Phaeodactylum tricornutum (ASM15095v2)

Phaeodactylum tricornutum Assembly and Gene Annotation

This genome has been re-annotated through a collaboration between Ensembl Genomes @ EMBL-EBI, the Ecole Normale Superieure, Pari,s and the J. Craig Venter Institute, San Diego

About the Phaeodactylum tricornutum genome

Phaeodactylum tricornutum is a cosmopolitan marine pennate diatom, unicellular brown algae that likely arose from the endocytobiosis of a red alga into a single-celled heterotroph. P. tricornutum cells can undergo morphological transitions between three possible morphotypes, change in the cell shape stimulated by environmental conditions.

Assembly

The genome was assembled by JGI and is also available from the EMBL/Genbank/DDBJ databases under the accession 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).

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.

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

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyASM15095v2, INSDC Assembly GCA_000150955.2, Feb 2010
Database version98.1
Base Pairs27,568,093
Golden Path Length27,568,093
Genebuild byEBI
Genebuild methodMaker Build by Ensembl Genomes
Data sourceEnsembl Protists

Gene counts

Coding genes12,178
Non coding genes177
Small non coding genes175
Long non coding genes1
Misc non coding genes1
Pseudogenes37
Gene transcripts12,392

Other

Short Variants468,051

About this species