Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Panova, Marina, Johansson, Tomas, Canbäck, Björn, Bentzer, Johan, Rosenblad, Magnus Alm, Johannesson, Kerstin, Tunlid, Anders, André, Carl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148934/
https://www.ncbi.nlm.nih.gov/pubmed/25135785
http://dx.doi.org/10.1186/1471-2164-15-687
_version_ 1782332683818369024
author Panova, Marina
Johansson, Tomas
Canbäck, Björn
Bentzer, Johan
Rosenblad, Magnus Alm
Johannesson, Kerstin
Tunlid, Anders
André, Carl
author_facet Panova, Marina
Johansson, Tomas
Canbäck, Björn
Bentzer, Johan
Rosenblad, Magnus Alm
Johannesson, Kerstin
Tunlid, Anders
André, Carl
author_sort Panova, Marina
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4148934
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-41489342014-09-05 Species and gene divergence in Littorina snails detected by array comparative genomic hybridization Panova, Marina Johansson, Tomas Canbäck, Björn Bentzer, Johan Rosenblad, Magnus Alm Johannesson, Kerstin Tunlid, Anders André, Carl BMC Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-18 /pmc/articles/PMC4148934/ /pubmed/25135785 http://dx.doi.org/10.1186/1471-2164-15-687 Text en © Panova et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Panova, Marina
Johansson, Tomas
Canbäck, Björn
Bentzer, Johan
Rosenblad, Magnus Alm
Johannesson, Kerstin
Tunlid, Anders
André, Carl
Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
title Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
title_full Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
title_fullStr Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
title_full_unstemmed Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
title_short Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
title_sort species and gene divergence in littorina snails detected by array comparative genomic hybridization
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148934/
https://www.ncbi.nlm.nih.gov/pubmed/25135785
http://dx.doi.org/10.1186/1471-2164-15-687
work_keys_str_mv AT panovamarina speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT johanssontomas speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT canbackbjorn speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT bentzerjohan speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT rosenbladmagnusalm speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT johannessonkerstin speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT tunlidanders speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization
AT andrecarl speciesandgenedivergenceinlittorinasnailsdetectedbyarraycomparativegenomichybridization