Publications

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 20218 | 2017 | 2016 |2015

2024

Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution
Lin CY, Marlétaz F, Pérez-Posada A, Martínez-García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Skarmeta JLG, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS, Yu JK, Su YH
Plos Biology, 22, ARTN e3002661, https://doi.org/10.1371/journal.pbio.3002661 (2024)

The hagfish genome and the evolution of vertebrates
Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS
Nature, 627, 811–820, https://doi.org/10.1038/s41586-024-07070-3 (2024)

Cryptic biodiversity in the commercial diamondback squid Thysanoteuthis rhombus Troschel 1857
Deville D, Mori S, Kawai K, Escánez A, Macali A, Lishchenko F, Braid H, Githaiga-Mwicigi J, Mohamed KS, Bolstad KSR, Miyahara K, Sugimoto C, Fernández-Álvarez FA, Sanchez G
Reviews in Fish Biology and Fisheries, 34, 293-313, https://doi.org/10.1007/s11160-023-09813-3 (2024)

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs
Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS
Nature Communications, 15, ARTN 579, https://doi.org/10.1038/s41467-023-43012-9 (2024)

2023

Transposon signatures of allopolyploid genome evolution
Session AM, Rokhsar DS
Nature Communications, 14, ARTN 3180, https://doi.org/10.1038/s41467-023-38560-z (2023)

Ancient gene linkages support ctenophores as sister to other animals
Schultz DT, Haddock SHD, Bredeson JV, Green RE, Simakov O, Rokhsar DS
Nature, 618, 110–117, https://doi.org/10.1038/s41586-023-05936-6 (2023)

Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid
Rouressol L, Briseno J, Vijayan N, Chen GY, Ritschard EA, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O
iScience, 26, ARTN 107091, https://doi.org/10.1016/j.isci.2023.107091 (2023)

The little skate genome and the evolutionary emergence of wing-like fins
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 A, Bogdanovic O, Gibcus JH, Yang LY, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T, Tena JJ, Lupiañez DG, Rokhsar DS, Gómez-Skarmeta JL
Nature, 616, 495–503, https://doi.org/10.1038/s41586-023-05868-1 (2023)

Cephalopod behaviour
Gutnick T, Rokhsar DS, Kuba MJ
Current Biology, 33, R1083-R1086, https://doi.org/10.1016/j.cub.2023.08.094 (2023)

Molecular evidence of anteroposterior patterning in adult echinoderms
Formery L, Peluso P, Kohnle I, Malnick J, Thompson JR, Pitel M, Uhlinger KR, Rokhsar DS, Rank DR, Lowe CJ
Nature, 623, 555–561, https://doi.org/10.1038/s41586-023-06669-2 (2023)

Atlantic Oceanic Squids in the "Grey Speciation Zone"
Fernández-Álvarez FA, Sanchez G, Deville D, Taite M, Villanueva R, Allcock AL
Integrative and Comparative Biology, 63, 1214-1225, https://doi.org/10.1093/icb/icad116 (2023)

Tracing cancer evolution and heterogeneity using Hi-C
Erdmann-Pham DD, Batra SS, Turkalo TK, Durbin J, Blanchette M, Yeh I, Shain H, Bastian BC, Song YS, Rokhsar DS, Hockemeyer D
Nature Communications, 14, ARTN 7111, https://doi.org/10.1038/s41467-023-42651-2 (2023)

Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology
Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Krol M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB
Integrative and Comparative Biology, 63, 1226-1239, https://doi.org/10.1093/icb/icad087 (2023)

Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity
Ahuja N, Hwaun E, Pungor JR, Rafiq R, Nemes S, Sakmar T, Vogt MA, Grasse B, Quiroz JD, Montague TG, Null RW, Dallis DN, Gavriouchkina D, Marletaz F, Abbo L, Rokhsar DS, Niell CM, Soltesz I, Albertin CB, Rosenthal JJC
Current Biology, 33, 2774-2783, https://doi.org/10.1016/j.cub.2023.05.066 (2023)

2022

Deeply conserved synteny and the evolution of metazoan chromosomes
Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O'Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS
Science Advances, 8, ARTN eabi5884, https://doi.org/10.1126/sciadv.abi5884 (2022)

