quota_Anchor: a strand and whole genome duplication–aware collinear gene identification tool

Whole-genome duplication (WGD) events have occurred in numerous branches of the tree of life and are particularly prominent within plant lineages. The significant disparity in the frequency of WGD events across different species imposes specific technical requirements on collinearity alignment tools. Here we present quota_Anchor, a tool for conducting strand- and WGD-aware collinear gene identification. This tool was designed to strictly control the alignment depth and directionality of adjacent gene pairs when searching collinear blocks. We explored the ability of quota_Anchor to position WGD events and classify homologous genes based on different gene duplication modes. User-friendly modules were employed for generating high-quality plots, which revealed that relatively inverted gene pairs tend to exhibit less similar expression patterns than non-relatively inverted gene pairs. Notably, we determined that WGD-derived genes are more frequently associated with plant growth and developmental processes, while genes derived from tandem duplication and proximal duplication are often enriched in stress response and defense-related functions. The accuracy and flexibility of quota_Anchor make it a powerful toolkit for comparative genomics research.