| Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae | Dorrell RG, Kuo A, Fussy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novak Vanclova AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV and Lovejoy C | Life Sci Alliance 6 (3), , 2023 |  | | Priorities for ocean microbiome research | Abreu A, Bourgois E, Gristwood A, Trouble R, Acinas SG, Bork P, Boss E, Bowler C, Budinich M, Chaffron S, de Vargas C, Delmont TO, Eveillard D, Guidi L, Iudicone D, Kandels S, Morlon H, Lombard F, Pepperkok R, Karlusich JJP, Piganeau G, Regimbeau A, Sommeria-Klein G, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Zablocki O, Arendt D, Bilic J, Finn R, Heard E, Rouse B, Vamathevan J, Casotti R, Cancio I, Cunliffe M, Kervella AE, Kooistra W, Obst M, Pade N, Power DM, Santi I, Tsagaraki TM, Vanaverbeke J, Tara Ocean F, Tara O, European Mol Biol Lab E and European Marine Biol Resource C | | | | Postglacial species arrival and diversity buildup of northern ecosystems took millennia | Alsos IG, Rijal DP, Ehrich D, Karger DN, Yoccoz NG, Heintzman PD, Brown AG, Lammers Y, Pellissier L, Alm T, Brathen KA, Coissac E, Merkel MKF, Alberti A, Denoeud F, Bakke J and PhyloNorway C | | | | Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding | Aury JM, Engelen S, Istace B, Monat C, Lasserre-Zuber P, Belser C, Cruaud C, Rimbert H, Leroy P, Arribat S, Dufau I, Bellec A, Grimbichler D, Papon N, Paux E, Ranoux M, Alberti A, Wincker P and Choulet F | | | | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection | Canaguier A, Guilbaud R, Denis E, Magdelenat G, Belser C, Istace B, Cruaud C, Wincker P, Le Paslier MC, Faivre-Rampant P and Barbe V | | | | Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France | Clavel B, Lepetz S, Chauvey L, Schiavinato S, Tonasso-Calviere L, Liu XX, Fages A, Khan N, Seguin-Orlando A, Sarkissian CD, Clavel P, Estrada O, Alioglu D, Gaunitz C, Aury JM, Barme M, Bodu P, Olive M, Bignon-Lau O, Castel JC, Boudadi-Maligne M, Boulbes N, Bourgois A, Decanter F, Foucras S, Frere S, Gardeisen A, Jouanin G, Mela C, Morand N, Espinet AN, Perdereau A, Putelat O, Riviere J, Robin O, Salin M, Valenzuela-Lamas S, Vallet C, Yvinec JH, Wincker P and Orlando L | | | | Patterns of eukaryotic diversity from the surface to the deep-ocean sediment | Cordier T, Angeles IB, Henry N, Lejzerowicz F, Berney C, Morard R, Brandt A, Cambon-Bonavita MA, Guidi L, Lombard F, Arbizu PM, Massana R, Orejas C, Poulain J, Smith CR, Wincker P, Arnaud-Haond S, Gooday AJ, de Vargas C and Pawlowski J | | | | The expanding Asgardÿarchaea and their elusive relationships with Eukarya | Da Cunha V, Ga‹a M and Forterre P | | | | Giant Viruses Encode Actin-Related Proteins | Da Cunha V, Gaia M, Ogata H, Jaillon O, Delmont TO and Forterre P | | | | Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea | Da Silva O, Ayata SD, Ser-Giacomi E, Leconte J, Pelletier E, Fauvelot C, Madoui MA, Guidi L, Lombard F and Bittner L | | | | Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale | de Vargas C, Le Bescot N, Pollina T, Henry N, Romac S, Colin S, Ha‰ntjens N, Carmichael M, Berger C, Le Guen D, Decelle J, Mah‚ F, Poulain J, Malpot E, Beaumont C, Hardy M, Guiffant D, Probert I, Gruber DF, Allen AE, Gorsky G, Follows MJ, Pochon X, Troubl‚ R, Cael BB, Lombard F, Boss E, Prakash M, tPPct, Bazile R, Boss E, Bourdin G, Cael B, Casati R, Colin Sb, Vargas Cd, Gorsky G, Guiffant D, Haentjens N, Henry N, Larson A, Bescot NL, Lombard F, Mirambeau G, Moulin Cm, Oddone A, Prakash M, Prazuck C, Raimbault V, Trellu C and Trouble? R | | | | Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean | Delmont TO, Gaia M, Hinsinger DD, Fr‚mont P, Vanni C, Fernandez-Guerra A, Eren AM, Kourlaiev A, d'Agata L, Clayssen Q, Villar E, Labadie K, Cruaud C, Poulain J, Da Silva C, Wessner M, Noel B, Aury J-M, Sunagawa S, Acinas SG, Bork P, Karsenti E, Bowler C, Sardet C, Stemmann L, de Vargas C, Wincker P, Lescot M, Babin M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Jaillon O, Kandels S, Iudicone D, Ogata H, Pesant S, Sullivan MB, Not F, Lee K-B, Boss E, Cochrane G, Follows M, Poulton N, Raes J, Sieracki M, Speich S, de Vargas C, Bowler C, Karsenti E, Pelletier E, Wincker P and Jaillon O | | | | Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean | Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P