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

• Published in: BMC plant biology Vol. 24; no. 1; p. 88
• Main Authors: Aversano, Riccardo, Iovene, Marina, Esposito, Salvatore, L'Abbate, Alberto, Villano, Clizia, Di Serio, Ermanno, Cardone, Maria Francesca, Bergamini, Carlo, Cigliano, Riccardo Aiese, D'Amelia, Vincenzo, Frusciante, Luigi, Carputo, Domenico
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 06.02.2024; BioMed Central; BMC
• Subjects: Amino acids; Analysis; Annotations; Biosynthesis; Chromosomes; Cloning; Comparative analysis; Copy number; Crop yields; Cultivars; Cultivation; Deoxyribonucleic acid; DNA; DNA Transposable Elements - genetics; DNA, Satellite; Fruit cultivation; Fruits; Gene sequencing; Genes; Genetic aspects; Genomes; Genomics; Grapes; Humans; Management; Nucleotide sequence; Plant Breeding; Production management; Repetitive elements; Resequencing; Satellite DNA; Variant calling; Vitaceae; Vitis - genetics; Vitis vinifera L; Italy; Satellite DNA; Vitis vinifera L; Resequencing; Repetitive elements; Variant calling
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-024-04778-2

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.