of Vitis vinifera using

Transcription

1 Characterisation of the pan-genome of Vitis vinifera using Next Generation Sequencing Plant Biology Europe June Copenhagen Gabriele Magris (gmagris@appliedgenomics.org)

2 Genetic variation in grapevine NorthAmerican grapevines Asian grapevines Vitis rupestris Vitis vinifera Vitis armata Dicot outcrossing perennial species

3 The pan-genome concept CORE GENOME Tettelin et al. Proc Natl Acad Sci USA, 2005 DISPENSABLE GENOME single-copy sequences multiple-copy sequences transposable elements transposable elements multiple sequences CNVs + PAVs Morgante et al. Curr Opin Pl Biol, 2007 all individuals only in some individuals

4 Structural variation calling reference sample deletion excision insertion Deletion Insertion V. vinifera V. armata V. rupestris V. vinifera V. armata V. rupestris V V A A R R V V A A R R

5 SV composition Deletions (7,856) Insertions (54,500) double strand breaks + defective repair events movement of transposable elements

6 SV location

7 Methylation before and after insertion Methylation Gypsy Copia LINE Pinot noir is one of the two parents of the highly homozygous PN40024 reference CG CHG CHH Pinot Noir PN40024 INS DEL GENOMIC REGION Reference Alternative Reference Pinot noir is one of the two parents of the highly homozygous PN40024 reference

8 Methylation before and after insertion Methylation Gypsy Copia LINE DNA DNA -2K -1K 0 +1K +2K -2K -1K 0 +1K +2K -2K -1K 0 +1K +2K haplotype CG CHG non- haplotype -2K -1K 0 +1K +2K -2K -1K 0 +1K +2K -2K -1K 0 +1K +2K -2K -1K 0 +1K +2K -2K -1K 0 +1K +2K Distance from insertion (bp)

9 Functional role of the dispensable genome RNAseq data Leaves Tendrils Berries Wine Cabernet Franc Rkatsiteli Sangiovese

10 Haplotype phasing & Allele-Specific Expression analysis Balanced bi-allelic RESEQUENCING OF F1 SELFED INDIVIDUALS HEROZYGOUS INSERTIONS Unbalanced bi-allelic + HET. SNPs GENOMIC REGION Monoallelic Cabernet Franc Rkatsiteli Sangiovese Maternal Paternal Adapted from Kukurba et al. (2014) Phase inference for SNPs and SVs allows to perform allele-specific analysis of gene in heterozygous individuals

11 SVs and Monoallelic Expression (MAE): berries colour Balanced bi-allelic Unbalanced bi-allelic VvmybA1c VvmybA1a Gret1 Adapted from Morgante et al. (2007) The insertion of the retroelement Gret1 in the promoter region of VvmybA1 was in strong association with the white-fruited phenotype Gret1 insertion Chr2:14,239,584-14,241,983 Monoallelic Adapted from Kukurba et al. (2014) Predicted gene Predicted transcripts cultivars Cabernet Franc Sangiovese (-) (+) (-) (+) ASE berries

12 SVs and Monoallelic Expression (MAE) Balanced bi-allelic DNA transposon insertion Chr16: Unbalanced bi-allelic Predicted gene Predicted transcripts in Rkatsiteli Monoallelic Adapted from Kukurba et al. (2014) Rkatsiteli allele-specific counts cultivars Sangiovese Rkastiteli (-) (+) berries /- -/+ genotype leaves leaves tendrils FPKM FPKM tendrils 43.3 berries 34.0 insertion increases of a myb transcription factor and changes gene structure Kishmish Vatkana genotype -/- -/+ +/+ leaves tendrils berries

13 SVs and Monoallelic Expression (MAE) Balanced bi-allelic Chr5: Copia LTR-retrotransposon insertion Unbalanced bi-allelic Monoallelic Adapted from Kukurba et al. (2014) Gene A (NB-LRR) Gene B (unknown protein) Predicted gene A Predicted gene B Allele-specific counts Cabernet Franc (-/+) Rkatsiteli (-/+) Sangiovese (-/-) (-) (+) (-) (+) (-) (-) berries leaves tendrils berries leaves tendrils insertion shuts down of 2 genes (under bidirectional promoter)

14 Conclusions Grapevine has a pan-genome composed by a core and a dispensable fraction The dispensable genome originates from deletions and insertions of transposable elements (). Cultivated varieties are highly heterozygous / hemizygous Transposable elements affect DNA methylation in flanking regions Spreading of heterochromatin marks is observed for all classes of Effects of different on local chromatin are variable and depend on insertionsite methylation status Structural variants affect allelic of flanking genes insertions may knock-out genes, contributing to genetic load insertions can produce new patterns of gene Grapevine chromosomes differ structurally as well as epigenetically

15 Acknowledgements Novabreed ERC-2011-ADG Fabio Marroni Sara Pinosio Michele Vidotto Alice Fornasiero Eleonora Paparelli Mirko Celii Rachel Schwope Aldo Tocci Mara Miculan Gabriele Di Gaspero Michele Morgante Federica Cattonaro Davide Scaglione Irena Jurman Emanuele De Paoli Nicoletta Felice Giusi Zaina