The forthcoming genome data generated by the Earth BioGenome Project opens up a new era of comparative genomics, whereby genome synteny analysis provides a necessity framework. Profiling of genome synteny between extant species or between ancestor and extant species represents an essential step for elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Based on the published algorithms or tools developed by our and other groups, we introduce a detailed protocol for the most comprehensive and up-to-date genome synteny pipeline (called PanSyn) and provides step-by-step instructions as well as application examples for demonstrating how to use it. The PanSyn pipeline includes three major modules (microsynteny analysis, macrosynteny analysis, and integrated micro & macro analysis). PanSyn inherits both basic and advanced functions from existing popular tools and also gains several additional advantages over many existing tools, including: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis with many features about inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny that allows for pan-evolutionary profiling of genome architecture, regulatory blocks as well as integration with external functional genomics datasets from 3D/4D genome and ENCODE projects. The PanSyn pipeline not only fills a gap in available software packages for a user-friendly, highly-customized tool for genome macrosynteny analysis but also allows for integrated pan-evolutionary and regulatory analysis of genome microsynteny and macrosynteny which are not yet available in public synteny software or tools.
Pan-evolutionary and regulatory genome architecture delineated by integrated macro- and microsynteny approach