and Pelletier E | | | | Diversity and ecological footprint of Global Ocean RNA viruses | Dominguez-Huerta G, Zayed AA, Wainaina JM, Guo JR, Tian FN, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Coordinators TO, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S and Sullivan MB | | | | Restructuring of plankton genomic biogeography in the surface ocean under climate change | Fremont P, Gehlen M, Vrac M, Leconte J, Delmont TO, Wincker P, Iudicone D and Jaillon O | | | | Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria | Grebert T, Garczarek L, Daubin V, Humily F, Marie D, Ratin M, Devailly A, Farrant GK, Mary I, Mella-Flores D, Tanguy G, Labadie K, Wincker P, Kehoe DM and Partensky F | | | | Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence | Gu‚rin N, Ciccarella M, Flamant E, Fr‚mont P, Mangenot S, Istace B, Noel B, Belser C, Bertrand L, Labadie K, Cruaud C, Romac S, Bachy C, Gachenot M, Pelletier E, Alberti A, Jaillon O, Wincker P, Aury J-M and Carradec Q | | | | Viral origin of eukaryotic type IIA DNA topoisomerases | Guglielmini J, Gaia M, Da Cunha V, Criscuolo A, Krupovic M and Forterre P | | | | A robust approach to estimate relative phytoplankton cell abundances from metagenomes | Karlusich JJP, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C and Bowler C | | | | Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans | Lang-Yona N, Flores JM, Haviv R, Alberti A, Poulain J, Belser C, Trainic M, Gat D, Ruscheweyh HJ, Wincker P, Sunagawa S, Rudich Y, Koren I and Vardi A | | | | Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei | Lu YAT, Ruault S, Daguin-Thiebaut C, Castel J, Bierne N, Broquet T, Wincker P, Perdereau A, Arnaud-Haond S, Gagnaire PA, Jollivet D, Hourdez S and Bonhomme F | | | | Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros | Nef C, Madoui MA, Pelletier E and Bowler C | | | | Biosynthetic potential of the global ocean microbiome | Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlstrom CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sanchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J and Sunagawa S | | | | Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex | Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J and Coelho MA | | | | In-depth characterization of denitrifier communities across different soil ecosystems in the tundra | Pessi IS, Viitamaki S, Virkkala AM, Eronen-Rasimus E, Delmont TO, Marushchak ME, Luoto M and Hultman J | | | | Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems | Richter DJ, Watteaux R, Vannier T, Leconte J, Fremont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernandez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Tara Oceans C, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcala M, Iudicone D and Jaillon O | | | | Tempo and drivers of plant diversification in the European mountain system | Smycka J, Roquet C, Boleda M, Alberti A, Boyer F, Douzet R, Perrier C, Rome M, Valay JG, Denoeud F, Semberova K, Zimmermann NE, Thuiller W, Wincker P, Alsos IG, Coissac E, Layergne S and PhyloAlps C | | | | The genomic history and global expansion of domestic donkeys | Todd ET, Tonasso-Calviere L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pardal LP, Rosa LP, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Gianni GB, Tagliacozzo A, Tine V, Alhaique F, Cardoso JL, Valente MJ, Antunes MT, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Oztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD and Orlando L | | | | Unifying the known and unknown microbial coding sequence space | Vanni C, Schechter MS, Acinas SG, Barberan A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sanchez P, Siren K, Steinegger M, Gloeckner FO and Fernandez-Guerra A | | | | The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes | Vernette C, Lecubin J, Sanchez P, Sunagawa S, Delmont TO, Acinas SG, Pelletier E, Hingamp P, Lescot M and Tara Oceans C | | | | Reply to: When did mammoths go extinct? | Wang Y, Prohaska A, Dong H, Alberti A, Alsos IG, Beilman DW, Bjork AA, Cao J, Cherezova AA, Coissac E, De Sanctis B, Denoeud F, Dockter C, Durbin R, Edwards ME, Edwards NR, Esdale J, Fedorov GB, Fernandez-Guerra A, Froese DG, Gusarova G, Haile J, Holden PB, Kjeldsen KK, Kjaer KH, Korneliussen TS, Lammers Y, Larsen