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

Panova, Marina; Johansson, Tomas LU ; Canbäck, Björn LU ; Bentzer, Johan LU ; Rosenblad, Magnus Alm; Johannesson, Kerstin; Tunlid, Anders LU and Andre, Carl (2014) In BMC Genomics 15.
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"... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Comparative genomic hybridization, Oligonucleotide arrays, Littorina, Ecotypes, Genome evolution, Gene divergence
in
BMC Genomics
volume
15
publisher
BioMed Central
external identifiers
  • wos:000341037200001
  • scopus:84906829147
ISSN
1471-2164
DOI
10.1186/1471-2164-15-687
project
BECC
language
English
LU publication?
yes
id
30255f97-c1ab-4e30-b780-1258d3846ab5 (old id 4649031)
date added to LUP
2014-09-24 09:28:09
date last changed
2017-01-01 06:17:29
@article{30255f97-c1ab-4e30-b780-1258d3846ab5,
  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.},
  articleno    = {687},
  author       = {Panova, Marina and Johansson, Tomas and Canbäck, Björn and Bentzer, Johan and Rosenblad, Magnus Alm and Johannesson, Kerstin and Tunlid, Anders and Andre, Carl},
  issn         = {1471-2164},
  keyword      = {Comparative genomic hybridization,Oligonucleotide arrays,Littorina,Ecotypes,Genome evolution,Gene divergence},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Genomics},
  title        = {Species and gene divergence in Littorina snails detected by array comparative genomic hybridization},
  url          = {http://dx.doi.org/10.1186/1471-2164-15-687},
  volume       = {15},
  year         = {2014},
}