Beyond "living fossils": Can comparative genomics finally reveal novelty?
Sanchez G, Simakov O, Rokhsar DS
Molecular Ecology Resources, 22, 9-11, https://doi.org/10.1111/1755-0998.13488 (2022)

De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza
Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H
New Phytologist, 233, 2094-2110, https://doi.org/10.1111/nph.17738 (2022)

Lifecycle, culture, and maintenance of the emerging cephalopod models Euprymna berryi and Euprymna morsei
Jolly J, Hasegawa Y, Sugimoto C, Zhang L, Kawaura R, Sanchez G, Gavriouchkina D, Marlétaz F, Rokhsar D
Frontiers in Marine Science, 9, ARTN 1039775, https://doi.org/10.3389/fmars.2022.1039775 (2022)

Chromosome evolution and the genetic basis of agronomically important traits in greater yam
Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hribová E, Parker M, Nwogha J, Shu SQ, Carlson J, Kariba R, Muthemba S, Knop K, Barton GJ, Sherwood AV, Lopez-Montes A, Asiedu R, Jamnadass R, Muchugi A, Goodstein D, Egesi CN, Featherston J, Asfaw A, Simpson GG, Dolezel J, Hendre PS, Van Deynze A, Kumar PL, Obidiegwu JE, Bhattacharjee R, Rokhsar DS
Nature Communications, 13, ARTN 2001, https://doi.org/10.1038/s41467-022-29114-w (2022)

Genome and transcriptome mechanisms driving cephalopod evolution
Albertin CB, Medina-Ruiz S, Mitros T, Schmidbaur H, Sanchez G, Wang ZY, Grimwood J, Rosenthal JJC, Ragsdale CW, Simakov O, Rokhsar DS
Nature Communications, 13, ARTN 2427, https://doi.org/10.1038/s41467-022-29748-w (2022)

2021

Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals
Xu F, Marlétaz F, Gavriouchkina D, Liu X, Sauka-Spengler T, Zhang GF, Holland PWH
Nature Communications, 12, ARTN 3117, https://doi.org/10.1038/s41467-021-23216-7 (2021)

Diversification of mandarin citrus by hybrid speciation and apomixis
Wu GA, Sugimoto C, Kinjo H, Azama C, Mitsube F, Talon M, Gmitter FG, Rokhsar DS
Nature Communications, 12, ARTN 4377, https://doi.org/10.1038/s41467-021-24653-0 (2021)

Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)
Sanchez G, Fernández-Álvarez FA, Taite M, Sugimoto C, Jolly J, Simakov O, Marlétaz F, Allcock L, Rokhsar DS
Communications Biology, 4, ARTN 819, https://doi.org/10.1038/s42003-021-02348-y (2021)

2020

Deeply conserved synteny resolves early events in vertebrate evolution
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
Nature Ecology & Evolution, 4, 820–830, https://doi.org/10.1038/s41559-020-1156-z (2020)

The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle
Peijnenburg KTCA, Janssen AW, Wall-Palmer D, Goetze E, Maas AE, Todd JA, Marlétaz F
PNAS, 117, 25609-25617, https://doi.org/10.1073/pnas.1920918117 (2020)

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS
Communications Biology, 3, ARTN 480, https://doi.org/10.1038/s42003-020-1096-9 (2020)

Unravelling spiral cleavage
Martín-Durán JM, Marlétaz F
Development, 147, ARTN dev181081, https://doi.org/10.1242/dev.181081 (2020)

The citrus genome
Gmitter FG, Wu GA, Rokhsar DS, Talon M
In: The Genus Citrus (ed Caruso M, Talon M, Gmitter FG), Chapter 1, 1-8, Woodhead Publishing, https://doi.org/10.1016/B978-0-12-812163-4.00001-2 (2020)

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance
Choo LQ, Bal TMP, Choquet M, Smolina I, Ramos-Silva P, Marlétaz F, Kopp M, Hoarau G, Peijnenburg KTCA
BMC Genomics, 21, ARTN 11, https://doi.org/10.1186/s12864-019-6372-z (2020)

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
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
Nature Communications, 11, ARTN 2631, https://doi.org/10.1038/s41467-020-16284-8 (2020)

