Abstract
BackgroundHigh-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data.ResultsIn this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates:1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D).Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices.2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats.ConclusionsOur experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies.SNiPlay is available at: http://sniplay.cirad.fr/.
Highlights
High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events in many plant species
The SNP pipeline section constitutes a freely accessible, user-friendly, customizable pipeline with which users can select the analysis steps to be performed, alternative programs being available at some steps
All pipeline results are accessible through a tabulated menu facilitating navigation, and examples are provided to familiarize users with the correct input and expected results (Figure 2C)
Summary
High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The combination of high-throughput re-sequencing and genotyping technologies with the availability of reference genome sequences allows Single Nucleotide Polymorphisms (SNPs) and insertion/deletion (indels) to be extensively characterized in many plant species [1,2,3], including in grapevine [4,5,6]. Two large projects have recently been launched: one to produce a SNP diversity map of the entire grapevine genome and the other to estimate linkage disequilibrium between SNPs in four genomic regions These grapevine projects are based on the present ability to obtain highthroughput sequences and subsequent SNP genotypes using the recently available complete genomic sequence. In this context, our objective was to conceive an original web-based tool, called SNiPlay, dedicated to polymorphism discovery and analysis in genetic diversity studies. It sends sequences and genotyping data into an integrative pipeline executing a series of modules in charge of various types of post-processing of the collected polymorphisms and associated genotyping data
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