Plant pan-genomes

Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) have differentially shaped individual genomes, which differ among interfertile individuals of the same species. Unbalanced SVs are DNA sequences present only in some individuals. They are referred to as the dispensable genome because they are not necessary for survival. This aspect of genome biology is poorly investigated. How SVs are generated, purged or maintained in the population may have direct and indirect effects on phenotypic diversity. In addition to altering the DNA sequence of genes, promoters and chromosomes, SVs may also alter methylation patterns and chromatin structure, widening the effect of localized SVs to neighboring genomic regions.

Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) have differentially shaped individual genomes, which differ among interfertile individuals of the same species. Unbalanced SVs are DNA sequences present only in some individuals. They are referred to as the dispensable genome because they are not necessary for survival. This aspect of genome biology is poorly investigated. How SVs are generated, purged or maintained in the population may have direct and indirect effects on phenotypic diversity. In addition to altering the DNA sequence of genes, promoters and chromosomes, SVs may also alter methylation patterns and chromatin structure, widening the effect of localized SVs to neighboring genomic regions.

Marroni et al (2014) Structural variation and genome complexity: is dispensable really dispensable? Current Opinion in Plant Biology 18:31-36

Pinosio et al (2016) Characterization of the poplar pan-genome by genome-wide identification of structural variation. Molecular and Biology Evolution 33:2706-2719

Novabreed is an ERC Advanced Grant awarded to Michele Morgante for investigating intraspecific variation of plant genomes. Plant genomes are characterized by high levels of structural variation, consisting of small insertion/deletions, mostly due to the movement of transposable elements, large insertion/deletion (Copy Number Variants, CNVs), and chromosomal rearrangements. Thus, the genome of a single individual does not reflect the entire genomic complement of a species. We proposed the concept of plant Pan-genome, which includes a Core Genome common to all individuals of a species and a Dispensable Genome (DG) composed of DNA with presence/absence variation among individuals. Transposable systems usually account for a large fraction of the DG, but not for its entirety. Uncovering the composition, origin and structure of the DG represents a step forward towards an understanding of the processes generating genetic diversity and phenotypic variation in crops. Since the DG is a dynamic component of the pan genome, we want to assess if DG is a major contributor to genetic variation useful for breeding. This variation may include changes in gene content and cis-regulatory elements, as well as epigenetic marks and allele specific expression. Novabreed addresses these questions in two crop species, grapevine and corn. The Novabreed team focuses on de-novo assembly, structural variation and allele specific gene expression, DNA methylation and chromatin conformation analysis.

The final report is accessible at the cordis webpage

Funded by the European Research Council

 

Status: Novabreed, completed

 

List of the main dissemination activities

A TOCCI ABCD Salerno 2016

A TOCCI PHD Sissapresentation 2016

Fornasiero PhD presentation 2016

Fornasiero SIGA 2016

Fornasiero Tocci SIGA poster 2017

Gabbo_VIB-Ghent_poster2017

Marroni_IGApresentation_2016

Morgante_VeronaBiotechCongress_2017

Paparelli_SIGA_2017

Scaglione_PAGXXV_2017

Schwope_VIB-Ghent_poster2017

Schwope-EPIGEN_2016

Vidotto_IGApresentation_2016

Vidotto_SIGA_2017

Vidotto_TGAC-BITS_poster2015

Zapparoli_PhDpresentation_2016

Zapparoli_SIGA2016

Fornasiero_PBE2018

Magris_PBE2018

Schwope_PBE2018