Publications

2023

Marlétaz, F., de la Calle-Mustienes, E., Acemel, R.D., Paliou, C., Naranjo, S., Martínez-García, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., González-Rajal, Á., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldón, T., Nakamura, T., Tena, J.J., Lupiáñez, D.G., Rokhsar, D.S., Gómez-Skarmeta, J.L.2023. The little skate genome and the evolutionary emergence of wing-like fins. Nature, 616, 495–503. https://doi.org/10.1038/s41586-023-05868-1

2022

Jolly, J., Hasegawa, Y., Sugimoto, C., Zhang, L., Kawaura, R., Sanchez, G., Gavriouchkina, D., Marlétaz, F., Rokhsar, D. 2022. Lifecycle, culture, and maintenance of the emerging cephalopod models Euprymna berryi and Euprymna morsei. Front. Mar. Sci. 9:1039775. doi: 10.3389/fmars.2022.1039775

Albertin, C.B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z.Y., Grimwood, J., Rosenthal, J.J.C., Ragsdale, C.W., Simakov, O., Rokhsar, D.S. 2022. Genome and transcriptome mechanisms driving cephalopod evolution. Nat Commun. 13(1):2427. doi: 10.1038/s41467-022-29748-w.

Bredeson, J.V., Lyons, J.B., Oniyinde, I.O., Okereke, N.R., Kolade, O., Nnabue, I., Nwadili, C.O., Hřibová, E., Parker, M., Nwogha, J., Shu, S., Carlson, J., Kariba, R., Muthemba, S., Knop, K., Barton, G.J., Sherwood, A.V., Lopez-Montes, A., Asiedu, R., Jamnadass, R., Muchugi, A., Goodstein, D., Egesi, C.N., Featherston, J., Asfaw, A., Simpson, G.G., Doležel, J., Hendre, P.S., Van Deynze, A., Kumar, P.L., Obidiegwu, J.E., Bhattacharjee, R., Rokhsar, D.S. 2022. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nat Commun. 13(1):2001. doi: 10.1038/s41467-022-29114-w.

Simakov, O., Bredeson, J., Berkoff, K., Marletaz, F., Mitros, T., Schultz, D.T., O'Connell, B.L., Dear, P., Martinez, D.E., Steele, R.E., Green, R.E., David, C.N., Rokhsar, D.S. 2022. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci Adv. 8(5):eabi5884. doi: 10.1126/sciadv.abi5884.

Sanchez, G., Simakov, O., Rokhsar, D.S. 2022. Beyond "living fossils": Can comparative genomics finally reveal novelty? Mol. Ecol. Resour. 22(1):9-11. https://doi.org/10.1111/1755-0998.13488.

2021

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. 233(5):2094-2110. doi: 10.1111/nph.17738.

Wu, G.A., Sugimoto, C., Kinjo, H., Azama, C., Mitsube, F., Talon, M., Gmitter, F.G. Jr., Rokhsar, D.S. 2021. Diversification of mandarin citrus by hybrid speciation and apomixis. Nat. Commun. 12:4377. doi: 10.1038/s41467-021-24653-0.

Sanchez, G., Fernández-Álvarez, F.Á., Taite, M., Sugimoto, C., Jolly, J., Simakov, O. Marlétaz, F., Allcock., L., Rokhsar, D.S. 2021. Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Commun. Biol. 4:819. doi: 10.1038/s42003-021-02348-y.

Xu, F., Marlétaz, F., Gavriouchkina, D., Liu, X., Sauka-Spengler, T., Zhang, G., Holland, P. W. H. 2021. Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals. Nat. Commun. 12(1):3117. doi: 10.1038/s41467-021-23216-7.

2020

Mitros, T., Session, A.M., James, B.T., Wu, G.A., Belaffif, M.B., Clark, L.V., Shu, S., Dong, H., Barling, A., Holmes, J.R., Mattick, J.E., Bredeson, J.V., Liu, S., Farrar, K., Głowacka, K., Jeżowski, S., Barry, K., Chae, W.B., Juvik, J.A., Gifford, J., Oladeinde, A., Yamada, T., Grimwood, J., Putnam, N.H., De Vega, J., Barth, S., Klaas, M., Hodkinson, T., Li, L., Jin, X., Peng, J., Yu, C.Y., Heo, K., Yoo, J.H., Ghimire, B.K., Donnison, I.S., Schmutz, J., Hudson, M.E., Sacks, E.J., Moose, S.P., Swaminathan, K., Rokhsar, D.S. 2020. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun. 11(1):5442. doi: 10.1038/s41467-020-18923-6.

