Online Resource for
Community Annotation of Eukaryotes

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 built 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. You can click the key icon button to request write access to a genome.

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.

Taxa

Aculy
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The mite Aculops lycopersici, which has a highly reduced body plan, is an important pest of tomatoes, manipulating its host plant to facilitate feeding. This species has the smallest arthropod genome yet identified, at 32 Mb, due to remarkable patterns of DNA sequence loss. It presents a striking and unprecedented example of how a multicellular eukaryote can exist without genetic material that might be essential in most other eukaryotes.

Genome streamlining in a minute herbivore that manipulates its host plant
R Greenhalgh, W Dermauw, JJ Glas, S Rombauts, N Wybouw, J Thomas, ...
Elife 9, e56689

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Amacr
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Amaranthus cruentus

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Artal
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Breadfruit (Artocarpus altilis) is a species of flowering tree in the mulberry and jackfruit family (Moraceae). The trees are widely cultivated in tropical regions, including lowland Central America, northern South America, and the Caribbean. The fruit is as a staple food in many cultures. The light-weight yet sturdy timber is also used as a building material.

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Artfr
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Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Late Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed.

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments.
Stephanie De Vos, Stephane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer & Peter Bossier
BMC Genomics volume 22, Article number: 635 (2021)
DOI: 10.1186/s12864-021-07937-z

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Arthe
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The jackfruit (Artocarpus heterophyllus) is a species of tree in the fig, mulberry, and breadfruit family (Moraceae). Its native range is unknown, however it is hypothesized to have oringinated in the region spanning southern India to the rainforests of Borneo. The jackfruit tree grows well in the tropical lowlands, and it bears the largest fruit of all trees, sometimes reaching an impressive 55 kg in weight. The immature fruit is used as a meat substitute in vegeterian dishes. The ripe fruit has a high sugar content and is often used as a dessert.

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Arung
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Collodictyon triciliatum from Russell Orr

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Bathy
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Bathycoccus prasinos is a tiny single-cell coccoid prasinophycean. The prasinophyceae are marine flagellates that form the pico-plankton. Bathycoccus however is one of the few species that seems to lack a flagellate stage in his life-cycle. Bathycoccus has about the same size as a bacterium and is very common in the northern Atlantic Ocean. The cells are covered by delicate overlapping scales, which have a spider 's-web structure and are formed within vesicles (probably Golgi vesicles). The organelles are tightly packed within the cell.

Genome paper:
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage.
Moreau H, Verhelst B, Couloux A, Derelle E, Rombauts S, Grimsley N, Van Bel M, Poulain J, Katinka M, Hohmann-Marriott MF, Piganeau G, Rouzé P, Da Silva C, Wincker P, Van de Peer Y, Vandepoele K. Genome Biol. 2012 Aug 24;13(8):R74. (http://genomebiology.com/2012/13/8/R74)

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Bpa
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Brevipalpus is a genus of mites in the family Tenuipalpidae, the flat mites. The genus includes several species that are among the most important economic pests in the flat mite family.Some Brevipalpus species are made up mostly of female individuals that reproduce via thelytoky, producing offspring without fertilization. Male individuals occur but often become feminized by Cardinium bacteria that colonize their bodies.

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Bph
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Brevipalpus is a genus of mites in the family Tenuipalpidae, the flat mites. The genus includes several species that are among the most important economic pests in the flat mite family.Some Brevipalpus species are made up mostly of female individuals that reproduce via thelytoky, producing offspring without fertilization. Male individuals occur but often become feminized by Cardinium bacteria that colonize their bodies.

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Cabom
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The yeast Candida bombicola is known to produce sophorolipids and is widely used in industry for the production of surfactans. C. bombicola produces sophorolipid molecules with surfactant properties when grown in a medium composed of two different carbon sources (usually sugar and oil) and a nitrogen source (frequently yeast extract). Sophorolipids are extracellular glycolipids and typically consist of a dimeric sophorose connected by a glycosidic bond to the penultimate hydroxyl group of an 18-carbon fatty acid.
The genome sequence of C. bombicola can lead us to develop an efficient transformation and expression system and the key regulators to engineer a strain for specific glycolipid synthesis.

