Structural variation, movement of transposable elements and epigenetics.
Genome research at IGA focuses on the investigation of mechanisms that generate structural, genetic, regulatory and epigenetic variation exploitable in agriculture
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
The Morgante lab has a long-lasting commitment to studying the dynamics of transposable elements in plants and how they shaped the genome of crop species. In addition to characterizing this portion of the genome in the frame of collaborative sequencing projects, Morgante’s lab has recently published papers on this specific subject in melon, olive, and conifers, extending to other crops past groundbreaking findings in corn.
Sanseverino et al (2015) Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome. Molecular Biology and Evolution 32(10):2760-2774.
Barghini et al (2015) LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Research 22(1):91-100
Zuccolo et al (2015) The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution. Gene 568(1):89-99
Epigenetic modifications are vital for allowing long-lived and/or complex organisms to adapt to challenging environments. IGA has recently specialized in whole-genome mapping of DNA methylation, chromatin modifications and chromatin interactions. There is considerable excitement for the impact of epigenetics on agriculture, in particular in perennial crops.
EPIGEN is a flagship project funded by the National Research Council of Italy. The goal of EPIGEN is to understand how epigenetic mechanisms regulate biological processes, determine phenotypic variation and contribute to the onset and the progression of human diseases (see an EPIGEN short movie for a brief description of what epigenetic is about).
The EPIGEN team is highly multidisciplinary and involves 70 Italian research groups. Under investigation are a variety of organisms ranging from animals (humans, mouse) to plants (maize, grapevine, Arabidopsis). In humans, topics include epigenetic control of cellular identity and human cancer, and epigenetic drugs for leukemia and muscular dystrophy. In plants, IGA is studying the role of transposons as mediators of epigenetic variation in both grape and maize.
IGA is the centralized EPIGEN platform for Next Generation Sequencing, serving the whole partnership. Two Illumina Hi-Seq 2500 sequencers are dedicated to the project partners. Centralization of NGS allows reduction of costs, optimization of equipment use and efficient transfer of the data to the project’s bioinformatics platform. Technologies accessible through the EPIGEN NGS Service platform include Whole Genome Shotgun Bisulfite Sequencing, Bisulfite conversion followed by capture and sequencing, MeDIP, ChIP-sequencing, RNA sequencing, and small RNA sequencing.
EPIGEN – Flagship Project Epigenomics
Funded by the National Research Council Italy
The transcriptional regulatory structure of plant genomes is still relatively unexplored. We are using model genetic systems to analyze factors that influence expression variation in plants.
A first example was provided by the analysis of berry transcriptomes during fruit development and ripening in 10 grape sequenced varieties, which showed the association of gene expression variation with genetic and epigenetic properties.
Magris et al (2019) Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties. The Plant Journal 99:895-909
A second study made use of Hi-C, ChIP-seq and ATAC-seq to measure how chromatin features correlates to the expression of 31 845 grapevine genes. This study provided an inventory of intergenic open chromatin regions that can be considered potential candidates for cis-regulatory regions in the grapevine genome.
Schwope et al (2021) Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. The Plant Journal 107(6):1631-1647
Funded by the Italian Ministry of Agriculture (MIPAAF), project VIGNETO
Phenotypic variation within a cultivated species may arise from a multitude of genetic mechanisms. Fruit colour is one of the most conspicuous plant traits that attract human attention. Thus, genetic mutations that alter genes involved in fruit pigmentation are more frequently retained than mutations in any other trait. Unsurprisingly, sequencing of fruit colour variants reveals genetic architecture and mutational mechanisms of unexpected complexity.
Yellow fleshed peach
The degradation of carotenoids causes the peach flesh to exhibit white colour. Loss-of-function variants at a gene encoding the carotenoid cleavage dioxygenase 4 (PpCCD4) account for the difference between white and yellow fleshed varieties. Yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions. All these mutations, despite being located within the transcribed portion of the gene, resulted in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a plant gene for which humans, in their quest to diversify fruit appearance and qualitative characteristics of food, unconsciously selected multiple mutations resulting from a variety of mechanisms.
Falchi et al (2013) Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach. Plant Journal 76(2):175-187