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Pungitus pungitius; Gasterosteus aculeatus; comparative genomics; transcriptome; substitution rate; adaptive evolution
Abstract:
Background: Comparative genomics approaches help to shed light on evolutionary processes that shape
differentiation between lineages. The nine-spined stickleback (Pungitius pungitius) is a closely related species of the
ecological ‘supermodel’ three-spined stickleback (Gasterosteus aculeatus). It is an emerging model system for evolutionary
biology research but has garnered less attention and lacks extensive genomic resources. To expand on these
resources and aid the study of sticklebacks in a phylogenetic framework, we characterized nine-spined stickleback
transcriptomes from brain and liver using deep sequencing.
Results: We obtained nearly eight thousand assembled transcripts, of which 3,091 were assigned as putative oneto-
one orthologs to genes found in the three-spined stickleback. These sequences were used for evaluating overall
differentiation and substitution rates between nine- and three-spined sticklebacks, and to identify genes that are
putatively evolving under positive selection. The synonymous substitution rate was estimated to be 7.1 × 10-9 per
site per year between the two species, and a total of 165 genes showed patterns of adaptive evolution in one or
both species. A few nine-spined stickleback contigs lacked an obvious ortholog in three-spined sticklebacks but
were found to match genes in other fish species, suggesting several gene losses within 13 million years since the
divergence of the two stickleback species. We identified 47 SNPs in 25 different genes that differentiate pond and
marine ecotypes. We also identified 468 microsatellites that could be further developed as genetic markers in
nine-spined sticklebacks.
Conclusion: With deep sequencing of nine-spined stickleback cDNA libraries, our study provides a significant
increase in the number of gene sequences and microsatellite markers for this species, and identifies a number of
genes showing patterns of adaptive evolution between nine- and three-spined sticklebacks. We also report several
candidate genes that might be involved in differential adaptation between marine and freshwater nine-spined
sticklebacks. This study provides a valuable resource for future studies aiming to identify candidate genes underlying
ecological adaptation in this and other stickleback species.