Mudd, A.B., Bredeson, J.V., Baum, R., Hockemeyer, D., Rokhsar, D.S. 2020. Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Commun Biol. 3(1):480. doi: 10.1038/s42003-020-1096-9.

Simakov, O.*, Marlétaz, F.*, Yue, J.X., O’Connell, B., Jenkins, J., Brandt, A., Calef, R., Tung, C.H., Huang, T.K., Schmutz, J. and Satoh, N., Yu, J.-K., Putnam, N.H., Green, R.E. & Rokhsar, D.S., 2020. Deeply conserved synteny resolves early events in vertebrate evolution. Nature Ecology & Evolution, 4:820–830. doi: 10.1038/s41559-020-1156-z.

Martín-Durán, J.M., Marlétaz, F., 2020. Unravelling spiral cleavage. Development. 147(1):dev181081. doi: 10.1242/dev.181081. PMID: 31898583.

Almudi, I., Vizueta, J., Wyatt, C.D.R., de Mendoza, A., Marlétaz, F., Firbas, P.N., Feuda, R., Masiero, G., Medina. P., Alcaina-Caro, A., Cruz, F., Gómez-Garrido, J., Gut, M., Alioto, T.S., 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.

Choo, L.Q., Bal, T.M.P., Choquet, M., Smolina, I., Ramos-Silva, P., Marlétaz, F., Kopp, M., Hoarau, G., Peijnenburg, K.T.C.A. 2020 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. PMID: 31900119.

Gmitter Jr, F.G., Wu, G.A., Rokhsar, D.S. and Talon, M., 2020. The citrus genome. In The Genus Citrus (pp. 1-8). Woodhead Publishing.

2019

Marlétaz, F., Peijnenburg, K.T., Goto, T., Satoh, N. and Rokhsar, D.S., 2019. A new spiralian phylogeny places the enigmatic arrow worms among gnathiferans. Current Biology, 29(2), pp.312-318.

Sanchez, G., Jolly, J., Reid, A., Sugimoto, C., Azama, C., Marlétaz, F., Simakov, O. and Rokhsar, D.S., 2019. New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis. Communications biology, 2(1), pp.1-15.

Mitros, T., Lyons, J.B., Session, A.M., Jenkins, J., Shu, S., Kwon, T., Lane, M., Ng, C., Grammer, T.C., Khokha, M.K. and Grimwood, J., Schmutz, J., Harland, R.M., Rokhsar, D.S., 2019. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. Developmental biology, 452(1), pp.8-20.

Belcaid, M., Casaburi, G., McAnulty, S.J., Schmidbaur, H., Suria, A.M., Moriano-Gutierrez, S., Pankey, M.S., Oakley, T.H., Kremer, N., Koch, E.J. and Collins, A.J.,  Nguyen, H.,  Lek, S., Goncharenko-Foster, I., Minx, P., Sodergren, E., Weinstock, G., Rokhsar, D.S., McFall-Ngai, M., Simakov, O., Foster, J.S. & Nyholm S.V., 2019. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. Proceedings of the National Academy of Sciences, 116(8), pp.3030-3035.

Simeonov, D.R., Brandt, A.J., Chan, A.Y., Cortez, J.T., Li, Z., Woo, J.M., Lee, Y., Carvalho, C.M., Indart, A.C., Roth, T.L. and Zou, J., May, A.P., Lupski, J.R., Anderson, M.S., Buaas, F.W., Rokhsar, D.S., & Marson, A., 2019. A large CRISPR-induced bystander mutation causes immune dysregulation. Communications biology, 2(1), pp.1-6.

Mudd, A.B., Bredeson, J.V., Baum, R., Hockemeyer, D. and Rokhsar, D.S., 2019. Muntjac chromosome evolution and architecture. bioRxiv, p.772343.

2018

Marlétaz, F.*, Firbas, P.N.*, 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

Wu, G.A., Terol, J., Ibanez, V., López-García, A., Pérez-Román, E., Borredá, C., Domingo, C., Tadeo, F.R., Carbonell-Caballero, J., Alonso, R. and Curk, F., Du, D., Ollitrault, P., Roose, M.L., Dopazo, J., Gmitter, F.G.,  Rokhsar, D.S., &  Talon M.  2018. Genomics of the origin and evolution of Citrus. Nature, 554(7692), pp.311-316

2017

Suzuki, A., Uno, Y., Takahashi, S., Grimwood, J., Schmutz, J., Mawaribuchi, S., Yoshida, H., Takebayashi-Suzuki, K., Ito, M., Matsuda, Y. and Rokhsar, D., 2017. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Developmental biology, 426(2), pp.236-244.

