Thalassiosira pseudonana Assembly and Gene Annotation

About Thalassiosira pseudonana CCMP1335

Thalassiosira pseudonana is a species of marine centric Bulka diatoms. It was chosen as the first eukaryotic marine phytoplankton for whole genome sequencing. T. pseudonana was selected for this study because it is a model for diatom physiology studies, belongs to a genus widely distributed throughout the world's oceans, and has a relatively small genome at 34 mega base pairs. Scientists are researching on diatom light absorption, using the marine diatom of Thalassiosira. The diatom requires a high enough concentration of CO2 in order to utilize C4 metabolism (Clement et al. 2015).

Taxonomy ID 296543 (Text from Wikipedia.) Picture credit: (Image source)

More information General information about this species can be found in Wikipedia

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.