BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing.

Numerous genes that determine the outcome of plant-pathogen interactions are currently being discovered and include, for example, immune receptors, susceptibility factors and pathogen effectors and their host targets. Target enrichment sequencing provides a means to preferentially resequence these genes of interest without the need to first generate a genotype-specific genome assembly. The Basic Local Alignment Search Tool (BLAST), in combination with the here developed BLASTmap, can be used to design probes that specifically target such gene(s), either by using the target species or the closest related genus as a reference. BLAST is a ubiquitous tool in biological sequence analysis and a multitude of programs are available for the visualization of BLAST alignments. However, there are currently no dedicated programs for visual comparison of large-scale BLAST output attributes such as bit score. The need to quickly and efficiently compare many thousands of BLAST results led to the development of BLASTmap, an interactive web application created using the Shiny R package, customized for clustering and viewing BLAST results as an interactive heat map. Here we show an example of how BLASTmap was successfully applied to analyze custom DNA/RNA probe sequences and to visually determine that four probes are sufficient for the specific yet inclusive enrichment of the potato R2 disease resistance gene family.

[1]  Bang Wong,et al.  Points of view: Into the third dimension , 2012, Nature Methods.

[2]  Guangfeng Song,et al.  HIV-1, human interaction database: current status and new features , 2014, Nucleic Acids Res..

[3]  Derek J. Van Booven,et al.  HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline , 2014, Source Code for Biology and Medicine.

[4]  Surendra Kumar,et al.  BLAST output visualization in the new sequencing era , 2014, Briefings Bioinform..

[5]  Jonathan D. G. Jones,et al.  Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations , 2013, The Plant journal : for cell and molecular biology.

[6]  Jonathan D. G. Jones,et al.  Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing , 2016, Nature Biotechnology.

[7]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[8]  Burkhard Rost,et al.  HeatMapViewer: interactive display of 2D data in biology , 2014, F1000Research.

[9]  Jaak Vilo,et al.  ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap , 2015, Nucleic Acids Res..

[10]  K. McLean,et al.  A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages , 2015, BMC Plant Biology.

[11]  M. Spector,et al.  A comparative analysis of exome capture , 2011, Genome Biology.

[12]  P. Bentzen,et al.  Ultra‐deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata) , 2014, Molecular ecology resources.

[13]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[14]  D. Melton,et al.  Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. , 1984, Nucleic acids research.

[15]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[16]  G. Bryan,et al.  Utilizing “Omic” Technologies to Identify and Prioritize Novel Sources of Resistance to the Oomycete Pathogen Phytophthora infestans in Potato Germplasm Collections , 2016, Front. Plant Sci..

[17]  Jonathan D. G. Jones,et al.  Targeted capture and sequencing of gene-sized DNA molecules. , 2016, BioTechniques.