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

Journal article
Authors Marina Panova
T. Johansson
B. Canbäck
J. Bentzer
Magnus Alm Rosenblad
Kerstin Johannesson
A. Tunlid
Carl André
Published in BMC Genomics
Volume 15
Pages 687
Publication year 2014
Published at Department of Biological and Environmental Sciences, Tjärnö Marine Biological Laboratory
Department of Chemistry and Molecular Biology
Pages 687
Language en
Links dx.doi.org/10.1186/1471-2164-15-687
Keywords Comparative genomic hybridization , Ecotypes , Gene divergence , Genome evolution , Littorina , Oligonucleotide arrays
Subject categories Marine ecology

Abstract

© 2014 Panova et al.; licensee BioMed Central Ltd. 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.

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