Abstract
The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).
Highlights
The threespine stickleback (Gasterosteus aculeatus) is a small teleost fish widely distributed in both marine and freshwater habitats across the northern hemisphere [1,2]
Genes 2019, 10, 426 and assembled stickleback genomes appears desirable, given the wide geographic distribution of the species, and the extensive population structure and phenotypic and genetic diversity exhibited across its range
AUGUSTUS predictions were trained on zebrafish genes, SNAP was trained using the 2586 highly conserved vertebrate genes predicted by BUSCO [19,20], while GeneMark was self-trained
Summary
The threespine stickleback (Gasterosteus aculeatus) is a small teleost fish widely distributed in both marine and freshwater habitats across the northern hemisphere [1,2]. Such research has been facilitated by the release in 2006 of a high-quality reference genome assembled from Sanger-sequenced plasmids, fosmids, and BAC clones derived from a freshwater individual from Alaska [6]. This genome, hereafter called the “reference genome”, has a total ungapped size of 447 Mb, of which 95% has been anchored to the 21 chromosomes through three rounds of re-assembly of the original sequence scaffolds or contigs [7,8,9]. Genes 2019, 10, 426 and assembled stickleback genomes appears desirable, given the wide geographic distribution of the species, and the extensive population structure and phenotypic and genetic diversity exhibited across its range. We report the generation and annotation of four de novo stickleback genome assemblies
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