Organization, diversity, expression and evolutionary dynamics of the NB resistance gene family in grapevine and related species

Transcription

1 Organization, diversity, expression and evolutionary dynamics of the NB resistance gene family in grapevine and related species Rustenholz Camille Merdinoglu Didier

2 Downy Mildew (Plasmopara viticola) Hévin - INRA Hévin - INRA Bugaret - INRA Powdery Mildew (Erysiphe necator) Bugaret - INRA Botrytis (Botrytis cinerea) Phylloxera (Daktulosphaira vitifoliae) Grape Fanleaf Disease (Grape Fanleaf Virus) Bugaret - INRA Cartolaro - INRA Larignon - IFV Grape Trunk Diseases Demangeat - INRA

3 33 American Vitis species Vitis vinifera ca 2000 varieties 26 Asian Vitis species Sources of resistance among Vitis species

4 Scientific background NB genes, major resistance genes in plants

5 Scientific background NB genes, major resistance genes in plants

6 Scientific background Characterization of the NB gene family Structural organization The grapevine reference genome PN40024

7 Scientific background Characterization of the NB gene family Structural organization Expression analysis The grapevine reference genome PN40024 RNA-seq data from 59 experimental conditions

8 Scientific background Characterization of the NB gene family Structural organization Expression analysis The grapevine reference genome PN40024 RNA-seq data from 59 experimental conditions Diversity throughout the Vitis genus 54 re-sequenced genomes among cultivated and wild Vitis Listan Resseguier Berlandieri Riesling Riparia Savagnin Humagne

9 Structural organization Annotation of NB genes Total : 829

10 Structural organization Annotation of NB genes Total :

11 Structural organization Gene and cluster homology CNL Intra-chromosomic link Inter-chromosomic link Large segmental duplication events TNL

12 Expression analysis Expression analysis of NB genes Norm. FPKM 0 1 Average expression level lower than other gene families Leaves Downy mildew Powdery mildew Flowers Young berries Ripe berries

13 Expression analysis Expression analysis of NB genes Norm. FPKM 0 1 A Average expression level lower than other gene families B C 8 contrasted expression profiles D E F G H Leaves Downy mildew Powdery mildew Flowers Young berries Ripe berries

14 Expression analysis Expression analysis of NB genes Norm. FPKM 0 1 A Average expression level lower than other gene families B C 8 contrasted expression profiles D 211 NB genes constitutively expressed E F G H Leaves Downy mildew Powdery mildew Flowers Young berries Ripe berries

15 Expression analysis Expression analysis of NB genes Norm. FPKM 0 1 A Average expression level lower than other gene families B C 8 contrasted expression profiles D 211 NB genes constitutively expressed E F G 208 NB genes expressed during powdery mildew infection H Leaves Downy mildew Powdery mildew Flowers Young berries Ripe berries

16 Expression analysis Expression analysis of NB genes Inter-cluster correlation Intra-cluster correlation Average expression level lower than other gene families 8 contrasted expression profiles 211 NB genes expressed constitutively 208 NB genes expressed during a powdery mildew infection Distribution of the median expression correlation values between NB genes NB genes in the same cluster preferentially co-expressed

17 Diversity among genus Copy Number Variation at gene and cluster levels Cluster1 Cluster2 gene1 gene2 gene3 gene4 gene5 gene6 Reference genome Expected depth Accession reads Detected Duplicated Not detected Detected Duplicated Duplicated Gene level

18 Diversity among genus Copy Number Variation at gene and cluster levels Cluster1 Cluster2 gene1 gene2 gene3 gene4 gene5 gene6 Reference genome Expected depth Accession reads Detected Duplicated Not detected Detected Duplicated Duplicated Gene level Detected Duplicated Cluster level

19 Diversity among genus Copy Number Variation at gene and cluster levels V. vinifera V. sylvestris Other Vitis M. rotundifolia genes

20 Diversity among genus Copy Number Variation at gene and cluster levels V. vinifera V. sylvestris Other Vitis M. rotundifolia genes clusters

21 NB gene family in the grapevine genome TNL and CNL display contrasted distribution throughout the genome

22 NB gene family in the grapevine genome TNL and CNL display contrasted distribution throughout the genome Two large segmental duplication events for the TNL

23 NB gene family in the grapevine genome CNL and TNL display different evolution histories

24 NB gene family in the grapevine genome CNL and TNL display different evolution histories Many NB genes are specifically expressed during a powdery mildew infection

25 NB gene family in the grapevine genome CNL and TNL display different evolution histories Many NB genes are specifically expressed during a powdery mildew infection NB genes in the same cluster preferentially share the same expression profile

26 NB gene family in the grapevine genome CNL and TNL display different evolution histories NB genes clusters are ideal structures to trigger efficient responses against pathogen attacks

27 NB gene family in the grapevine genome CNL and TNL display different evolution histories NB genes clusters are ideal structures to trigger efficient responses against pathogen attacks Clusters are highly conserved among Vitis

28 NB gene family in the grapevine genome CNL and TNL display different evolution histories NB genes clusters are ideal structures to trigger efficient responses against pathogen attacks Clusters are highly conserved among Vitis Variations occur mostly at the gene level

29 NB gene family in the grapevine genome CNL and TNL display different evolution histories NB genes clusters are ideal structures to trigger efficient responses against pathogen attacks NB genes clusters are conserved factories able to catalyze rearrangements leading to adaptive novelties

30 Acknowledgements Didier Merdinoglu Pere Mestre Camille Rustenholz Sophie Blanc Gautier Arista Marie-Christine Le Paslier Dominique Brunel Maharaja Ponnaiah Patricia Faivre-Rampant Sébastien Aubourg Cécile Guichard Nadia Bentahar Anne-Françoise Adam-Blondon

31 Thanks for your attention.