Abstract
Reconstructing synteny blocks is an essential step in comparative genomics studies. Different methods were already developed to answer various needs such as genome (re-)annotation, identification of duplicated regions and whole genome duplication events or estimation of rearrangement rates. We present SynChro, a tool that reconstructs synteny blocks between pairwise comparisons of multiple genomes. SynChro is based on a simple algorithm that computes Reciprocal Best-Hits (RBH) to reconstruct the backbones of the synteny blocks and then automatically completes these blocks with non-RBH syntenic homologs. This approach has two main advantages: (i) synteny block reconstruction is fast (feasible on a desk computer for large eukaryotic genomes such as human) and (ii) synteny block reconstruction is straightforward as all steps are integrated (no need to run Blast or TribeMCL prior to reconstruction) and there is only one parameter to set up, the synteny block stringency . Benchmarks on three pairwise comparisons of genomes, representing three different levels of synteny conservation (Human/Mouse, Human/Zebra Finch and Human/Zebrafish) show that Synchro runs faster and performs at least as well as two other commonly used and more sophisticated tools (MCScanX and i-ADHoRe). In addition, SynChro provides the user with a rich set of graphical outputs including dotplots, chromosome paintings and detailed synteny maps to visualize synteny blocks with all homology relationships and synteny breakpoints with all included genetic features. SynChro is freely available under the BSD license at http://www.lcqb.upmc.fr/CHROnicle/SynChro.html.
Highlights
Synteny block reconstruction consists on the identification of a series of homologous genes whose order is conserved between two genomes
For very distantly related genomes, detection of synteny conservation requires the development of statistical models or the construction of synteny profiles obtained from different genomes [5,6,7]
For genomes sharing intermediate phylogenetic proximity, protein-coding genes may have retained enough sequence similarity and physical collinearity along chromosomes to allow synteny block reconstruction which can help infering the history of chromosomal rearrangements and the structure of ancestral genomes [10]
Summary
Synteny block reconstruction consists on the identification of a series of homologous genes whose order is conserved between two (or more) genomes. For very distantly related genomes, detection of synteny conservation requires the development of statistical models or the construction of synteny profiles obtained from different genomes [5,6,7]. In this case, synteny can help to the gene annotation process based on conservation of gene clusters [6,8] or can be used to estimate the number of whole genome duplication events [9]. For genomes sharing intermediate phylogenetic proximity, protein-coding genes may have retained enough sequence similarity and physical collinearity along chromosomes to allow synteny block reconstruction which can help infering the history of chromosomal rearrangements and the structure of ancestral genomes [10]
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