Micro-Syntenies Detected by MicSyn Make It Possible to Show Clearly The Vestige of Ancient WGDs of Plants

Synteny is the homologous region between or within chromosomes caused by genome duplication and speciation events. Particularly, detection of the synteny in plants is very important to understand plant genome because there were many WGD events. Thus, many programs such as MCScan and i-ADHoRe had been developed. Synteny tends to get smaller over time because of many evolutionary events such as recombination between chromosomes. However, there are not currently appropriate methods to identify the small synteny block (micro-synteny) containing, in generally, less than five genes. To detect micro-synteny precisely, a step to exclude the false-positive micro-synteny blocks is essential because small homologous regions were able to appear by chance. Thus, we developed MicSyn, a program to detect micro-synteny within/between genomes. The tool determines small homologous regions by DAGchainer then excludes the false-positive micro-synteny regions by the fisher’s exact test for the number of substitution and non-substitution in the synonymous site between corresponding genes. As an application of the program, we determined micro-syntenies within a genome for several plants and drew a heatmap (keatmap) with Ks values between paralogs determined from the micro-syntenies. The map more clearly shows a vestige of the eudicot hexaploidy event as well as the monocot tetraploidy event, in contrast to a map from relatively long syntenies.