Danio Species Sequencing Project - Danio albolineatus-sc-2010-08-02
Danio Species Sequencing Project - Danio albolineatus
The Zebrafish (Danio rerio) genome is essentially finished. There are many other members of the Danio genus that are closely related, and can even be interbred with the Zebrafish to make hybrids. They differ in many attributes to the zebrafish, most obviously in external appearance, size, shape and skin patterning. Danio rerio (zebrafish) has distinctive stripes of black melanophores and silver xanthrophores, whereas Danio albolineatus has almost uniformly dispersed melanophores, xanthopores, iridophores and erythrophores. For more details see Quigley et al. Development 131. 2004 and http://protist.biology.washington.edu/dparichy/. We believe this, in combination with the dozens of extant zebrafish mutants affecting skin colour and patterning, is an excellent model to study the differentiation of neural crest stem cells into different pigment cell types, and the patterning of these pigment cells into large structures - stripes and spots. Here we are sequencing a heterozygous (but inbred) individual of Danio albolineatus from the Parichy lab. Based on public sequences in NCBI this possesses ~92% identity in transcripts (coding and UTR) with Danio rerio. Hybrid crosses have been made with Danio rerio, see Quigley et al. Development 131. 2005. In addition to working towards a better understanding of neural crest stem cells and skin patterning one can also use the genome sequence comparatively to identify conserved sequences, and those evolving at a faster rate. Similar approaches with Caenorhabditis, Drosophila species and primate genome comparisons have been shown to be highly informative. Due to the high level of polymorphism between Danio albolineatus and the Danio rerio reference genome, mapping of reads as a resequencing project (expecting ~1% polymorphism or 2-3 SNP maximum) is likely to perform poorly.  Studies using this data should cite the “Sanger-University of Washington Danio species sequencing project” or the relevant paper(s) by Matthew Clark and David Parichy.   . This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
The Zebrafish (Danio rerio) genome is essentially finished. There are many other members of the Danio genus that are closely related, Danio rerio (zebrafish) has distinctive stripes of black melanophores and silver xanthrophores, whereas Danio albolineatus has almost uniformly dispersed melanophores, xanthopores, iridophores and erythrophores. This is an excellent model to study the differentiation of neural crest stem cells into different pigment cell types, and the patterning of these pigment cells into large structures - stripes and spots. In addition to working towards a better understanding of neural crest stem cells and skin patterning one can also use the genome sequence comparatively to identify conserved sequences, and those evolving at a faster rate. Due to the high level of polymorphism between Danio albolineatus and the Danio rerio reference genome, mapping of reads as a resequencing project (expecting ~1% polymorphism or 2-3 SNP maximum) is likely to perform poorly.