Thalassiosira pseudonana (ASM14940v2)

Thalassiosira pseudonana Assembly and Gene Annotation

About the Thalassiosira pseudonana genome

Thalassiosira pseudonanais a centric diatom that belongs to the diverse algal group, likely arose from a common secondary endosymbiotic event, involving at least five different genomes. Diatoms are involved in various biogeochemical cycles most notably involving carbon, nitrogen and silicon, and contribute 30% to 40% of marine primary productivity. Consequently, they are responsible for approximately one fifth of the oxygen that is generated each year through global photosynthesis.

Assembly

The genome assembly was done at JGI and is also available from the EMBL/Genbank/DDBJ databases under the accession GCA_000149405.1

Annotation

The protein coding genes in this site are a direct import from JGI. 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). Publications using this data should cite the following publication:

References

  1. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.
    Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M et al. 2004. Science. 306:79-86.
  2. Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana.
    Montsant Anton, Allen AndrewE, Coesel Sacha, Martino AlessandraDe, Falciatore Angela, Mangogna Manuela, Siaut Magali, Heijde Marc, Jabbari Kamel, Maheswari Uma et al. 2007. J. Phycol.. 43:585-604.
  3. Update of the Diatom EST Database: a new tool for digital transcriptomics.
    Maheswari U, Mock T, Armbrust EV, Bowler C. 2009. Nucleic Acids Res.. 37:D1001-5.

Picture credit: Joint Genome Institute. Artistic rendering by Leila Hornick.

Other Data

T. pseudonana ESTs were sequenced from 7 different cDNA libraries. These ESTs were aligned to the genome using exonerate.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyASM14940v2, INSDC Assembly GCA_000149405.2, May 2014
Database version104.2
Golden Path Length32,437,365
Genebuild by
Genebuild methodImport
Data sourceJGI

Gene counts

Coding genes11,672
Non coding genes98
Small non coding genes98
Pseudogenes99
Gene transcripts11,870

About this species