Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina

Abstract

Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.

Keywords: Repetitive elements; Resequencing; Satellite DNA; Variant calling; Vitis vinifera L.

Fig. 1

a SNP distribution and abundance in Aglianico (left) and Falanghina (right) genomes relative to the Pinot Noir reference genome (PN40024_12X.v2). From the inner circle the plots show: chromosome size; GC content in 100 Kbp bins; gene content in 100 Kbp bins; SNPs/INDELs in 100 Kbp bins; GAIN in 100 Kbp bins; LOSS in 100 Kbp bins; Duplications in 100 Kbp bins. b Gene Ontology Enrichment Analysis (GOEA) results performed on AGL (left) and FAL (right) genes harboring missense mutations and genes including polymorphisms altering CDS length. Enriched terms related to biological process are reported. c Summary of high-impact variants found in AGL and FAL within enzyme-coding genes involved in the terpenoids (TPS, terpene synthase), GLVs (MCC, Methylcrotonyl-CoA carboxylase), BCAA (AAT, alcohol acetyltransferase) and phenylpropanoid (PAL, phenylalanine ammonia-lyase; 4CL, 4-coumarate: CoA ligase; CHS, chalcone synthase) biosynthetic pathways. * stands for stop codon

Fig. 2

a Principal Component Analysis (PCA) of 23 V. vinifera whole-genome resequenced genotypes by [9]. The samples selected in this study to perform the repeatome comparative analysis are red-dotted, namely Adjaruli Tetri (ADJ), Aglianico (AGL), Airen (ARN), Chardonnay (CHR), Chasselas Blanc (CHS), Enantio (ENT), Falanghina (FAL), Gamay Noir (GMY), Greco Bianco (GRC), Lambrusco di Sorbara (LBS), Mgaloblishvili (MGL), Mtsvane Kachuri (MTS), Muscat of Alexandria (MSL), Muscat Petits Grains Blanc (MSP), Nebbiolo (NBL), Nosiola (NSL), Ojaleshi (OJL), Pinot Noir (PNT), Schiava Gentile (SCH), Semillon (SML), Sultanina (SLT), Terbash (TRB), Tschvediansis Tetra (TSC). b Proportion of DNA repetitive sequences identified. (C) PCA of different grape cultivars based on their repeats landscape. Clustering was performed with K-means and colors were assigned according to the cluster. c Boxplots showing the most significant and enriched families of repeats in clusters 1 and 2 of PCA shown in (c). Wilcoxon test results are shown for each repeat class

Fig. 3

Fluorescence in situ hybridization (FISH) of VvSat67 (green signals) and VvSat214 (red) repeats on the mitotic metaphase chromosomes (stained in blue) of different grape accessions: (A1–3) Falanghina (FAL); (B1–3) Aglianico (AGL); (C1–3) Greco Bianco (GRC). Arrowheads point to VvSat67 signals (greens) that are located independently from VvSat214, on different chromosomes. Arrows (in A1–3 and B1–3) point to VvSat67 and VvSat214 signals that co-localize on the same chromosome(s). Scale bars = 5 μm

Fig. 4

FISH mapping of VvSat67 and VvSat214 repeats on the meiotic pachytene chromosome of Falanghina (FAL), Aglianico (AGL) and Greco Bianco (GRC) grapes. Black and white images of DAPI stained pachytene chromosomes of (A1) FAL; (B1) AGL; and (B1) GRC. Middle column: Signals derived from VvSat67 (green) and VvSat214 (red). Third column: Merged images. Arrowheads point to VvSat214 signals (in red) that are located on a different chromosome from VvSat67 signals (green). Arrows (in A1–3 and B1–3) point to VvSat67 and VvSat214 signals that co-localize on the same chromosome. Scale bars = 5 μm