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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Mycology and Nematology Genetic Diversity and Biology Laboratory » Research » Publications at this Location » Publication #326392

Research Project: Systematics and Diagnostics of Emerging and Quarantine-Significant Plant Pathogenic Fungi

Location: Mycology and Nematology Genetic Diversity and Biology Laboratory

Title: SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species

Author
item Veltri, Daniel - Orise Fellow
item Wight, Martha - Animal And Plant Health Inspection Service (APHIS)
item Crouch, Joanne

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2016
Publication Date: 5/3/2016
Citation: Veltri, D., Wight, M.M., Crouch, J. 2016. SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species. Nucleic Acids Research. 44(W1):W41-W45.

Interpretive Summary: With the recent proliferation of new DNA sequencing technologies that are capable of generating massive datasets, the need for novel computer-based analytics becomes increasingly important for scientists. However, not all biological scientists have the computer programming training and experience needed to effectively make use of these powerful new resources. Many existing computer software pipelines assume that the user possesses knowledge of specialized programming languages that are implemented as text at the command line. In this research we developed a new, user-friendly computer program called SimpleSynteny that works through a web server using a graphical, point-and-click interface. The program functions to compare the order of genes along chromosome segments, and can be used to compare sections of the genomes of 2-10 different organisms simultaneously. The analysis is highly customizable, and yields a final graphical image that is suitable for inclusion in scientific journal publications, web sites, trade journals, or any venue where there is a need to summarize and communicate information about gene order. Although the SimpleSynteny pipeline is provided as a graphical web interface, it is built around a set of advanced computer tools and scripts that work in the background to make it a powerful platform for comparative genome analysis. This easily implemented and open-access computer program will be useful for scientists studying the genes and genomes of any living organism, including plants, microorganisms, insects, nematodes and animals.

Technical Abstract: Defining syntenic relationships among orthologous gene clusters is a frequent undertaking of biologists studying organismal evolution through comparative genomic approaches. With the increasing availability of genome data made possible through next-generation sequencing technology, there is a growing need for user-friendly tools capable of assessing synteny. Here we present SimpleSynteny, a new web-based platform capable of directly interrogating collinearity of local genomic neighbors across multiple species in a targeted manner. SimpleSynteny provides a pipeline for evaluating the synteny of a preselected set of gene targets across multiple organismal genomes. An emphasis has been placed on ease-of-use, and users are only required to submit FASTA files for their genomes and genes of interest. SimpleSynteny then guides the user through an iterative process of exploring and customizing genomes individually before combining them into a final high-resolution figure. Because the process is iterative, it allows the user to customize the organization of multiple contigs and incorporate knowledge from additional sources, rather than forcing complete dependence on the computational predictions. Additional tools are provided to help the user identify which contigs in a genome assembly contain gene targets and to optimize analyses of circular genomes. SimpleSynteny is freely available at: http://www.SimpleSynteny.com.