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Catro
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The medicinal plant Catharanthus roseus (Madagascar periwinkle) synthesizes over 150 different terpenoid indole alkaloids (TIAs) including the pharmaceutically important molecules ajmalicine and serpentine. In addition, it is the sole source of the commercial anticancer TIA compounds vinblastine and vincristine (van Der Heijden et al., Curr Med Chem 11: 607-628, 2004; Verma et al., Protoplasma 249: 255-268, 2012).
To accommodate analyses we concatenated the 31,450 C. roseus RNA-Seq contigs joined by a spacer of 2000 N. This resulted in 7 fake chromosomes, of which the first 6 contain 5,000 transcripts each. For some contigs more than one open reading frame is reported due to sequence issues at the contig level. These will be curated carefully in time.

Pathways recovered from the functional annotation of the C. roseus transcripts can be found here: CathaCyc

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CCMP2099
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Arctic Micromonas CCMP2099 with Alex Worden

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Cerbe
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Cercospora is among the most speciose genera in all Fungi. First described in 1863, the genus has sustained a long history largely due to notoriety as the causal agent of leaf spot diseases in an extensive range of plant hosts. Cercospora species generally share a number of characteristics associated with pathogenicity including penetration through natural openings such as stomata and extracellular growth between mesophyll cells without formation of obvious feeding structures. The fungus Cercospora beticola causes Cercospora leaf spot, an economically devastating disease of sugar beet worldwide. Here we report the 37.1 Mbp draft genome sequence of C. beticola that encodes 12,281 genes and 12,495 transcripts.

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Cerze
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Restricted annotation effort for C.zeina

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Chbra
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Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.
CELL, Volume 174, Issue 2, 12 July 2018, Pages 448-464.e24

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Cohum
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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

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Cruhi
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Crucihimalaya himalaica (Edgew.) Al-Shehbaz, O’Kane and R.A.Price, a selfing, diploid (2n=16) relative of A. thaliana, was previously recognized as A. himalaica (Edgew.) O.E.Schulz, and thenames A. rupestris Edgew. and A. brevicaulis Jafri are also accepted as synonyms. Crucihimalaya himalaica mainly grows on rocky hillsides, sandy slopes, alpine meadows, and screes in the Himalayas and Hengduan Mountains. Previous estimates suggested that Crucihimalaya diverged from the closely related Pachycladon approximately 10.94 million years ago (Mya).


Published in: DOI: 10.1073/pnas.1817580116.

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Degal
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This is the Dermanyssus gallinae (Red poultry mite) annotation.

The poultry red mite, Dermanyssus gallinae, is a major worldwide concern in the egg-laying industry. Here, we report the first draft genome assembly and gene prediction of Dermanyssus gallinae, based on combined PacBio and MinION long-read de novo sequencing. The ∼959-Mb genome is predicted to encode 14,608 protein-coding genes.
Paper

intro movie

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Digex
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Digitaria exilis , commonly known as Fonio or Achu is an annual tropical grass grown in West Africa. The tiny seeds are rich in starch. Fonio plays an important role in food security, the seeds ripen fast and can thus be harvested before other cereals like maize or millet, thus preventing food shortages. Fonio grains contain amino acids that are not found in wheat, rice, maize or sorghum. Fonio is resilient and can withstand drought stress. Annotation was done with Maker.97.99% of the BUSCO genes were found as complete genes, while this representation number increased to 99.31% if partially covered BUSCO genes were added. A total of 12.4% of the BUSCO genes were single copy, while 85.6% of the BUSCO genes were found in duplicate. Approximately 1.3% of the BUSCO genes were fragmented and ~0.7% were missing.

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Ectsi
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This is the updated version of the Ectocarpus genome. Update consisted of improved genome assembly (including genetic maps to create pseudochromosomes) and of a re-annotation effort taking into account recently produced RNAseq data.

The annotation of the Ectocarpus genome is done by the Roscoff group in collaboration with the Ghent bioinfo group. To produce automated annotations we adapted the EuGene system to the specificities of the Ectocarpus genome in order to produce a high quality annotation.
The automated prediction and subsequent manual curation resulted in a total of ~18000 genes in the Ectocarpus genome.

