MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species

Abstract

Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies.

Keywords: detection; multiple synteny; plant; visualization; webtool.

Figure 1

Architecture of MultiSyn webtool. Notes: Architecture shows two configurations, the client-side and server-side. The client-side provides the interface for input and output for the MultiSyn user using HTML5 and jQuery. The user performs an analysis to enter the proteins (pep) and annotation (simplified BED) file or select species, chromosome, locus in a Web browser. The server-side consists of the core script for processing in connection with the webtool and for the determination and visualization of synteny. In the core script using python, phylip, shell script to connect the user to enter data and other utilities to detect and visualize synteny treated as a result. Input information is stored in the user information for the file DB and the analysis conducted provides the final output product.

Figure 2

Progress of MultiSyn in webtool. Notes: The yellow progress status in (A) is also presented in steps 2 and step 3 of the homepage. A: Step 1: users can upload their protein file (pep format) and annotation file (simplified bed format) or select species and set the range of chromosomal region of interest. B: Step 2: select species to compare. After species selection, synteny among user’s data and species are determined by MCScanX. C: Step 3: select pivot chromosome to align species and set colors for species and specific genes. D: Step 4: download the plot or modify the plot by going back to previous.

Figure 3

Multiple synteny plot of PSY1. Notes: PSY1 encodes first dedicated step in lycopene biosynthesis, showing an expansion of genes by whole-genome triplication, neofunctionalization. The synteny of PSY1 regions (chromosome 3, 8.6 Mb ~ 9.0 Mb) are aligned with B. rapa (BR), G. max (GM), S. bicolor (SB), S. tuberosum (ST), and V. vinifera (VV). Red and blue lines mean same and opposite directional alignment, respectively. Magenta, blue, purple, cyan, and green boxes represent PSY1 (phytoene synthase, Solyc03g031860.2), ARF8 (Auxin response factor 8, Solyc03g031970.2), AEC (Auxin efflux carrier family protein, Solyc03g031990.2), HMGCR (3-hydroxy-3-methylglutaryl-coenzyme A, Solyc03g032010.2), and UBQLN (Ubiquilin-1, 4, Solyc03g032160.2), respectively.