Amphioxus functional genomics (AmphiENCODE)

Amphioxus functional genomics (AmphiENCODE)

Lab members: Demián Burguera, Chris Wyatt
Funding: CRG; Genoscope and many other funding sources of the Consortium members (coordinator Hector Escriva). 

As part of a large collaborative effort with many labs integrating the European Amphioxus Genome Consortium (coordinated by Hector Escriva (CNRS/UPMC)), Genoscope, and the lab of Jose Luis Gómez-Skarmeta (CADB-CSIC), we are participating in the sequencing, assembly and functional annotation of the European amphioxus, Branchiostoma lanceolatum. The work of this Consortium will provide unprecedented amounts of functional data for this slow-evolving invertebrate chordate, including RNA-Seq for multiple adult tissues and developmental stages, ChIP-Seq of chromatin modifications, ATAC-Seq, CAGE-Seq and Bisulphite-seq. These data will be integrated in public resources and will facilitate studies to understand the evolutionary origins of vertebrates by providing functional data for the best outgroup to our lineage.  

Related publications:

  • Venkatesh, B., Lee, A.P., Ravi, V., Lian, M.M., Maurya, A.K., Swann, J.B., Ohta, Y., Flajnik, M.F., Sutoh, Y., Kasahara, M., Hoon, S., Gangu, V., Roy, S.W., Irimia, M., Korzh, V., Kondrychyn, I., Tay, B., Tohari, S., Lim, Z.W., Kong, K.W., Ho, S., Lorente-Galdos, B., Quilez, J., Marques-Bonet, T., Raney, B.J., Ingham, P.W., Tay, A., Hillier, L.W., Minx, P., Boehm, T., Wilson, R.K., Brenner, S. (2014). The elephant shark genome provides unique insights into gnathostome evolution. Nature, 505(7482):174-9