Phaeodactylum tricornutum

PLEASE NOTE: The Phaeodactylum tricornutum genome sequence is composed of "finished chromosomes" (Phatr2) and "unmapped sequence"(Phatr2_bd), which were annotated separately. Please use both portals to make a complete analysis of the genome.


v.2.0 finished chromosomes and unmapped sequence (May 2007): This Phaeodactylum tricornutum genome sequence assembly was initially assembled using the JGI assembler, Jazz, constructed from whole genome shotgun paired end sequencing reads. That draft assembly was finished by JGI/Stanford Human Genome Center which produced the Phaeodactylum_tricornutum_v2.051706 genome assembly reported here.

There are two parts to the P. tricornutum genome sequence assembly and annotation reported here: the Phatr2 "finished chromosomes" and the Phatr2_bd "unmapped sequence". The finished chromosomes consist of the finished genome sequence that could be reliably assembled into chromosomes. The "unmapped sequence" consists of assembled scaffolds that could neither be mapped to finished chromosomes nor assigned to organelles, but that could be aligned to P. tricornutum ESTs which were not represented in the finished chromosomes. Because some ESTs not represented on the finished chromosomes are represented on the unmapped sequence scaffolds, these scaffolds are indicated as possible regions of the P. tricornutum genome not present in the finished chromosomes, as opposed to being alternate haplotypes of sequence already contained in the finished chromosomes. The finished chromosomes of the nuclear genome sequence from that assembly were annotated using the JGI Genome Annotation Pipeline and custom analyses, and are reported here as the Phatr2 annotation. The unmapped sequence were annotated in the same manner, and are reported here as the Phatr2_bd annotation.

Summary statistics for the 3.0 release (Phatr2 and Phatr2_bd), including comparison to the previous v1.0 release (Phatr1, the previous public release), are below.

Nuclear Genome Assembly Phatr1 Phatr2 Phatr2_bd
Nuclear genome size (Mbp) 31.0 26.1 1.3
Sequencing read coverage depth ~10.4x ~9.6x ~9.6x
Total # of fasta sequences (nuclear) 588 33 55
Total # of fasta sequences (>2 Kbp) 363 33 49
Three largest Scaffolds (Mbp) 2.4

Gene Models Phatr11 Phatr22 Phatr2_bd3 Phatr2_bd / Phatr2 Phatr1 / Phatr2
length (bp) of: average average average ratio ratio
gene 1,571.5 1,620.8 1,614.2 100% 97%
transcript 1,465.4 1,513.6 1,476.5 98% 97%
exon 823.6 843.4 789.5 94% 98%
intron 138.3 136.9 160.3 117% 101%
protein length (aa) 453.3 462 454.2 98% 98%
exons per gene 1.78 1.8 1.87 104% 99%
# of gene models in track 10,681 10,025 377 4% 107%

[1] FilteredModels1

[2] Filtered gene models v2.0

[3] FilteredModels1



Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV. The Phaeodactylum genome reveals the evolutionary history of diatom genomes Nature. 2008 Nov 13;456(7219):239-44.



This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.