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Orcae

Introduction

ORCAE is an online genome annotation resource offering users the necessary tools and information to validate and correct gene annotations. The system is build on the wiki philosophy, all modifications to a certain gene are stored and can be found back in the annotation history of that gene. To be able to modify genes however you will need to have a user account. Anonymous users can browse the public genomes but don't have editing rights.
To get started select one of the genomes from the list below or log in directly to go to the restricted access section.
If you would like to apply for a user account, so that you are able to edit records, send a mail to explaining your request.

How to cite this resource

Sterck, L., Billiau, K., Abeel, T., Rouzé, P., Van de Peer, Y.
ORCAE: online resource for community annotation of eukaryotes. Nat. Methods (2012) 9, 1041.

Please note that although care was taken to make this website as much as possible cross-browser compatible, it will work best with FireFox > 3.5, Safari and Google Chrome.

Public Genomes

Amoebophrya species A25

Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms. This is the Nanopore scaffolded assembly.

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp
S Farhat, P Le, E Kayal, B Noel, E Bigeard, E Corre, F Maumus, I Florent, ...
BMC biology 19 (1), 1-21

Brevipalpus yothersi Brasil

This is the Brevipalpus yothersi Brasil assembly and annotation. (picture from http://www.padil.gov.au )

Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi
D Navia, VM Novelli, S Rombauts, J Freitas-Astúa, ...
Microbiology resource announcements 8 (6), e01563-18

Coffea humblotiana

Coffea humblotiana

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago
N Raharimalala, S Rombauts, A McCarthy, A Garavito, S Orozco-Arias, ... Scientific reports 11 (1), 1-14

Ostreococcus tauri

This is the updated genome. The genome size of Ostreococcus tauri is the smallest of all known eukaryotes. The nuclear genome is about 12 Mb, fragmented into 20 chromosomes, ranging in size from 120 to 1500 Kb. Phylogenetic analysis placed Ostreococcus tauri within the Prasinophyceae, an early branch of the Chlorophyta (green algae).

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies.
Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G1.
BMC Genomics. 2014 Dec 13;15:1103.
doi: 10.1186/1471-2164-15-1103.

Ostreococcus tauri

The genome size of Ostreococcus tauri is the smallest of all known eukaryotes. The nuclear genome is about 12 Mb, fragmented into 20 chromosomes, ranging in size from 120 to 1500 Kb. Phylogenetic analysis placed Ostreococcus tauri within the Prasinophyceae, an early branch of the Chlorophyta (green algae).

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.
Derelle E1, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piégu B, Ball SG, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y, Moreau H.
Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11647-52.

Psoroptes ovis

This is the Psoroptes ovis (sheep scab mite) assembly and annotation.

Draft genome assembly of the sheep scab mite, Psoroptes ovis STG Burgess, K Bartley, EJ Marr, HW Wright, RJ Weaver, JC Prickett, ... Genome announcements 6 (16), e00265-18

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding-and stage-specific patterns of allergen expression
STG Burgess, EJ Marr, K Bartley, FG Nunn, RE Down, RJ Weaver, ...
BMC genomics 20 (1), 1-23

Pyrus communis (European pear)

Pyrus communis (European pear)

Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
G Linsmith, S Rombauts, S Montanari, CH Deng, JM Celton, P Guérif, ...
Gigascience 8 (12), giz138

Tetranychus urticae

In spider-mites known genome size varies from ~723Mbp in Tetragnatha elongata to ~5.5 Gbp in Habronattus decorus suggesting poliploidisation of the genome. So far no chelicerate genome has been sequenced. The annotation of the Tetranychus urticae genome, representing a major plant pest, will be important for plant science and agriculture. Toward this goal we're developing the spider mite Tetranychus urticae as a plant-eating arthropod model. This project capitalizes on multidisciplinary collaboration between our lab, the laboratory of Dr. Grbic (with expertise in developmental biology and pest control who is leading the sequencing project of the T. urticae genome) and the Joint Genome Institute.

The genome of Tetranychus urticae reveals herbivorous pest adaptations.
Grbić M1, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P, Grbić V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernández-Crespo P, Diaz I, Martinez M, Navajas M, Sucena É, Magalhães S, Nagy L, Pace RM, Djuranović S, Smagghe G, Iga M, Christiaens O, Veenstra JA, Ewer J, Villalobos RM, Hutter JL, Hudson SD, Velez M, Yi SV, Zeng J, Pires-daSilva A, Roch F, Cazaux M, Navarro M, Zhurov V, Acevedo G, Bjelica A, Fawcett JA, Bonnet E, Martens C, Baele G, Wissler L, Sanchez-Rodriguez A, Tirry L, Blais C, Demeestere K, Henz SR, Gregory TR, Mathieu J, Verdon L, Farinelli L, Schmutz J, Lindquist E, Feyereisen R, Van de Peer Y.
Nature. 2011 Nov 23;479(7374):487-92. doi: 10.1038/nature10640.

Vitis vinifera

Re-annotation effort of Vitis vinifera V2

A new version of the grapevine reference genome assembly (12X. v2) and of its annotation (VCost. v3)
A Canaguier, J Grimplet, G Di Gaspero, S Scalabrin, E Duchêne, ...
Genomics data 14, 56
Restricted Genomes

Terms of Service:
This tool is provide "free to use for all". We made every attempt to ensure the accuracy and reliability of the results provided through this webservice. However, the information is provided "as is" without responsibility or liability of any kind. We don't claim ownership and/or copyright on the input data nor the generated image(s) using our serivce.

Please note that although care was taken to make this website as much as possible cross-browser compatible, it will work best with FireFox > 3.5, Safari and Google Chrome.