Species biology: A keystone ecosystem engineer and important food for flatfish and crayfish. This echinoderm has exceptional adult regenerative abilities and can regenerate fully functional arms in a matter of weeks, making this species an emerging model for regeneration and stem cell biology in biomedical research. Major scientific targets include cellular and molecular mechanisms underlying regeneration with important links to neuroscience, stem cell biology and neuropeptide structure and function in the absence of a centralised nervous system.
Rationale for genome sequencing: Echinoderms have the potential to offer viable and tractable models for molecular and cellular research on stem cells and regeneration, aided by the fact that echinoderms are characterised by a simple genomic structure. Genetic information between this species is highly conserved, compared to humans, but the nature of the common molecular regulatory pathways that facilitate regeneration is still unclear. A bit effort on transcriptomics is being made, but genome information will provide key information to fully understand the process.
Key references: Dupont and Thorndyke (2006) Journal of Experimental Biology, Wood et al. (2008) Proceedings of the Royal Society B, Bannister et al. (2005) Development Genes and Evolution, Bannister et al. (2008) Development Genes and Evolution, Dupont et al. (2009) Development Genes and Evolution, Burns et al. (2011) Journal of Experimental Marine Biology and Ecology, Burns et al. (2012) Journal of Experimental Marine Biology and Ecology
Estimated Genome size: 3.0 Gbp
Available sequence information: EST database available at http://www.echinobase.org/Echinobase/
Reads in NCBI/SRA: SRS591028.
Genome sequencing progress: (last updated 2016-08-25)
Illumina libraries, bp - 200, 300, 550, 3000, 5 000-8 000
Total sequences data, Gbp - 420
Total size assembly, Gbp - 3.4
Scaffold NG50, bp - 74 200
Max scaffold size, bp - 785 350
Additional genetic resources:
Other resources: -
Database resources: albiorix.bioenv.gu.se
In culture: Not at the moment, but we are able to get them all year around and we are able to culture them and have larvae during the summer months.
Contact: Olga Ortega-Martinez - firstname.lastname@example.org
Bioinformatician: Tomas Larsson - email@example.com
AFI annotation team