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Elsfa
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Elsinoe fawcettii is an important pathogens of citrus. It is known to produce red or orange pigments, called elsinochrome. Elsinochrome is a nonhost-selective phytotoxin and is required for full fungal virulence and lesion formation. E. fawcettii (anamorph: Sphaceloma fawcettii) is classified in the Phylum Ascomycota, Class Dothideomycetes, Order Myriangiales and Family Elsinoaceae. E. fawcettii causes citrus scab (formerly sour orange scab and common scab) on various species and hybrids in the Rutaceae family worldwide. Citrus tissues infested with Elsinoë often display erumpent scab pustules with a warty appearance.Elsinochrome and many perylenequinone-containing phytotoxins of fungal origin are grouped as photo-sensitizing compounds that are able to absorb light energy, react with oxygen molecules and produce reactive oxygen species, such as superoxide and singlet oxygen. Elsinochrome has been documented to cause peroxidation of cell membranes and to induce rapid electrolyte leakage from citrus tissues. Elsinochrome biosynthesis and conidiation are coordinately regulated in E. fawcettii, and the environmental and physiological inducers commonly involved in both processes have begun to be elucidated.

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Eugra
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The DOE Joint Genome Institute has completed whole-genome (8X) shotgun sequencing for E. grandis (est. genome size 640 Mbp, n = 11). High-density linkage maps guided the assembly of 11 large chromosome (pseudomolecule) scaffolds containing 88% (605 Mbp) of the draft assembly. Similarity searches with 1.6 million ESTs from BRASUZ1 suggest that a large proportion (96%) of expressed gene loci are located in these super-scaffolds. Ab initio and homology-based annotation performed at JGI and the University of Ghent was further supported by over 4 million 454-FLX-Titanium ESTs produced by JGI, as well as Sanger and Illumina EST data provided by collaborators.

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Faial
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Faidherbia albida belongs to the monotypic genus Faidherbia, and was previously a member of the Acacia genus (previously known as as Acacia albida). It is a leguminous plant native to Africa and the Middle East. Vernacular names for it include apple-ring acacia, ana tree, balanzan tree, gao tree and winter thorn. The plant has many uses: seed pods are used as fodder for livestock, chopped branches are used to build fences, wood is used for building canoes, wooden tools and is burned as fuel. Ashes of the wood are used in making soap and as a depilatory and tanning agent for hides. In times of scarcity, humans eat the boiled seeds. Other uses include nitrogen fixation, erosion control and traditional-medicine.

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Geca
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Geotrichum candidum (the most familiar name and also the anamorph of the species Galactomyces candidus) has recently being classified as a yeast belonging to the Saccharomycotina subphylum. G. candidum strains are morphologically highly variable, from yeast-like forms to mould-like forms, which explains why it was initially thought to be a filamentous fungus. G. candidum is found commonly in the environment, in foodstuffs and as an integral part of the natural human microbiota. It is found naturally in cheese and fermented milk and it is widely used as adjunct culture in the maturation of cheese. It is also involved in various biotransformation and biodegradation processes and has been shown to inhibit bacterial pathogens.

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Kaba
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TODO

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Kasa
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Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Presented here is the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764T (= CBS 14374T). The genome has a total length of 12.9 Mb and contains 5,326 putative protein-coding genes, excluding pseudogenes and transposons.

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Labpu
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Lablab purpureus is the only specis in the monotypic genus Lablab which belongs to the family Fabacea. The plant is indiginous to Africa, and is widely cultivated in India and South-East Asia. It is known as the Dolichos bean, Hyacinth bean or Field bean, and is one of the most ancient crops among cultivated plants. The plant is variable due to extensive breeding in cultivation.The fruit and beans are edible if boiled well. Otherwise, they are toxic due to the presence of cyanogenic glycosides. Thy cyanogenic potential differs between varieties. The leaves and flowers can be eaten raw, steamed or cooked. The roots can be boiled or baked.

