Publications
2024
Marlétaz F, Timoshevskaya N, Timoshevskiy V, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith J§, Rokhsar DS§. 2024. The hagfish genome and the evolution of vertebrates. Nature. 627:811–820 doi:10.1038/s41586-024-07070-3
2023
Piovani L, Marlétaz F. 2023. Single-cell transcriptomics refuels the exploration of spiralian biology. Brief Funct Genomics. 22(6):517–524 doi:10.1093/bfgp/elad038. [review article]
Piovani L, Leite DJ, Yañez-Guerra LA, Simpson F, Musser JM, Salvador-Martinez I, Marlétaz F, Jekely G, Telford MJ. 2023. Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories. Sci Adv. 9(31):eadg6034. doi:10.1126/sciadv.adg6034.
Ahuja N, Hwaun E, Pungor JR, Rafiq R, Nemes S, Sakmar T, Vogt MA, Grasse B, Diaz Quiroz J, Montague TG, Null RW, Dallis DN, Gavriouchkina D, Marlétaz F, Abbo L, Rokhsar DS, Niell CM, Soltesz I, Albertin CB, Rosenthal JJC. 2023. Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity. Curr Biol. 10;33(13):2774-2783.e5. doi:10.1016/j.cub.2023.05.066
Marlétaz F, Couloux A, Poulain J, Labadie K, Da Silva C, Mangenot S, Noel B, Poustka AJ, Dru P, Pegueroles C, Borra M, Lowe EK, Lhomond G, Besnardeau L, Le Gras S, Ye T, Gavriouchkina D, Russo R, Costa C, Zito F, Anello L, Nicosia A, Ragusa MA, Pascual M, Molina MD, Chessel A, Di Carlo M, Turon X, Copley RR, Exposito JY, Martinez P, Cavalieri V, Ben Tabou de Leon S, Croce J, Oliveri P, Matranga V, Di Bernardo M, Morales J, Cormier P, Geneviève AM, Aury JM, Barbe V, Wincker P, Arnone MI, Gache C, Lepage T§. 2023. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. 2023. Cell Genomics. 5;3(4):100295. doi:10.1016/j.xgen.2023.100295
Marlétaz F, de la Calle-Mustienes E, Acemel RD*, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T§, Tena JJ§, Lupiáñez DG§, Rokhsar DS§, Gómez-Skarmeta JL. 2023. The little skate genome and the evolutionary emergence of wing-like fins. Nature. 616(7957):495-503. doi:10.1038/s41586-023-05868-1
Martín-Zamora FM, Liang Y, Guynes K, Carrillo-Baltodano AM, Davies BE, Donnellan RD, Tan Y, Moggioli G, Seudre O, Tran M, Mortimer K, Luscombe NM, Hejnol A, Marlétaz F§, Martín-Durán JM§. 2023. Annelid functional genomics reveal the origins of bilaterian life cycles. Nature. 615(7950):105-110. doi:10.1038/s41586-022-05636-7.
2022
Pisani D, Rossi ME, Marlétaz F, Feuda R. 2022. Phylogenomics: Is less more when using large-scale datasets? Curr Biol. Dec 19;32(24):R1340-R1342. doi:10.1016/j.cub.2022.11.019 [commentary]
Brasó-Vives M, Marlétaz F, Echchiki A, Mantica F, Acemel RD, Gómez-Skarmeta JL, Hartasánchez DA, Le Targa L, Pontarotti P, Tena JJ, Maeso I, Escriva H, Irimia M, Robinson-Rechavi M. 2022. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biology. 18;23(1):243. doi:10.1186/s13059-022-02808-6.
Simakov O, Bredeson J, Berkoff K, Marlétaz F, Mitros T, Schultz DT, O’Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS. 2022. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci Adv. 8(5):eabi5884. doi:10.1126/sciadv.abi5884.
Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H. 2021. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. New Phytol. Mar;233(5):2094-2110. doi:10.1111/nph.17738.
2021
Ramos-Silva P, Wall-Palmer D, Marlétaz F, Marin F, Peijnenburg KTCA. 2021. Evolution and biomineralization of pteropod shells. J Struct Biol. 213(4):107779. doi:10.1016/j.jsb.2021.107779.
Sanchez G, Fernández-Álvarez FÁ, Taite M, Sugimoto C, Jolly J, Simakov O, Marlétaz F, Allcock L, Rokhsar DS. 2021. Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Commun Biol. 4(1):819. doi:10.1038/s42003-021-02348-y.
