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

BACKGROUND: 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. 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. CONCLUSIONS: 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.

The functional resource of a gall-forming adelgid.

Interactions among shoots within plant modules could allow gall-insects to acquire resources from other plant parts near the feeding sites. As a result, nearby plant parts may act as a "functional resource", or extended resource base. We tested for functional interconections between galls and adjacent ungalled shoots in Adelges cooleyi Gil. (Homoptera: Adelgidae) on Picea engelmanni, Engelmann spruce. Observations of gall and surrounding shoot weights showed that gall weights were twice normal shoot weights, but that surrounding shoot weights were unaffected. Reducing photosynthate availability by covering galls or surrounding shoots with opaque cloth suggested that functional interconnections exist among them; covering galls reduced surrounding current-year ungalled shoot weight, and covering surrounding shoots reduced their weight even further, but neither covering treatment affected gall or gall-insect weight. These patterns suggest that surrounding shoots constitute an extended and flexibly utilized resource base for adelgid galls. Resources made available via functional interconnections appeared to be equally available throughout adelgid galls. No differences were found in gall-insect performance in parts of the gall closer to connections with surrounding shoots compared to more distantly-located gall-insects. Further studies are required to examine patterns of resource movement among unmanipulated galls and shoots. Functional resources may be common features of plant/gall-insect interactions, potentially playing an important role in gall-insect reproductive success and habitat selection.