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Madom
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The apple is the pomaceous fruit of the apple tree, Malus domestica in the rose family. It is one of the most widely cultivated tree fruits. Apple trees grow best in temperate countries with a cool climate and plenty of rain during the winter.
The annotation results presented here are produced in cooperation with Istituto Agrario S. Michele all'Adige (IASMA) in Italy.

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Masba
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Mastigamoeba balamuthi is a free-living relative of the parasitic amoeba Entamoeba histolytica. It can be found in the anoxic mud or fresh waters. The cells are amoeboid with several nuclei, sometimes carrying single flagellum. They possess anaerobic mitochondrion-related organelles, that produce molecular hydrogen.

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Medtr
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The data presented here for Medicago consists of a region on chromosome 5. This region was selected to be manually examined to be able to asses the quality of the automated prediction.
In a later stage we will also offer the complete annotated genome.

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Mipuc
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Miromonas
Micromonas is a motile unicell with a single chloroplast and mitochondrion and no scales on its cell surface. Micromonas pusilla was the first picoplanktonic species to be described and has been revealed as the dominating species within the picoplankton communities in coastal and open-oceanic regions. The species was originally named Chromulina pusilla Butcher, and was renamed later on. Currently, all Micromonas strains are assigned to this single species within the genus Micromonas. However, M. pusilla strains fall into distinct phylogenetic clades and therefore it is likely that the designation M. pusilla harbours several different (cryptic) species.

Introner Elements
During the annotation of two strains of the marine green alga Micromonas pusilla, intronic repeat elements were discovered in CCMP1545 that were absent from RCC299 and other published genomes. These Introner Elements (IEs) are highly conserved and are found at novel positions in genes. This is unlike canonical introns which are all different in sequence, but are found at conserved positions within genes. These ‘invasive introns’ lack any of the known characteristics of transposable elements and could be divided into four heterogeneously distributed subfamilies (IE1-4

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Mipur
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Micromonas sp. RCC299 (also known as NOUM17) was discovered during a research expedition at the Equatorial Pacific.

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MorolBGI
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Moringa oleifera is a crop plant that grows in tropical and subtropical regions. It is drought and frost-resistant, enabling widespread cultivation. Virtually all parts of the plant can be used as food source or in traditional herbal medicine.

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MorolUGent
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Moringa oleifera is a crop plant that grows in tropical and subtropical regions. It is drought and frost-resistant, enabling widespread cultivation. Virtually all parts of the plant can be used as food source or in traditional herbal medicine.

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Olea
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The olive genome project is coordinated by the iBG, Izmir, Turkey. The genome was sequenced by the BGI (China) and analysed by iBG and us. The Olive (Olea europaea) is a small evergreen tree that grows best in a Mediteranean climate. Spain, Italy, Greece, and other Mediterranean countries are major producers, but olives are also cultivated outside the Mediterranean region in regions with an appropriate climate (e.g., in in California and Argentina).

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Ost809
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TODO

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Ostlu
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The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Palenik B1, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7705-10. Epub 2007 Apr 25.

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Ostme
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Ostreococcus mediterraneus belongs to the basal branch of the phylogeny of Ostreococcus, the smallest photosynthetic eukaryotes. Its compact 13.86 Mb nuclear genome is slightly larger, and has a slightly lower GC content, than previously sequenced O. tauri and O. lucimarinus. Analysis of its genome sequence revealed the ancestral GC composition and gene content in this lineage. Unexpectedly, the sequenced strain RCC2590 coexists with a resident virus, OmV2, thereby providing insights into the genomic bases of phytoplankton-virus coexistence.

Yau et al. Virus-host coexistence in phytoplankton through the genomic lens, Science Advances 2020

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Ostsi
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TODO

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Ostta
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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.

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Panci
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P. citri is considered to be an economically important and widespread pest of citrus crops (Jeppson et al., 1975). Peak infestations of this pest can vary greatly both within and between seasons (McMurtry et al., 1992). However, Hare and co-workers (Hare and Phillips, 1992; Hare et al., 1992) were unable to confirm the seriousness of P. citri attack on foliage and subsequent economic loss. Following a detailed 4-year study on orange groves in California, USA, they concluded that infestations of up to 10 adult females per leaf could be tolerated without any significant economic loss, and with no cumulative injury over four consecutive generations. Moreover, they report that P. citri infestations can be beneficial in leading to increased fruit size.

