Cephalopod Genomics
A sequenced genome is a rich and important tool for understanding the biology of an organism. Well into the last decade, few sequence resources were available for cephalopods. In collaboration with the Ragsdale lab at the University of Chicago, the Rokhsar group at the University of California Berkeley and the Simakov lab at the University of Vienna, we have sequenced the genomes of Octopus bimaculoides, the California two-spot octopus, and Doryteuthis pealeii, the longfin inshore squid, a longstanding model organism in neuroscience. We have created chromosomal-scale assemblies for these species, as well as Euprymna scolopes. These sequence resources will be a key tool in identifying candidate genes and examining their deployment.
Key publications:
Albertin CB*, Mitros T, Medina S, Schmidbaur H, Sanchez G, Schmutz J, Rosenthal JJ, Ragsdale CW*, Simakov O*, Rokhsar DS*. 2022. Genome and transcriptome mechanisms driving cephalopod evolution. Nature Communications.13(1):2427
Schmidbaur H, Kawaguchi A, Gerguri T, Fu X, Hoang OP, Zimmerman B, Ritschard E, Weissenbacher A, Foster J, Nyholm S, Bates P, Albertin CB*, Tanaka E*, Simakov O*. 2022. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature Communications. 13(1):2127
Albertin CB, Simakov O. 2020. Cephalopod biology: at the intersection between genomic and organismal novelties. Annual Reviews of Animal Biosciences. 8:1.
Albertin CB, Simakov O, Mitros T, Wang YZ, Pungor JR, Edsinger-Gonzalez E, Brenner S, Ragsdale CW, Rokhsar DS. 2015. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 524(7564):220-4.
Albertin CB, Bonnaud L, Brown CT, Crookes-Goodson WJ, de Fonseca RR, Di Cristo C, Dilkes BP, Edsinger-Gonzales E, Freeman RM Jr., Hanlon RT, Koenig KM, Lindgren AR, Martindale MQ, Minx P, Moroz LL, Nödl MT, Nyholm SV, Ogura A, Pungor JR, Rosenthal JJ, Schwarz EM, Shigeno S, Strugnell JM, Wollesen T, Zhang G, Ragsdale CW. 2012. Cephalopod genomics: A plan of strategies and organization. Standards of Genomic Science. 7(1):175-88.