Phaeodactylum tricornutum Assembly and Gene Annotation

About Phaeodactylum tricornutum CCAP 1055/1

Phaeodactylum tricornutum is a diatom, the only species in the genus Phaeodactylum. Unlike other diatoms, P. tricornutum can exist in different morphotypes and changes in cell shape can be stimulated by environmental conditions. This feature can be used to explore the molecular basis of cell shape control and morphogenesis. Unlike most diatoms, P. tricornutum can grow in the absence of silicon and can survive without making silicified frustules. This provides opportunities for experimental exploration of silicon-based nanofabrication in diatoms.

Picture credit: Creative Commons Attribution 2.5 via Wikimedia Commons (Image source) Taxonomy ID 556484

(Text from Wikipedia.)

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

Assembly

The genome was assembled by JGI and is also available from the EMBL/Genbank/DDBJ databases under the accession GCA_000150955.1](http://www.ebi.ac.uk/ena/data/view/GCA_000150955.1). The assembly contains 34 chromosomes and 55 unassembled scaffolds.

Annotation

The Phaeodactylum tricornutum genome is a reannotation with 12,089 gene models predicted by usnig existing gene models, expression data and protein sequences from related species used to train the SNAP and Augustus gene prediction programs using the MAKER2 annotation pipeline. The inputs were:

• 10,402 gene models from a previous genebuild from JGI
• 13,828 non-redundant ESTs
• 42 libraries of RNA-Seq generated using Illumina technology
• 49 libraries of RNA-Seq data generated under various iron conditions using SoLiD technology
• 93,206 Bacillariophyta ESTs from dbEST, 22,502 Bacillariophyta and 118,041 Stramenopiles protein sequences from UniProt.

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).

References

1. The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
   Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP et al. 2008. Nature. 456:239-244.
2. 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: Image showing four fusiform morphotype cells of P. tricornutum , Taken by De Martino.A and Bowler.C, Departement de Biologie, Ecole Normale Superieure, Paris, France

Other Data

P. tricornutum ESTs were sequenced from 16 different cDNA libraries. These libraries were constructed from cells cultured under different conditions in order to investigate the molecular basis for responses to various nutrient and stress conditions and changes in cell morphotype. These ESTs were aligned to the genome using exonerate.

More information

General information about this species can be found in Wikipedia.