NK, Macleod R, Mangerud J, McColl H, Merkel MKF, Money D, Moller P, Nogues-Bravo D, Orlando L, Owens HL, Pedersen MW, Racimo F, Rahbek C, Rasic JT, Rouillard A, Ruter AH, Skadhauge B, Svendsen JI, Tikhonov A, Vinner L, Wincker P, Xing Y, Zhang Y, Meltzer DJ and Willerslev E | | | | Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome | Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Tara Oceans Coordinatorsdouble d, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, de Vargas C, Gorsky G, Guidi L, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Pesant S, Sardet C, Speich S, Stemmann L, Sullivan MB, Sungawa S and Wincker P | | | | Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome | Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo JR, Mohssen M, Tian FN, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB and Tara Oceans C | | | | Genome-wide supermatrix analyses of maples (Acer, Sapindaceae) reveal recurring inter-continental migration, mass extinction, and rapid lineage divergence | Areces-Berazain F, Hinsinger DD and Strijk JS | | | | Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing | Belser C, Baurens FC, Noel B, Martin G, Cruaud C, Istace B, Yahiaoui N, Labadie K, Hribova E, Dolezel J, Lemainque A, Wincker P, D'Hont A and Aury JM | | | | Macroscale patterns of oceanic zooplankton composition and size structure | Brandao MC, Benedetti F, Martini S, Soviadan YD, Irisson JO, Romagnan JB, Elineau A, Desnos C, Jalabert L, Freire AS, Picheral M, Guidi L, Gorsky G, Bowler C, Karp-Boss L, Henry N, de Vargas C, Sullivan MB, Stemmann L, Lombard F and Tara Oceans Consortium C | | | | Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA | Brandt MI, Pradillon F, Trouche B, Henry N, Liautard-Haag C, Cambon-Bonavita MA, Cueff-Gauchard V, Wincker P, Belser C, Poulain J, Arnaud-Haond S and Zeppilli D | | | | Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding | Brandt MI, Trouche B, Quintric L, Gunther B, Wincker P, Poulain J and Arnaud-Haond S | | | | Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms | Bulankova P, Sekulic M, Jallet D, Nef C, van Oosterhout C, Delmont TO, Vercauteren I, Osuna-Cruz CM, Vancaester E, Mock T, Sabbe K, Daboussi F, Bowler C, Vyverman W, Vandepoele K and De Veylder L | | | | Environmental vulnerability of the global ocean epipelagic plankton community interactome | Chaffron S, Delage E, Budinich M, Vintache D, Henry N, Nef C, Ardyna M, Zayed AA, Junger PC, Galand PE, Lovejoy C, Murray AE, Sarmento H, Acinas SG, Babin M, Iudicone D, Jaillon O, Karsenti E, Wincker P, Karp-Boss L, Sullivan MB, Bowler C, de Vargas C, Eveillard D and Tara Oceans C | | | | Relative Influence of Plastic Debris Size and Shape, Chemical Composition and Phytoplankton-Bacteria Interactions in Driving Seawater Plastisphere Abundance, Diversity and Activity | Cheng JG, Jacquin J, Conan P, Pujo-Pay M, Barbe V, George M, Fabre P, Bruzaud S, Ter Halle A, Meistertzheim AL and Ghiglione JF | | | | Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids | Clavel P, Dumoncel J, Sarkissian CD, Seguin-Orlando A, Calviere-Tonasso L, Schiavinato S, Chauvey L, Perdereau A, Aury JM, Wincker P, Onar V, Clavel B, Lepetz S, Braga J and Orlando L | | | | Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean | | | | | Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean | Delmont TO, Karlusich JJP, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P and Pelletier E | | | | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity | Denoyelle L, Talouarn E, Bardou P, Colli L, Alberti A, Danchin C, Del Corvo M, Engelen S, Orvain C, Palhiere I, Rupp R, Sarry J, Salavati M, Amills M, Clark E, Crepaldi P, Faraut T, Masiga CW, Pompanon F, Rosen BD, Stella A, Van Tassell CP, Tosser-Klopp G and VarGoats C | | | | A community perspective on the concept of marine holobionts: current status, challenges, and future directions | Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cardenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachoni CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lathier FH, Medina M, Marzinelli EM, Morganti TM, Pons LN, Prado S, Pintado J, Saha M, selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C and Not F | | | | Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes | Dorrell RG, Villain