Journal article
CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation
- Abstract:
- 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 assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid.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.The 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
Actions
Access Document
- Files:
-
-
(Preview, Version of record, pdf, 1.1MB, Terms of use)
-
- Publisher copy:
- 10.1186/s12864-016-3458-8
Authors
- Publisher:
- BioMed Central
- Journal:
- BMC Genomics More from this journal
- Volume:
- 18
- Issue:
- 1
- Article number:
- 97
- Publication date:
- 2017-01-18
- Acceptance date:
- 2016-12-22
- DOI:
- EISSN:
-
1471-2164
- Pmid:
-
28100184
- Language:
-
English
- Keywords:
- Pubs id:
-
pubs:675614
- UUID:
-
uuid:aecb93af-ca8f-4344-9e9a-792f030e2bce
- Local pid:
-
pubs:675614
- Source identifiers:
-
675614
- Deposit date:
-
2019-06-27
Terms of use
- Copyright holder:
- Prunier et al
- Copyright date:
- 2017
- Notes:
- © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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
- Licence:
- CC Attribution (CC BY)
If you are the owner of this record, you can report an update to it here: Report update to this record