Finet C, Kassner VA, Carvalho AB, Chung H, Day JP, Day S, Delaney EK, De Ré FC, Dufour HD, Dupim E, Izumitani HF, Gautério TB, Justen J, Katoh T, Kopp A, Koshikawa S, Longdon B, Loreto EL, Nunes MDS, Raja KKB, Rebeiz M, Ritchie MG, Saakyan G, Sneddon T, Teramoto M, Tyukmaeva V, Vanderlinde T, Wey EE, Werner T, Williams TM, Robe LJ, Toda MJ, Marlétaz F. 2021. DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics. Genome Biol Evol. 13(8):evab179. doi:10.1093/gbe/evab179.
Xu F, Marlétaz F, Gavriouchkina D, Liu X, Sauka-Spengler T, Zhang G, Holland PWH. Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals. 2021. Nat Commun. 12(1):3117. doi:10.1038/s41467-021-23216-7?
2020
Martín-Durán JM, Vellutini BC, Marlétaz F, Cetrangolo V, Cvetesic N, Thiel D, Henriet S, Grau-Bové X, Carrillo-Baltodano AM, Gu W, Kerbl A, Marquez Y, Bekkouche N, Chourrout D, Gómez-Skarmeta JL, Irimia M, Lenhard B, Worsaae K, Hejnol A. Conservative route to genome compaction in a miniature annelid. Nat Ecol Evol. 2020 Nov 16. doi:10.1038/s41559-020-01327-6
Peijnenburg KTCA, Janssen AW, Wall-Palmer D, Goetze E, Maas AE, Todd JA, Marlétaz F. The origin and diversification of pteropods precede past perturbations in the Earth’s carbon cycle. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25609-25617. doi:10.1073/pnas.1920918117
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, Casares F. 2020. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nat Commun. 11(1):2631. doi:10.1038/s41467-020-16284-8
Simakov O, Marlétaz F, Yue JX, O’Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. 2020. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol. 4(6):820-830. doi:10.1038/s41559-020-1156-z.
Martín-Durán JM, Marlétaz F. Unravelling spiral cleavage. 2020. Development. 147(1):dev181081. doi:10.1242/dev.181081
Choo LQ, Bal TMP, Choquet M, Smolina I, Ramos-Silva P, Marlétaz F, Kopp M, Hoarau G, Peijnenburg KTCA. Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance. 2020. BMC Genomics. 21(1):11. doi:10.1186/s12864-019-6372-z
2019
Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS. New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis. 2019. Commun Biol. 2(1):465. doi:10.1038/s42003-019-0661-6.
Marlétaz F, Peijnenburg KTCA, Goto T, Satoh N, Rokhsar D. A new spiralian phylogeny places the enigmatic arrow worms among gnathiferans. 2019. Curr Biol. 29, 1–7, doi:10.1016/j.cub.2018.11.042
2018
Marlétaz F, Firmbas PN, Maeso I, Tena J, Bogdanovic O, Perry M, Wyatt C, de la Calle-Mustienes E, van Heeringen S, Farahani E, Bertrand S, Burgera D, Aldea D, Subirana L, … , Mangenot S, Aury JM, Wincker P, Garcia-Fernandez J, Lenhard B, Lister R, Holland PWH, Irimia M, Escriva H, Skarmeta JL. 2018. Amphioxus functional genomics pinpoints the origin of chordate regulatory novelties. Nature. 564, 64–70.* doi:10.1038/s41586-018-0734-6
2017
Hargreaves A, Long Z, Christensen J, Marlétaz F, Liu S, Li F, Jansen PG, Spiga E, Hansen MT, Pedersen SVH, Biswas S, Serikawa K, Fox B, Taylor WR, Mulley JF, Zhan G, Heller RS, Holland PWH. 2017. Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster. Proc Nat Acad U S A early access doi:10.1073/pnas.1702930114.