A, Perez-Lamarque B, de Kerdrel GA, McCallum G, Watson AK, Ait-Mohamed O, Alberti A, Corre E, Frischkorn KR, Karlusich JJP, Pelletier E, Morlon H, Bowler C and Blanc G | | | | Community-led, integrated, reproducible multi-omics with anvi'o | Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen OC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjodin A, Scott JJ, Vazquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO and Willis AD | | | | Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp | Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai RB, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouze P, van de Peer Y, Wincker P, Rombauts S, Porcel BM and Guillou L | | | | Giant viruses and the origin of eukaryotic RNA polymerases | | | | | Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes | Garczarek L, Guyet U, Dore H, Farrant GK, Hoebeke M, Brillet-Gueguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguille G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury JM, Wincker P, Scanlan DJ and Partensky F | | | | Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization | Gauthier J, Boulain H, van Vugt J, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagne N, Boulogne I, Sabeti-Azad M, Maibeche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Consoli FL, Dupas S, Hua-Van A, Le Goff G, Bezier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA and Drezen JM | | | | Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant | Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T and Balesdent MH | | | | Population genomics of apricots unravels domestication history and adaptive events | Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrere S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen XL, Petriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T and Decroocq V | | | | VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses | Guo JR, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, Pratama AA, Gazitua MC, Vik D, Sullivan MB and Roux S | | | | Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case | Istace B, Belser C, Falentin C, Labadie K, Boideau F, Deniot G, Maillet L, Cruaud C, Bertrand L, Chevre AM, Wincker P, Rousseau-Gueutin M and Aury JM | | | | Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean | Kaneko H, Blanc-Mathieu R, Endo H, Chaffron S, Delmont TO, Gaia M, Henry N, Hernandez-Velazquez R, Nguyen CH, Mamitsuka H, Forterre P, Jaillon O, de Vargas C, Sullivan MB, Suttle CA, Guidi L and Ogata H | | | | Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods | Karlusich JJP, Pelletier E, Lombard F, Carsique M, Dvorak E, Colin S, Picheral M, Cornejo-Castillo FM, Acinas SG, Pepperkok R, Karsenti E, de Vargas C, Wincker P, Bowler C and Foster RA | | | | Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton | Kijima S, Delmont TO, Miyazaki U, Gaia M, Endo H and Ogata H | | | | Comparative genomics reveals new functional insights in uncultured MAST species | Labarre A, Lopez-Escard D, Latorre F, Leonard G, Bucchini F, Obiol A, Cruaud C, Sieracki ME, Jaillon O, Wincker P, Vandepoele K, Logares R and Massana R | | | | Niche adaptation promoted the evolutionary diversification of tiny ocean predators | Latorre F, Deutschmann IM, Labarre A, Obiol A, Krabberod AK, Pelletier E, Sieracki ME, Cruaud C, Jaillon O, Massana R and Logares R | | | | Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection | Le Luyer J, Schull Q, Auffret P, Lopez P, Crusot M, Belliard C, Basset C, Carradec Q, Poulain J, Planes S and Saulnier D | | | | Historical management of equine resources in France from the Iron Age to the Modern Period | Lepetz S, Clavel B, Alioglu D, Chauvey L, Schiavinato S, Tonasso-Calviere L, Liu XX, Fages A, Khan N, Seguin-Orlando A, Sarkissian CD, Clavel P, Estrada O, Gaunitz C, Aury JM, Barme M, Boulbes N, Bourgois A, Decanter F, Foucras S, Frere S, Gardeisen A, Jouanin G, Mela C, Morand N, Espinet AN, Perdereau A, Putelat O, Riviere J, Robin O, Salin M, Valenzuela-Lamas S, Vallet C, Yvinec JH, Wincker P and Orlando L | | | | The origins and spread of domestic horses from the Western Eurasian steppes | Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calviere L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Sarkissian CD, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregely