~120 Mbp.
AssemblyThe 121 Mbp draft sequence of the Chlamydomonas nuclear genome was generated at 13x coverage by whole-genome, shotgun sequencing of plasmid and fosmid libraries, followed by assembly into ~1500 contigs . Assembly into chromosomes was done on the basis of genetic mapping.
AnnotationThe set of gene predictions in version 5.5 incorporates new JGI gene expression data from 1M reads generated from nitrogen-starved cells on the 454 Titatnium platform as well as 239M 2x150 stranded Illumina reads and other smaller RNA-Seq datasets. The underlying gene prediction was performed by Mario Stanke using Augustus (annotation version u11.6)
The non-coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997) , RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007).
- The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marchal-Drouard L et al. 2007. Science. 318:245-250.
Picture credit: By Ninghui Shi [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0)], from Wikimedia Commons
General information about this species can be found in Wikipedia.
|Assembly||Chlamydomonas_reinhardtii_v5.5, INSDC Assembly GCA_000002595.3, Jan 2018|
|Golden Path Length||111,098,438|
|Genebuild method||Imported from ENA|
|Data source||Joint Genome Institute|
|Non coding genes||200|
|Small non coding genes||200|