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CINECA, Genomic pipelines: Peach-Var DB

TYPE
Big Data Platforms (PaaS), Infrastructure Access
REGION
Italy
LANGUAGE
English

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.

SERVICE DESCRIPTION

The ‘Search’ menu provides several tools to explore genomic variants in PeachVar-DB. All the query output can be easily downloaded in both text and VCF format, allowing users to perform downstream analysis on a customized subset of variants. Whenever a genetic variant present in PeachVar-DB falls into a known genetic marker interval, the output table displays a button named ‘Genetic Marker’. The ‘Search by region’ function runs the query on the genomic co-ordinates specified by the user. Furthermore, the selected genomic windows are hyperlinked to the ‘Synteny Viewer’ tool available under GDR, allowing the visualization of genome conservation and rearrangement patterns. Users interested in the variants occurring on a specific gene can use the ‘Search by gene ID’ function to retrieve this information. Genes can be queried either by typing their name (based on the JGI nomenclature for peach genome v2.1 transcript annotations) or through the provided full list of transcripts. The results can be visualized via JBrowse and are linked to a detailed functional annotation description in Phytozome.
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 NGSgenerated 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. PeachVar-DB is the first database specifically dedicated to the storing, sharing and querying of peach genomic variations identified by the analysis of WGRS data from a panel of peach and wild relative accessions. The final results presented in this database rely on the identification of a highly reliable and accurate consensus call-set, consisting of >5 millions peach genetic variants, detected by merging the results of multiple variant-calling algorithms. Genomic variants can be quickly and easily explored, visualized and retrieved by using a well-assorted set of tools ranging from BLAST similarity search to the JBrowse Genome Browser. In turn, this information can be used for a range of purposes, including germplasm characterization, SNP array design and experimental design for functional and evolutionary genomics.
The linking of genomic data with phenotypic traits remains one of the major challenges for crop improvement. In this perspective, the inclusion of phenotypic information has not been dictated solely by the need for a basic description of the input dataset, but rather it represents a first step towards the creation of a more comprehensive database devoted to functional genomics, which will be able to handle and analyze a plethora of both genomic and phenomic data.

CASE EXAMPLES

Peach is an economically important fruit tree species of temperate region. The pipeline can be used by researchers to:
leverage of basic knowledge in this species;
increase the efficiency of breeding activities;

LINKS

SERVICE OFFERED BY

MEMBER
CINECA
TYPE
DIH
COUNTRY
Italy

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