Applying AnchorWave to Address Plant Genome Alignment

Background

Recent technological advancements lead to a huge number of genomes being sequenced. We propose to unlock the secret of genome by genome comparison. Genome alignment is a fundamental step of genomics analysis, providing a set of intermediate results for downstream analysis. However, with previous genome alignment tools, it is difficult to deal with long (> 50 bp) inserts and deletions (InDels) and whole-genome duplication (WGD) that have taken place between two plant genomes. In addition, plants have a lower gene length and more complex structure variations and chromosome rearrangement than mammals. Software developed by the mammal research community cannot sensitively and accurately align plant genomes. This protocol illustrates AnchorWave, which can deal well with dispersed repeats, active TEs, high sequence diversity, and WGD (Song et al., 2022). AnchorWave combines a collinear region identification approach with a 2-piece affine gap cost global alignment strategy. This software firstly identifies collinear regions with conserved anchors and then performs base-pair resolved global sequence alignment for each anchor and inter-anchor region. AnchorWave provides a significant improvement for base-pair-resolved plant genome alignment.