CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation

BMC Genomics

Research Article

John MacKay¹  Sébastien Caron²  Julien Prunier³ 

[1] Department of Plant Sciences, University of Oxford, OX1 3RB, Oxford, UK;Centre for Forest Research, Université Laval, G1V 0A6, Quebec, QC, Canada;Institute for System and Integrative Biology (IBIS), Université Laval, G1V 0A6, Quebec, QC, Canada;Institute for System and Integrative Biology (IBIS), Université Laval, G1V 0A6, Quebec, QC, Canada;Centre for Forest Research, Université Laval, G1V 0A6, Quebec, QC, Canada;

关键词: Copy number variation;    Comparative genomic hybridization;    Non-model species;    Genomic structural variation;    Genome architecture;    Species hybridization;    Picea glauca;    Picea mariana;    Picea Engelmanni;    conifers;   

DOI  :  10.1186/s12864-016-3458-8

 received in 2016-10-28, accepted in 2016-12-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundCopy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid.ResultsWe discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs.ConclusionsThe approach we developed is of particular interest in non-model species lacking a reference genome. Our findings point to a role for CNVs in adaptation. Their reduced abundance in the hybrid may limit genetic variability and evolvability of hybrids. We propose that CNVs make a qualitatively distinct contribution to adaptation which could be important for short term change.

【 授权许可】

CC BY   
© The Author(s). 2017