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

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

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

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

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.

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

RNA viruses have recently been detected in association with house dust mites, including laboratory cultures, dust samples, and mite-derived pharmaceuticals used for allergy diagnosis. The aim of this study is to assess the incidence of viral infection on Dermatophagoides pteronyssinus physiology and on the allergenic performance of extracts derived from its culture. Transcriptional changes between genetically identical control and virus-infected mite colonies were analyzed by RNAseq with the support of a new D. pteronyssinus high-quality annotated genome (56.8 Mb, 108 scaffolds, N50=2.73 Mb, 96.7% BUSCO-completeness).

-1- RNA viruses alter house dust mite physiology and allergen production with no detected consequences for allergenicity

-2- RNA viruses in the house dust mite Dermatophagoidespteronyssinus, detection in environmental samples and in commercial allergen extracts used for in vivo diagnosis

-3- Dietary shifts have consequences for the repertoire of allergens produced by the European house dust mite

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.

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.

Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence …
Virus-host coexistence in phytoplankton through the genomic lens 2020,Science Advances
Sheree Yau, Marc Krasovec, L Felipe Benites, Stephane Rombauts, Mathieu Groussin, Emmelien Vancaester, Jean-Marc Aury, Evelyne Derelle, Yves Desdevises, Marie-Line Escande, Nigel Grimsley, Julie Guy, Hervé Moreau, Sophie Sanchez-Brosseau, Yves Van de Peer, Klaas Vandepoele, Sebastien Gourbiere, Gwenael Piganeau

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.

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.

This is version 2.1 of the O.tauri assembly and annotation.

Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence …
Virus-host coexistence in phytoplankton through the genomic lens 2020,Science Advances
Sheree Yau, Marc Krasovec, L Felipe Benites, Stephane Rombauts, Mathieu Groussin, Emmelien Vancaester, Jean-Marc Aury, Evelyne Derelle, Yves Desdevises, Marie-Line Escande, Nigel Grimsley, Julie Guy, Hervé Moreau, Sophie Sanchez-Brosseau, Yves Van de Peer, Klaas Vandepoele, Sebastien Gourbiere, Gwenael Piganeau

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)

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

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.

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.

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.

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