2019

A large CRISPR-induced bystander mutation causes immune dysregulation
Simeonov DR, Brandt AJ, Chan AY, Cortez JT, Li Z, Woo JM, Lee Y, Carvalho CMB, Indart AC, Roth TL, Zou J, May AP, Lupski JR, Anderson MS, Buaas FW, Rokhsar DS, Marson A
Communications Biology, 2, ARTN 70, https://doi.org/10.1038/s42003-019-0321-x (2019)

New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis
Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS
Communications Biology, 2, ARTN 465, https://doi.org/10.1038/s42003-019-0661-6 (2019)

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis
Mitros T, Lyons JB, Session AM, Jenkins J, Shu SQ, Kwon T, Lane M, Ng C, Grammer TC, Khokha MK, Grimwood J, Schmutz J, Harland RM, Rokhsar DS
Developmental Biology, 452, 8-20, https://doi.org/10.1016/j.ydbio.2019.03.015 (2019)

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
Marlétaz F, Peijnenburg KTCA, Goto T, Satoh N, Rokhsar DS
Current Biology, 29, 312-318, https://doi.org/10.1016/j.cub.2018.11.042 (2019)

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods
Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV
PNAS, 116, 3030-3035, https://doi.org/10.1073/pnas.1817322116 (2019)

2018

Genomics of the origin and evolution of Citrus
Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du DL, Ollitrault P, Roose ML, Dopazo J, Gmitter FG, Rokhsar DS, Talon M
Nature, 554, 311–316, https://doi.org/10.1038/nature25447 (2018)

Amphioxus functional genomics and the origins of vertebrate gene regulation
Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez É, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang SF, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu AL, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M
Nature, 564, 64–70, https://doi.org/10.1038/s41586-018-0734-6 (2018)

2017

Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis
Suzuki A, Uno Y, Takahashi S, Grimwood J, Schmutz J, Mawaribuchi S, Yoshida H, Takebayashi-Suzuki K, Ito M, Matsuda Y, Rokhsar D, Taira M
Developmental Biology, 426, 236-244, https://doi.org/10.1016/j.ydbio.2016.04.014 (2017)

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths
Marlétaz F, Le Parco Y, Liu SL, Peijnenburg KTCA
Genome Biology and Evolution, 9, 1374-1384, https://doi.org/10.1093/gbe/evx090 (2017)

New genes from old: asymmetric divergence of gene duplicates and the evolution of development
Holland PWH, Marlétaz F, Maeso I, Dunwell TL, Paps J
Philosophical Transactions of the Royal Society B, 372, ARTN 20150480, https://doi.org/10.1098/rstb.2015.0480 (2017)

Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster
Hargreaves AD, Zhou L, Christensen J, Marlétaz F, Liu SP, Li F, Jansen PG, Spiga E, Hansen MT, Pedersen SVH, Biswas S, Serikawa K, Fox BA, Taylor WR, Mulley JF, Zhang GJ, Heller RS, Holland PWH
PNAS, 114, 7677-7682, https://doi.org/10.1073/pnas.1702930114 (2017)

Time-calibrated molecular phylogeny of pteropods
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
Plos One, 12, e0177325, https://doi.org/10.1371/journal.pone.0177325 (2017)

2016

Genome evolution in the allotetraploid frog Xenopus laevis
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Ogdanovic OB, Lister R, Georgiou G, Paranjpe SS, Van Kruijsbergen I, Shu SQ, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Zutsu YI, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJC, Fujiyama A, Harland RM, Taira M, Rokhsar DS
Nature, 538, 336–343, https://doi.org/10.1038/nature19840 (2016)

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity
Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J, Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, Setter TL, Gleadow RM, Kulakow P, Ferguson ME, Rounsley S, Rokhsar DS
Nature Biotechnology, 34, 562-570, https://doi.org/10.1038/nbt.3535 (2016)

2015

Hemichordate genomes and deuterostome origins
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
Nature, 527, 459–465, https://doi.org/10.1038/nature16150 (2015)

The deuterostome context of chordate origins
Lowe CJ, Clarke DN, Medeiros DM, Rokhsar DS, Gerhart J
Nature, 520, 456-465, https://doi.org/10.1038/nature14434 (2015)

The octopus genome and the evolution of cephalopod neural and morphological novelties
Albertin CB, Simakov O, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS
Nature, 524, 220–224, https://doi.org/10.1038/nature14668 (2015)