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Open Access Research article

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization

Marina Panova1*, Tomas Johansson2, Björn Canbäck2, Johan Bentzer2, Magnus Alm Rosenblad3, Kerstin Johannesson1, Anders Tunlid2 and Carl André1

Author Affiliations

1 Department of Biological and Environmental Sciences - Tjärnö, Gothenburg University, Gothenburg, Sweden

2 Department of Biology, Microbial Ecology Group, Lund University, Lund, Sweden

3 Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden

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BMC Genomics 2014, 15:687  doi:10.1186/1471-2164-15-687

Published: 18 August 2014

Abstract

Background

Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis.

Results

We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis.

Conclusions

The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.

Keywords:
Comparative genomic hybridization; Oligonucleotide arrays; Littorina; Ecotypes; Genome evolution; Gene divergence