The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, (https://github.com/yhw320/PanSyn), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.

地球生物基因组计划即将产生的海量基因组数据将开启比较基因组学的新时代，基因组同线性分析为此提供了重要的框架。分析基因组同线性是阐明基因组结构、调控模块/元件及其进化历史的重要一步。在这里，我们描述了 PanSyn（https://github.com/yhw320/PanSyn），这是最全面、最新的基因组同线性管道，提供分步说明和应用示例来演示其用法。 PanSyn 继承了现有流行工具的基本和高级功能，为基因组宏同线性分析和基因组结构的集成泛进化和调控分析提供了用户友好的、高度定制的方法，这在公共同线性软件或工具中尚不可用。 PanSyn 的优点包括：(i) 通过微合线基因和相关调控元件的功能分析进行先进的微合线分析； (ii) 全面的宏观同线性分析，包括从祖先到现存物种的核型进化的推断； (iii) 微同线性和宏观同线性的功能集成，用于基因组结构和调控模块的泛进化分析，以及与来自三维或四维基因组和 ENCODE 项目的外部功能基因组数据集的集成。 PanSyn 需要 Linux 环境和 Perl 编程语言的基本知识以及访问计算机集群的能力，特别是对于大规模基因组比较。我们的协议可以由有能力的研究生或博士后轻松实施，并且需要几天到几周的时间来执行数十到数百个基因组。 PanSyn 为整合进化和功能基因组学提供了最全面、最强大的工具。