A super-pangenome of the North American wild grape species

Abstract

Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. We generated a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the full resolution of genomic diversity among wild grape species from sequence to gene level. The pangenome graph captured genomic variation between haplotypes within a species and across the different species, and it accurately assessed the similarity of hybrids to their parents. The species selected to build the pangenome ensured a comprehensive representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis (pan-GWAS), we demonstrated the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of the adaptive traits from wild relatives, potentially accelerating crop breeding research.

Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

“…Therefore, predicting the type of change generated by these variants and their impact is crucial to better describe the genomic variability of the species (73, 74). Our results are consistent with previous studies (75) indicating that low-impact variants are generally more abundant in the core genome, whereas high and medium-impact variants tend to be more prevalent in the dispensable regions of the genome.…”

“…A greater proportion of genes in the variable regions of the pangenome exhibited rapid changes, with the core regions being the least influenced by the expansion and contraction of these gene families. The evolutionary trends revealed in our findings align with that of prior research (75), in which BGCs gene families are undergoing frequent changes in E. lata and P. minimum . Moreover, our results corroborated earlier observations indicating dynamic changes in the gene families associated with cellular transporters in P. minimum (3, 5).…”

“…By incorporating a comprehensive view of the genomic variation, which a single reference genome of a species cannot achieve, the pangenomes developed in this study are valuable tools for future forward genetic analyses like pangenome wide-association analysis (panGWAS; (75)) approaches, aimed at uncovering the genetic basis of specific pathogenic and virulence-related phenotypes, or metatranscriptomic profiling of gene expression of fungal populations during natural infections(93).…”

“…Genomic variants were extracted and categorized from the pangenome graph using vg deconstruct v1.40.0 (114) and bcftools v1.8 (111) following the protocol in https://github.com/noecochetel/North_American_Vitis_Pangenome (75). The functional impact of the different types of variants was predicted SnpEff v.5.1 (74).…”

“…The final estimation of family expansion and contraction was done with diamond v0.9.24.125 (130), mcl v14-137 (131) and CAFE v.5.0 (48) as described in (75). The estimated lambda parameter for P. minimum was 0.00416, for E. lata was 0.00251, and for N. parvum was 0.000975.…”