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Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
The algorithms implemented in Stacks are reported and demonstrated to be efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio. Expand
Preservation of duplicate genes by complementary, degenerative mutations.
Focusing on the regulatory complexity of eukaryotic genes, it is shown how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. Expand
The zebrafish reference genome sequence and its relationship to the human genome
A high-quality sequence assembly of the zebrafish genome is generated, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map, providing a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebra fish-specific genes on chromosome 4 and chromosomal regions that influence sex determination. Expand
Zebrafish hox clusters and vertebrate genome evolution.
Teleosts, the most species-rich group of vertebrates, appear to have more copies of these developmental regulatory genes than do mammals, despite less complexity in the anterior-posterior axis. Expand
The zebrafish glypican knypek controls cell polarity during gastrulation movements of convergent extension.
Experimental and genetic evidence is provided that glypican Knypek acts during vertebrate gastrulation as a positive modulator of noncanonical Wnt signaling to establish polarized cell behaviors underlying convergent extension movements. Expand
The cloche and spadetail genes differentially affect hematopoiesis and vasculogenesis.
The studies demonstrate that the molecular mechanisms that regulate hematopoietic and vasculogenic cells in normal zebrafish have been conserved throughout vertebrate evolution and the clo and spt genes are key regulators of these programs. Expand
Zebrafish smoothened functions in ventral neural tube specification and axon tract formation.
Sonic hedgehog (Shh) signaling patterns many vertebrate tissues. shh mutations dramatically affect mouse ventral forebrain and floor plate but produce minor defects in zebrafish. Zebrafish have twoExpand
Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos.
The work presented here suggests that snail1 is involved in morphogenetic events during gastrulation, somitogenesis and development of the cephalic neural crest, and that no tail may act as a positive regulator of snail1. Expand
A homeobox gene essential for zebrafish notochord development
It is shown that floating head is the zebrafish homologue of Xnot, a homeobox gene expressed in the amphibian organizer and notochord, and it is proposed that flh regulates notochords precursor cell fate. Expand
A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development
Analysis of mutant phenotypes strongly supports the interpretation that ancestral gene functions partitioned spatially and temporally between Sox9 co-orthologs, and shows that sox9 helps regulate other early crest genes, including foxd3, sox10, snai1b and crestin. Expand