Genomics

Dataset Information

36

CNV in spruce


ABSTRACT: 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. Results: We 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. Overall design: CNV analysis of descendent and parental White Spruce (Picea glauca), Interior Spruce (Picea engelmannii x Picea glauca) and Black Spruce (Picea mariana)

INSTRUMENT(S): Agilent-052809 Genotypic_Custom_WhiteSpruce_4x180K_CGH_Array [Probe name version]

SUBMITTER: Julien Prunier 

PROVIDER: GSE92329 | GEO | 2016-12-14

SECONDARY ACCESSION(S): PRJNA357252

REPOSITORIES: GEO

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Publications

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

Prunier Julien J   Caron Sébastien S   MacKay John J  

BMC genomics 20170118 1


Copy 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  ...[more]

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