Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors

BMC Genomics

Martien A M Groenen²  Richard P M A Crooijmans²  Mirte Bosse²  Laurent A F Frantz²  Hendrik-Jan Megens²  Ole Madsen²  Yogesh Paudel¹ 

[1] Current address: Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland;Animal Breeding and Genomics Centre, Wageningen University, Wageningen, 6700 AH, The Netherlands

关键词: Read depth method;    Next generation sequencing data;    Copy number variation;    Structural variation;    Speciation;   

Others  :  1177258
DOI  :  10.1186/s12864-015-1449-9

 received in 2014-08-14, accepted in 2015-03-09,  发布年份 2015

【 摘 要 】

Background

Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation.

Results

In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture.

Conclusion

We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation.

【 授权许可】

   
2015 Paudel et al.; licensee BioMed Central.

【 图 表 】

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