title: Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.
abstract: Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.
authors: Istituto di Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy Istituto di Genomica Applicata (IGA), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.
authors: Sara
authors: S
authors: Pinosio
authors: Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.
authors: Stefania
authors: S
authors: Giacomello
authors: INRA US 1279 EPGV/CEA/CNG, Evry, France.
authors: Patricia
authors: P
authors: Faivre-Rampant
authors: School of Biological Sciences, University of Southampton, Southampton, United Kingdom.
authors: Gail
authors: G
authors: Taylor
authors: INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.
authors: Veronique
authors: V
authors: Jorge
authors: INRA US 1279 EPGV/CEA/CNG, Evry, France.
authors: Marie Christine
authors: MC
authors: Le Paslier
authors: Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.
authors: Giusi
authors: G
authors: Zaina
authors: INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.
authors: Catherine
authors: C
authors: Bastien
authors: IGA Technology Services (IGATS), Udine, Italy.
authors: Federica
authors: F
authors: Cattonaro
authors: Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.
authors: Fabio
authors: F
authors: Marroni
authors: Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.
authors: Michele
authors: M
authors: Morgante
mesh_terms: D056915:DNA Copy Number Variations; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D054643:INDEL Mutation; D032107:Populus / Q000235:genetics*; D013329:Structure-Activity Relationship
keywords: pan-genome; poplar; structural variation; transposable elements