T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpre M, Hoyo MMD, Wilczynski J, Pospula S, Lasota-Kus A, Tunia K, Nowak M, Rannamae E, Saarma U, Boeskorov G, Lougas L, Kysely R, Peske L, Balasescu A, Dumitrascu V, Dobrescu R, Gerber D, Kiss V, Szecsenyi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsar G, Gal E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Lamas SV, Canadell SA, Espinet AN, Iborra MP, Garrido JL, Gonzalez ER, Celestino S, Olaria C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Gianni GB, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muniz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A and Orlando L | | | | Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10(-/-) Mice | Miyoshi J, Miyoshi S, Delmont TO, Cham C, Lee STM, Sakatani A, Yang KR, Shan Y, Kennedy M, Kiefl E, Yousef M, Crosson S, Sogin M, Antonopoulos DA, Eren AM, Leone V and Chang EB | | | | Bacterial Abundance, Diversity and Activity During Long-Term Colonization of Non-biodegradable and Biodegradable Plastics in Seawater | Odobel C, Dussud C, Philip L, Derippe G, Lauters M, Eyheraguibel B, Burgaud G, Ter Halle A, Meistertzheim A-L, Bruzaud S, Barbe V and Ghiglione J-F | | | | Estimating the Travel Time and the Most Likely Path from Lagrangian Drifters | O'Malley M, Sykulski AM, Laso-Jadart R and Madoui MA | | | | AI-based mobile application to fight antibiotic resistance | Pascucci M, Royer G, Adamek J, Al Asmar M, Aristizabal D, Blanche L, Bezzarga A, Boniface-Chang G, Brunner A, Curel C, Dulac-Arnold G, Fakhri RM, Malou N, Nordon C, Runge V, Samson F, Sebastian E, Soukieh D, Vert JP, Ambroise C and Madoui MA | | | | Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia | Pouchon C, Lavergne S, Fernandez A, Alberti A, Aubert S and Mavarez J | | | | Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts | Rasmussen JA, Villumsen KR, Duchene DA, Puetz LC, Delmont TO, Sveier H, Jorgensen LV, Praebel K, Martin MD, Bojesen AM, Gilbert MTP, Kristiansen K and Limborg MT | | | | Evolutionary origins and species delineation of the two Pyrenean endemics Campanula jaubertiana and C. andorrana (Campanulaceae): evidence for transverse alpine speciation | Roquet C, Smycka J, Alberti A, Boleda M, Coissac E, Denoeud F, Komac B, Lavergne S, Pladevall C and Saez L | | | | Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean | Royo-Llonch M, Sanchez P, Ruiz-Gonzalez C, Salazar G, Pedros-Alio C, Sebastian M, Labadie K, Paoli L, Ibarbalz FM, Zinger L, Churcheward B, Chaffron S, Eveillard D, Karsenti E, Sunagawa S, Wincker P, Karp-Boss L, Bowler C, Acinas SG and Tara Oceans C | | | | Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients | Schauberger C, Glud RN, Hausmann B, Trouche B, Maignien L, Poulain J, Wincker P, Arnaud-Haond S, Wenzhofer F and Thamdrup B | | | | Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology | Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TLP, Erkens RHJ, Sauquet H, Pirie MD, Thomas DC and Cao KF | | | | Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis | Sugier K, Laso-Jadart R, Vacherie B, Kafer J, Bertrand L, Labadie K, Martins N, Orvain C, Petit E, Wincker P, Jamet JL, Alberti A and Madoui MA | | | | Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient | Trouche B, Brandt MI, Belser C, Orejas C, Pesant S, Poulain J, Wincker P, Auguet JC, Arnaud-Haond S and Maignien L | | | | Late Quaternary dynamics of Arctic biota from ancient environmental genomics | Wang YC, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MKF, Fernandez-Guerra A, Rouillard A, Lammers Y, Alberti A, Denoeud F, Money D, Ruter AH, McColl H, Larsen NK, Cherezova AA, Edwards ME, Fedorov GB, Haile J, Orlando L, Vinner L, Korneliussen TS, Beilman DW, Bjork AA, Cao JL, Dockter C, Esdale J, Gusarova G, Kjeldsen KK, Mangerud J, Rasic JT, Skadhauge B, Svendsen JI, Tikhonov A, Wincker P, Xing YC, Zhang YB, Froese DG, Rahbek C, Nogues DB, Holden PB, Edwards NR, Durbin R, Meltzer DJ, Kjaer KH, Moller P and Willerslev E | | | | Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy | Woo ACC, Gaia M, Guglielmini J, Da Cunha V and Forterre P | | | | Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench | Zhang WJ, Zhang C, Zhou SY, Li XG, Mangenot S, Fouteau S, Guerin T, Qi XQ, Yang J, Bartlett DH and Wu LF | | | | The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material | Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Puscas M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM and Coissac E | | | | Plastome comparative genomics in maples resolves the infrageneric backbone relationships | Areces-Berazain F, Wang YX, Hinsinger DD and Strijk JS | | | | Continued Adaptation of C-4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses | Bianconi ME, Hackel J, Vorontsova MS, Alberti A, Arthan W, Burke SV, Duvall MR, Kellogg EA, Lavergne S, McKain MR, Meunier A, Osborne CP, Traiperm P, Christin PA and Besnard G | | | | TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages | Bottai D, Frigui W, Sayes F, Di Luca M, Spadoni D, Pawlik A, Zoppo M, Orgeur M, Khanna V, Hardy D, Mangenot S, Barbe V, Medigue C, Ma L, Bouchier C, Tavanti A, Larrouy-Maumus G and Brosch R | | | | An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities | Brandt MI, Trouche B, Henry N, Liautard-Haag C, Maignien L, de Vargas C, Wincker P, Poulain J, Zeppilli D and Arnaud-Haond S | | | | Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean | Busseni G, Caputi L, Piredda R, Fremont P, Mele BH, Campese L, Scalco E, de Vargas C, Bowler C, d'Ovidio F, Zingone A, d'Alcala MR and Iudicone D | | | | Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach | Cai RB, Kayal E, Alves-de-Souza C, Bigeard E, Corre E, Jeanthon C, Marie D, Porcel BM, Siano R, Szymczak J, Wolf M and Guillou L | | | | Metagenomic Mining for Amine Dehydrogenase Discovery | Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, de Berardinis V, Zaparucha A, Champion JA, Bommarius AS and Vergne-Vaxelaire C | | | | A framework for in situ molecular characterization of coral holobionts using nanopore sequencing | Carradec Q, Poulain J, Boissin E, Hume BCC, Voolstra CR, Ziegler M, Engelen S, Cruaud C, Planes S and Wincker P | | | | Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria | Dore H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Gueguen L, Hoebeke M, Bisch A, Le Corguille G, Corre E, Labadie K, Aury JM, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F and Garczarek L | | | | Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions | Endo H, Blanc-Mathieu R, Li YZ, Salazar G, Henry N, Labadie K, de Vargas C, Sullivan MB, Bowler C, Wincker P, Karp-Boss L, Sunagawa S and Ogata H | | | | Tara Pacific Expedition's Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results | Flores JM, Bourdin G, Altaratz O, Trainic M, Lang-Yona N, Dzimban E, Steinau S, Tettich F, Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Douville E, Forcioli D, Furla P, Galand PE, Sullivan MB, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sunagawa S, Thomas OP, Trouble R, de Vargas C, Thurber RV, Voolstra CR, Wincker P, Zoccola D, Bowler C, Gorsky G, Rudich Y, Vardi A and Koren I | | | | Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes | Foucher A, Evrard O, Ficetola GF, Gielly L, Poulain J, Giguet-Covex C, Laceby JP, Salvador-Blanes S, Cerdan O and Poulenard J | | | | Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2 | Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lievremont D, Coppee JY, Barbe V and Arsene-Ploetze F | | | | REPLY TO KU AND SUN: Ancestors of modern giant and large eukaryotic dsDNA viruses infected proto-eukaryotes | Guglielmini J, Woo AC, Krupovic M, Forterre P and Gaia M | | | | Biogeography of soil microbial habitats across France | Karimi B, Villerd J, Dequiedt S, Terrat S, Boure NCP, Djemiel C, Lelievre M, Tripied J, Nowak V, Saby NPA, Bispo A, Jolivet C, Arrouays D, Wincker P, Cruaud C and Ranjard L | | | | Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection | Kayal E, Alves-de-Souza C, Farhat S, Velo-Suarez L, Monjol J, Szymczak J, Bigeard E, Marie D, Noel B, Porcel BM, Corre E, Six C and Guillou L | | | | metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics | Laso-Jadart R, Ambroise C, Peterlongo P and Madoui MA | | | | Investigating population-scale allelic differential expression in wild populations ofOithona similis(Cyclopoida, Claus, 1866) | Laso-Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet JL and Madoui MA | | | | Genome Resolved Biogeography of Mamiellales | Leconte J, Benites LF, Vannier T, Wincker P, Piganeau G and Jaillon O | | |
|