Burridge AK, Hörnlein C, Janssen AW, Hughes M, Bush SL, Marlétaz F, Gasca R, Pierrot-Bults AC, Michel E, Todd JA, Young JR, Osborn KJ, Menken SBJ, Peijnenburg KTCA 2017. Time-calibrated molecular phylogeny of pteropods. PLoS One. 12(6):e0177325. doi:10.1371/journal.pone.0177325
Marlétaz F, Le Parco Y, Liu S, Peijnenburg K 2017. Extreme Mitogenomic Variation Without Cryptic Speciation in Chaetognaths. Genome Biol Evol. 9(6):1374-1384. doi:10.1093/gbe/evx090
Holland PWH, Marlétaz F,Maeso I, Dunwell TL, Paps J. 2017. New genes from old: asymmetric divergence of gene duplicates and the evolution of development. Phil. Trans. R. Soc. B. 372: 20150480. doi:10.1098/rstb.2015.0480 [review article]
2016
Maeso I, Dunwell TL, Wyatt CD, Marlétaz F, Vetö B, Bernal JA, Quah S, Irimia M, Holland PW. 2016. Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals. BMC Biol. 14(1):45. doi:10.1186/s12915-016-0267-0
Feuda R, Marlétaz F, Bentley M, Holland PWH. Conservation, duplication and divergence of five opsin genes in insect evolution. 2016. Genome Biol Evol. 8(3):579-87. doi:10.1093/gbe/evw015
Acemel RD, Tena JJ, Irastorza I,* Marlétaz F*, Gómez-Marín C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PWH, Devos DP, Maeso I, Escrivá H, Gómez-Skarmeta JL. 2016. A single 3D chromatin compartment in the amphioxus Hox cluster reveals the stepwise evolution of vertebrate Hox bimodal regulation. Nature Genetics. 48(3):336-41. doi:10.1038/ng.3497
2015
Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J. 2015. Hemichordate genomes and deuterostome origins. 2015. Nature. 527, 459–465. doi:10.1038/nature16150
Kenny NJ, Namigai EK, Marlétaz F, Hui JH, Shimeld SM. 2015. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics. epub Aug 26. doi:10.1016/j.margen.2015.07.004
Marlétaz F, Maeso I, Faas L, Isaacs HV, Holland PWH. 2015. Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution. BMC Biology 13:56 doi:10.1186/s12915-015-0165-x
2014
Ferguson L, Marlétaz F, Carter JM*, Taylor W, Gibbs M, Breuker C, Holland PWH. 2014. Ancient expansion of the Hox cluster in Lepidoptera has generated four homeobox genes implicated in extra-embryonic tissue formation. PLoS genetics. 10(10): e1004698. doi:10.1371/journal.pgen.1004698
2012
Marlétaz F, Maeso I, Paps J, Holland PWH. 2012. Discovery and classification of homeobox genes in animal genomes. Methods in Molecular Biology. 1196: 3-18 [review article]
Simakov O, Marlétaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS. 2013. Insights into bilaterian evolution from three spiralian genomes. Nature 493(7433):526-31. doi:10.1038/nature11696
Finet C, Berne-Dedieu A, Scutt CP, Marlétaz F. 2012. Evolution of the ARF Gene Family in Land Plants: Old Domains, New Tricks. Mol Biol Evol 30(1):45-56. doi:10.1093/molbev/mss220
2011
Sobreiraa TJP, Marlétaz F, Simões-Costa M*, Schechtmane D, Pereiraa AC, Brunet F, Sweeney S, Pani A, Aronowicz J, Lowe CJ, Davidson B, Laudet V, Bronner-Fraser M, de Oliveira PSL, Schubert M, and Xavier-Neto J. 2011. Structural Shifts of ALDH Enzymes Were Instrumental for the Early Evolution of Retinoid-Dependent Axial Patterning in Metazoans. Proc Nat Acad U S A 108(1):226-31 doi:10.1073/pnas.1011223108
2010
Finet C, Timme RE, Delwiche CF, Marlétaz F. 2010. Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants. Curr Biol 20(24):2217-22. doi:10.1016/j.cub.2010.11.035
Marlétaz F, Gyapay G, Le Parco Y. 2010. High Level of Structural Polymorphism Driven by Mobile Elements in the Hox Genomic Region of the Chaetognath Spadella cephaloptera. Genome Biol Evol 2:665-667. doi:10.1016/j.cub.2010.11.035
2008
Campo-Paysaa F, Marlétaz F, Laudet V, Schubert M. 2008. Retinoic Acid Signaling in Development: Tissue-Specific Functions and Evolutionary Origins. Genesis. 46(11):640-56. doi:10.1002/dvg.20444 [review article]
Marlétaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco Y. 2008. Chaetognath Transcriptome Reveals Ancestral and Unique Features Among Bilaterians. Genome Biol 9(6):R94. doi:10.1186/gb-2008-9-6-r94
Marlétaz F, Le Parco Y. Careful with Understudied Phyla: the Case of Chætognath. 2008. BMC Evol Biol 8(1):251. doi:10.1186/1471-2148-8-251
2006
Marlétaz F Martin E, Perez Y, Papillon D, Caubit X, Fasano L, Dossat C, Wincker P, Weissenbach J, Le Parco Y. 2006. Chætognath Phylogenomics: a Protostome with Deuterostome-Like Development. Curr Biol 16:R577-8. doi:10.1016/j.cub.2006.07.016
Marlétaz F, Holland LZ, Laudet V, Schubert M. 2006. Retinoic Acid Signaling and the Evolution of Chordates. Int J Biol Sci. 2:38-47 doi:10.7150/ijbs.2.38 [review article]