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Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
- J. Catchen, A. Amores, Paul A Hohenlohe, W. Cresko, J. Postlethwait
- BiologyG3: Genes | Genomes | Genetics
- 1 August 2011
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.
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.
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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.