Open Access Open Badges Research article

Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations

Maria Raffaella Ercolano1*, Adriana Sacco1, Francesca Ferriello1, Raffaella D’Alessandro1, Paola Tononi2, Alessandra Traini13, Amalia Barone1, Elisa Zago2, Maria Luisa Chiusano1, Genny Buson2, Massimo Delledonne2 and Luigi Frusciante1*

Author Affiliations

1 Department of Agriculture Sciences, University of Naples Federico II, Via Universita’ 100, 80055 Portici, Italy

2 Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy

3 Present address: East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK

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BMC Genomics 2014, 15:138  doi:10.1186/1471-2164-15-138

Published: 18 February 2014



Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits.


Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars.


The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.

Combined assembling; Fruit quality; NGS sequencing; SNPs; Solanum lycopersicum