We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition-duplication (tr-d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr-d events and had a higher chance of being expressed. We also found an enrichment of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history.

中文翻译：

---

十字花科家族内的基因转座-复制景观。

我们开发了CLfinder-OrthNet管道，该管道可检测多个紧密相关的基因组之间的共线性，找到直系同源基因组，并将每个直系同源物组的进化历史编码为一个有代表性的网络（OrthNet）。使用基于网络拓扑的搜索，我们从六个十字花科基因组中识别出的17,432个中，识别出1,394个OrthNet，其中包括基因转座-复制（tr-d）事件。十字花科基因组子集共享的tr-d的出现反映了基因组及其重复内容之间的差异时间。大多数tr-d事件导致重复基因座中的开放阅读框（ORF）被截短。但是，具有完整ORF的重复项比随机事件预期的发生率要高得多。这些来自较旧的tr-d事件，被表达的可能性更高。我们还发现了丰富的tr-d事件，而原始位点和重复位点之间的基因间序列保守性完全丧失。最后，我们确定了在六个十字花科基因组中的两个极端植物中唯一发现的tr-d事件，包括与它们的适应性进化相关的盐耐受性32和锌转运蛋白3的tr-d。CLfinder-OrthNet提供了一个灵活的工具包，可以比较基因顺序，将直向同源物之间的进化路径可视化为网络，以及识别共享进化史的基因位点。我们鉴定了在六个十字花科基因组中的两个极端植物中唯一发现的tr-d事件，包括与它们的适应性进化相关的盐耐性32和ZINC TRANSPORTER 3的tr-d。CLfinder-OrthNet提供了一个灵活的工具包，用于比较基因顺序，将直向同源物之间的进化路径可视化为网络，以及识别共享进化史的基因位点。我们鉴定了在六个十字花科基因组中的两个极端植物中唯一发现的tr-d事件，包括与它们的适应性进化相关的盐耐性32和ZINC TRANSPORTER 3的tr-d。CLfinder-OrthNet提供了一个灵活的工具包，用于比较基因顺序，将直向同源物之间的进化路径可视化为网络，以及识别共享进化史的基因位点。