CNV in spruce
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA357252 | ENA |
REPOSITORIES: ENA
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Project description: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.
2016-12-14 | GSE92329 | GEO
Project description:Following previous work, we extend the use of a reliable detection method to a wide progeny in white spruce in order to genetically map a maximum of inherited gene CNVs and linked those to phenotypic traits related to adaptation. We selected probes targeting 3911 genes likely in CNV in this progeny and performed genetic mapping for those harboring a 1:1 segregation. In addition, the link between gene CNVs and phenotypic variation was tested using budburst, budset and growth data for the same samples. Results: We genetically mapped 82 gene CNVs inherited from the previous generation and harboring the expected segregation ratio. This mapping allowed to delineate a few hotspots of CNV that are likely shared with other conifer species. In addition, individual-specific gene CNVs likely representing de novo variation supported the hypothesis of a purifying selection against copy losses. Finally, 29 gene CNVs were significantly associated to adaptive trait variation; 13 were located on the genetic map, including 4 located within hotspots of CNVs.
2017-07-26 | GSE101876 | GEO
Project description:Bisulfite treatment libraries were made to characterize DNA methylation of Norway spruce
2016-11-22 | GSE86983 | GEO
Project description:We constructed four PARE libraries for the identification of miRNA target genes in Norway spruce.
2015-09-02 | GSE65248 | GEO
Project description:In past studies the hypothesis of "self-toxicity of natural regeneration barriers of Spruce tianshan" were proposed, and verified that 3, 4-dihydroxyacetophenone (DHAP) contained in litter of Spruce Tianshan was the direct cause of population regeneration barriers.The molecular basis of DHAP-induced autotoxicity was explored through transcriptomic analysis of young roots of spruce tianshan treated with DHAP (3,4 dihydroxyacetophenone).
2021-01-01 | GSE160134 | GEO
Project description:White pine weevil is a major pest of conifers in North America, especially for Spruce trees. Constitutive defenses are important in understanding defense mechanisms because they constitute the initial barrier to attacks by weevils and other pests. Resistant and susceptible trees exhibit constitutive differences in spruce. To improve our knowledge of their genetic basis, we compared the constitutive expression levels of 17,825 genes between 20 resistant and 20 susceptible trees in interior spruce (Picea glauca).
2011-11-28 | GSE27476 | GEO
Project description:The absence of meiosis and sex are expected to lead to mutation accumulation in asexual (apomictic) plants. We have performed a double-validated analysis of copy number variation (CNV) on 10 biological replicates each of diploid sexual and diploid apomictic Boechera using a high-density (>700K) custom microarray, in order to compare mutation accumulation in the form of CNV between the transcribing regions of their genomes. The Boechera genome demonstrated higher levels of depleted compared to enriched CNV, irrespective of reproductive mode. Genome-wide patterns of CNV revealed four divergent lineages, three of which were characterized by both sexual and apomictic genotypes. Hence genome-wide CNV is reflective of at least 3 independent origins (i.e. expression) of apomixis from different sexual genetic backgrounds. CNV distributions for different families of transposable elements (TEs) were lineage specific, and a trend for enrichment in LINE/L1 and LTR/Copia elements in lineage 3 apomicts is consistent with sex and meiosis being mechanisms for purging genomic parasites. We hypothesize that significant overrepresentation of specific gene ontology classes (e.g. pollen-pistil interaction) in apomicts implies that gene enrichment could be an adaptive mechanism for genome stability in diploid apomicts by providing a polyploid-like system for buffering the effects of deleterious mutations.
2014-04-07 | GSE51596 | GEO