Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.

植物基因组测序已大大增加，有些物种甚至具有多个高质量的参考版本。在进化时代，对进化枝特异性同源性推论和分析的需求增加了。在这里，我们提出了一种新颖的方法GeneTribe（https://chenym1.github.io/genetribe/），用于遗传相似基因组之间的同源性推断，该方法融合了基因共线性，并且在准确性方面比传统的基于序列相似性的方法表现出更好的性能。和可扩展性。Triticeae部落是典型的富含多倍体的进化枝，具有复杂的物种关系，其中包括许多重要的农作物，例如小麦，大麦和黑麦。我们建立了Triticeae-GeneTribe（http://wheat.cau.edu.cn/TGT/），这是一个同源数据库，通过整合12个Triticeae基因组和3个外联模型基因组，并实现了通用的分析和可视化功能。通过大共线性分析，我们能够构建一个精致的模型，说明小麦中4A-5A-7B染色体的结构重排是两个主要的易位事件。通过宏观和微观共线性分析，我们阐明了小麦春化基因同源物的复杂进化历史。Vrn2，是基因组易位，重复，多倍体化和基因丢失事件的综合结果。我们的工作为连接新兴的基因组装配体提供了有用的实践，并意识到植物中广泛的多倍体性，并将帮助研究人员有效地利用基因组序列资源。