PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data

Marco Cirilli; Tiziano Flati; Silvia Gioiosa; Ilario Tagliaferri; Angelo Ciacciulli; Zhongshan Gao; Stefano Gattolin; Filippo Geuna; Francesco Maggi; Paolo Bottoni; Laura Rossini; Daniele Bassi; Tiziana Castrignanò; Giovanni Chillemi

doi:10.1093/pcp/pcx183

PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data

Plant Cell Physiol. 2018 Jan 1;59(1):e2. doi: 10.1093/pcp/pcx183.

Authors

Affiliations

¹ Department of Agricultural Science (DISAA), University of Milan, Milan, Italy.
² Cineca, HPC High Performance Computing Department, Rome, Italy.
³ IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy.
⁴ Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.
⁵ Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy.
⁶ Department of Computer Science, 'Sapienza' University of Rome, Via Salaria 113, 00198 Rome, Italy.

PMID: 29216377
DOI: 10.1093/pcp/pcx183

Abstract

Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data.

Keywords: Database; Genome resequencing; Genomic variants; NGS; Peach.

MeSH terms

Computational Biology / methods*
Data Mining / methods
Databases, Genetic
Genetic Variation*
Genome, Plant / genetics*
High-Throughput Nucleotide Sequencing / methods
Internet
Phylogeny
Polymorphism, Single Nucleotide
Prunus persica / classification
Prunus persica / genetics*
Rosaceae / classification
Rosaceae / genetics