Hargreaves, A., Long, Z., Christensen, J., Marlétaz, F., Liu, S., Li, F., Jansen, P.G., Spiga, E., Hansen, M.T., Pedersen, S.V.H., Biswas, S., Serikawa, K., Fox, B., Taylor, W.R., Mulley, J.F., Zhan, G., Heller, R.S., Holland, P.W.H. 2017. Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster. Proc Nat Acad U S A. 114 (29) 7677-7682. doi:10.1073/pnas.1702930114

Holland, P.W.H., Marlétaz, F., Maeso, I., Dunwell, T.L., 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]

Burridge, A.K., Hörnlein, C., Janssen, A.W., Hughes, M., Bush, S.L., Marlétaz, F., Gasca, R., Pierrot-Bults, A.C., Michel, E., Todd, J.A., Young, J.R., Osborn, K.J., Menken, S.B.J., Peijnenburg, K.T.C.A., 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 

2016 

Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M. and Van Heeringen, S.J., Quigley, I., Heinz, S., Ogino, H., Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam, N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe, M., Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe, S.S, van Kruijsbergen, I., Shu, S. Carlson, J., Kinoshita, T., Ohta, Y.,  Mawaribuchi, S., Jenkins, J., Grimwood, J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y., Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller, K., Haudenschild, C., Kitzman, J., Nakayama, T., Izutsu, Y.,  Robert, J.,  Fortriede, J., Burns, K., Lotay, V., Karimi, K., Yasuoka, Y.,  Dichmann, D.S., Flajnik, M.F.,  Houston, D.W.,  Shendure, J.,  DuPasquier, L., Vize, P. D., Zorn, A.M., Ito, M., Marcotte, E.M., Wallingford, J.B.,  Ito, Y., Asashima, M., Ueno, N., Matsuda, Y., Veenstra, G.J.C., Fujiyama, A., Harland, R.M, Taira M., & Rokhsar, D.S., 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 538(7625), pp.336-343.

Bredeson, J.V., Lyons, J.B., Prochnik, S.E., Wu, G.A., Ha, C.M., Edsinger-Gonzales, E., Grimwood, J., Schmutz, J., Rabbi, I.Y., Egesi, C. and Nauluvula, P., Lebot, V., ​Ndunguru, J. Mkamilo, G., Bart, R.S., Setter, T.L., Gleadow, R.M., P., Ferguson, M.E., Rounsley S. & Rokhsar, D.S., 2016. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nature biotechnology, 34(5), pp.562-570.

2015

Albertin, C.B.*, Simakov, O.*, Mitros, T., Wang, Z.Y., Pungor, J.R., Edsinger-Gonzales, E., Brenner, S., Ragsdale, C.W. and Rokhsar, D.S., 2015. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature, 524(7564), pp.220-224.

Simakov, O., Kawashima, T., Marlétaz, F., Jenkins, J., Koyanagi, R., Mitros, T., Hisata, K., Bredeson, J., Shoguchi, E., Gyoja, F. and Yue, J.X., Chen, Y.-C., Freeman, R.M., Sasaki, A., Hikosaka-Katayama, T., Sato, A., Fujie, M., Baughman, K.W., Levine, J.,  Gonzalez, P.,  Cameron, C., Fritzenwanker, J.H., Pani, A.M,  Goto, H., Kanda, M., Arakaki, N., Yamasaki, S., Qu, J., Cree, A., Ding, Y., Dinh, H.H., Dugan, S., Holder, M., Jhangiani, S.N., Kovar, C.L.,  Lee, S.L., Lewis, L.R., Morton, D., Nazareth, L.V., Okwuonu, G., Santibanez, J., Chen, R., Richards, S.,  Muzny, D.M., Gillis, A., Peshkin, L., Wu, M., Humphreys, T., Su, Y.-H., Putnam, N.H., Schmutz, J.,  Fujiyama,  A., Yu, J.-K., Tagawa, K., Worley, K.C., Gibbs, R.A., Kirschner, M.W., Lowe,  C.J., Satoh,  N., Rokhsar D.S., & Gerhart J., 2015. Hemichordate genomes and deuterostome origins. Nature, 527(7579), pp.459-465.

Lowe, C.J., Clarke, D.N., Medeiros, D.M., Rokhsar, D.S. and Gerhart, J., 2015. The deuterostome context of chordate origins. Nature, 520(7548), pp.456-465.