Poster_MapSynteny_V04 - Automatizacion y Sistemas

MapSynteny: Software to create images of synteny
AC ,
CH ,
KA ,
Blair MW.
Sugarbeet and Bean Research Unit, Agricultural Research Service, United States Department of Agriculture, East Lansing, Michigan, United
States of America. 2 Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, K.U. Leuven, Heverlee,
MapSynteny is a macro in MS Excel® able to create images to show the relationship between genetic maps and large sequences
(scaffolds, chromosomes, BACs, etc.). Based on tab-delimited BLAST results and some formulas, a suitable image of syntenic
relationships or physical mapping can be obtained. This simple and versatile software can produce four types of outputs based
on traditional linkage map figures (Figure 1).
The software is written in Visual script of Microsoft Excel 2010®. The program uses BLAST result dataset in tab-delimited format
(BLAST Version 2.2.24). This dataset is the comparison between the markers sequences (defined in the program as: spB) and the
genome sequences of the comparison species (defined in the program as: spC). The linkage map (spB) could be imported using
the flat file obtained from MapDisto (Lorieux 2011)
Synteny between species
Macro-assembly of scaffolds
Many important crop plants have few genomic resources.
Those species are referred to as orphan crops. Often related
species are rich sources of genomic information. MapSynteny
is a useful tool to take advantage of this information.
Scaffolds are large DNA sequences produced by the next
generation sequence assembling processes. The Map
Synteny program can be used to graph linkage map and DNA
sequence relationships at the chromosome level (Figure 2).
The visualization with blocks is useful for macro-synteny
analysis. Large blocks allow visualization of poorly saturated
maps (Figure 1a). Small blocks can be used for a highly
saturated map (Figure 1b). Marker labels can also be added
(Figure 1c). The forth type is useful for micro-synteny
analyses and extrapolations (inSilico mapping) (Figure 1d).
Figure 2. Example in P. vulgaris of scaffold/ linkage map
This software and a tutorial is available at
The application of this program is shown in recent
publication by Galeano et al. (2009 and 2011).
Galeano CH, Fernandez AC, Franco N, Cichy K, McClean P,
Vanderleyden J. Blair MW. Saturation of an intra-gene pool
linkage map: towards a unified consensus linkage map for
fine mapping and synteny analysis in common bean. PLoS
ONE 2011 Dec 8.
Figure 1. Types of visualization. A) Large macro-synteny
blocks. B) Small macro-synteny blocks. C) Marker labeled
small synteny blocks. D) Micro-synteny relationship between
Phaseolus vulgaris and Glycine max.
Galeano CH, Fernandez AC, Gómez M, Blair MW. Single
strand conformation polymorphism based SNP and Indel
markers for genetic mapping and synteny analysis of common
bean (Phaseolus vulgaris L.). BMC Genomics. 2009 Dec
Lorieux M. 2011.

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