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Picpa
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We are involved in the genome project of P. pastoris, together with Prof. Dr. Nico Callewaert (Unit of Molecular Glycobiology). This is our first eukaryotic genome which is sequenced by the 454 pyrosequencing method. The gene prediction was done by the integrated gene prediction platform - EuGene . More than 80% of the gene structures were checked by expert annotators and assigned the proper function.

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Poptr
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The data presented here is that of the version 2 of the poplar genome. Additional sequencing and re-assembly have been performed to come to this version. The work was done by the DOE-JGI. The annotation produced for the first assembly of the poplar genome (which was also the basis for the version 2 annotation) was done in collaboration with our group using the EuGene gene prediction platform.

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Psote
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Winged bean (Psophocarpus tetragonolobus) is a tropical vining plant. All parts of the plant can be eaten, from the tubers to the immature pods. The mature seed have a high percentage of protein (c30-40%) and this crop has been described as the 'soybean of the tropics'. The genome has 9 chromosomes and the current genome assigned 98.9% of the scaffolds developed to pseudochromosome positions, to give a final assembly of 530 MB. The crop is one of the underutilised crops which have potential to help supply the future plant protein requirements of the growing populations, especially in South Asia and Africa, where it is grown.

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Psovi
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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

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Pycom
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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

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RCC4223
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Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature.
Work in collaboration with Banyuls (FR).
https://www.ncbi.nlm.nih.gov/pubmed/30113623

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Rhrob
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Rhizoglyphus robini (Bulb mite, inberd line : IW23_F14)

The bulb mite, Rhizoglyphus robini, is an important pest species with almost global distribution and can be found on the bulbs and tubers of a wide variety of different agricultural and ornamental plants. Males of this species are dimorphic in the expression of a sexually selected trait used in male-male competition. ‘Fighter’ males have a thickened terminally pointed pair of third legs, whereas, ‘scrambler’ males have unmodified legs which are all roughly equal thickness. This species is highly amenable to being kept in laboratory cultures. The genome of this species is 307.5 Mb.

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Sacja
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Brown macroalgae (kelps) belong to the phylum Stramenopiles, a phylogenetic lineage that is distantly related to terrestrial plants and animals. These macroalgae exhibit differentiated tissues during development, making them distinct from unicellular stramenopiles. The extensive submarine kelp forests are the largest biogenic structures within benthic marine communities, occupying 70% of the total biomass in cold and temperate marine systems. Specifically, Laminariales kelp species are essential for ecosystems and are economically important as a marine crop. Here we present the genome of Saccharina japonica, one of the most economically important seaweeds.
Ye N , Zhang X , Miao M , et al. Saccharina genomes provide novel insight into kelp biology[J]. Nature Communications, 2015, 6:6986.

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Sauch
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Saururus chinensis, commonly known as Asian lizard's tail, is an herb that grows in low, damp places to more than 1 meter high, endemic to China, India, Japan (including the Ryukyu Islands), Korea, Philippines, and Vietnam. Its leaves are green, papery, ribbed, densely glandular, and ovate to ovate-lanceolate, and (4-)10-20 × (2-)5-10 cm in size. Each flower spike resembles a lizard's tail.

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Schgr
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The desert locust, (Schistocerca gregaria) inhabits dry grasslands and deserts from Africa to the Punjab and can fly upward to about 1,500 metres in huge swarms. It is a dangerous migratory pest species that devastate crops and threatens food security. Desert locusts can transform between two extreme phases, solitarious and gregarious, depending on their population density. Locust plagues are essentially unpredictable.

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Sclbi
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Sclerocarya birrea (also known as the marula) is a medium-sized dioecious tree, indigenous to the miombo woodlands of Southern Africa, the Sudano-Sahelian range of West Africa, and Madagascar. The distribution of this species throughout Africa and Madagascar has followed the migration patterns of Bantu-speaking tribes from West Central Africa to Southern Africa, as their diet included the marula fruit. The fruits, have a light yellow skin and white flesh that is rich in vitamin C containing about eight times the amount found in an orange. Each fruit contain a walnut-sized, thick-walled stone which surrounds the seed. The seeds have a high protein and oil content. Marula oil is gaining popularity as an ingredient in beauty products.

