Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations
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- 作者：Maria Raffaella Ercolano (25)
Adriana Sacco (25)
Francesca Ferriello (25)
Raffaella D’Alessandro (25)
Paola Tononi (26)
Alessandra Traini (25) (27)
Amalia Barone (25)
Elisa Zago (26)
Maria Luisa Chiusano (25)
Genny Buson (26)
Massimo Delledonne (26)
Luigi Frusciante (25) - 关键词：Combined assembling ; Fruit quality ; NGS sequencing ; SNPs ; Solanum lycopersicum
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：809 KB
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Adriana Sacco (25)
Francesca Ferriello (25)
Raffaella D’Alessandro (25)
Paola Tononi (26)
Alessandra Traini (25) (27)
Amalia Barone (25)
Elisa Zago (26)
Maria Luisa Chiusano (25)
Genny Buson (26)
Massimo Delledonne (26)
Luigi Frusciante (25)
25. Department of Agriculture Sciences, University of Naples Federico II, Via Universita-100, 80055, Portici, Italy
26. Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134, Verona, Italy
27. East Malling Research, New Road, East Malling, Kent, ME19 6BJ, UK - ISSN：1471-2164
文摘
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.