title: Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.
authors.affiliation: Department of Agriculture Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy. ercolano@unina.it.
authors.forename: Maria Raffaella
authors.initials: MR
authors.lastname: Ercolano
authors.forename: Adriana
authors.initials: A
authors.lastname: Sacco
authors.forename: Francesca
authors.initials: F
authors.lastname: Ferriello
authors.forename: Raffaella
authors.initials: R
authors.lastname: D'Alessandro
authors.forename: Paola
authors.initials: P
authors.lastname: Tononi
authors.forename: Alessandra
authors.initials: A
authors.lastname: Traini
authors.forename: Amalia
authors.initials: A
authors.lastname: Barone
authors.forename: Elisa
authors.initials: E
authors.lastname: Zago
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Chiusano
authors.forename: Genny
authors.initials: G
authors.lastname: Buson
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.forename: Luigi
authors.initials: L
authors.lastname: Frusciante
mesh_terms: D002874:Chromosome Mapping; D005638:Fruit / Q000378:metabolism; D017353:Gene Deletion; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013045:Species Specificity