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Semro
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Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. The assembled genome sequence consisted of 4,754 genomic scaffolds covering 125.57 Mb. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Combined with re-sequencing data , our results offer new insights on the genetic diversity and gene functions in benthic diatoms.

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms
Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, Poulsen N, Bulankova P, Verhelst B, Audoor S, Belisova D, Pargana A, Russo M, Stock F, Cirri E, Brembu T, Pohnert G, Piganeau G, Ferrante MI, Mock T, Sterck L, Sabbe K, De Veylder L, Vyverman W, Vandepoele K.
Nat Commun. 2020 Jul 3;11(1):3320.

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Solly
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We are currently part of the International Tomato Annotation Group (ITAG) - a collaborative effort in efficiently and accurately annotating the tomato genome, and are largely responsible for the gene prediction. This is done using the EuGene software, which is able to integrate various probabilistic models, splice-site models, EST/cDNA alignment, and protein alignment.

The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium.
Nature. 2012 May 30;485(7400):635-41. doi: 10.1038/nature11119.

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Soltu
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This the iTAG annotation on potato. After the release of the potato genome (August 2011), and in order to make comparative analyses with tomato, we decided to run the iTAG annotation pipeline also on potato.

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Spil
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Sardines are a nutrient-rich small oily fish widely consumed by humans and as forage fish for larger fish species, seabirds and marine mammals. It is a source of omega-3 fatty acids.

The sardine genome project is a collaboration project between CCMAR and CIBIO.

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Tetur
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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.

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Ulvmu
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Ulva also known as Sea Lettuce is a multicellular green seaweed belonging to the Ulvophyceae. Apart from being ubiquitous in benthic communities around the world and notorious for its bloom formations in eutrophic coastal environments, Ulva is also an exciting novel model organism for studies of algal growth, development and morphogenesis. The key reasons that Ulva is potentially such a good model system are: (i) Ulva growth is symbiotic, with proper development requiring close association with bacterial epiphytes, (ii) Ulva is extremely developmentally plastic, which can shed light on the transition from simple to complex multicellularity and (iii) Ulva will provide critical information about the molecular evolution of the green lineage which is characterized by a huge variety of cyto-morphologies.

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Vigsu
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Vigna subterranea (also known by its common names: Bambara nut, Bambara-bean, Congo goober, earth pea, ground-bean, or hog-peanut) is a member of the family Fabaceae. The centre of origin of bambara groundnut is north-eastern Nigeria and northern Cameroon. It is now cultivated throughout tropical Africa, and to a lesser extent in tropical parts of the Americas, Asia and Australia. Its use as a food source in West Africa was recorded by Arabic travellers in the 14th Century. Its importance declined after the introduction of Arachis hypogaea (the peanut) from the New World tropics. V. subterranea is grown primarily for its seeds, which are dried and bioled. Seeds and leafy shoots are also used as fodder for pigs and poultry. In some parts of Africa the leaves are used in traditional medicine.

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Vitpa
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Vitellaria paradoxa is a unique agroforestry tree species central to sustaining local livelihoods and the farming environments of rural communities across Africa’s Sudano-Sahelian agroclimactic belt. Rural families in hundreds of thousands of villages across the so-called “shea belt”, a 500-750 km wide semi-arid area stretching 6,000 km and spanning 21 countries from Senegal to South Sudan, use shea in their daily lives as an edible butter/oil, soap, cosmetic, and medicine. Shea is also a multimillion dollar export commodity as a cocoa butter equivalent for chocolate confectionary and as an ingredient in luxury cosmetic, personal care, and pharmaceutical, products. The development of genomic resources for shea tree is part of the larger effort of the African Orphan Crops Consortium.

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ZMb104
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This is the draft assembly of maize b104. It's not a public release but intended for in-house to curate some b104 genes based on available RNAseq data as well as the b73 homologs

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Zosma
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Zostera is a small genus of widely distributed seagrass, commonly called marine eelgrass or simply eelgrass.

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