Open AccessAnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication
Author(s) -
Baoxing Song,
Santiago Marco-Sola,
Miquel Moretó,
Lynn Johnson,
Edward S. Buckler,
Michelle C. Stitzer
Publication year - 2021
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2113075119
Subject(s) - genome , indel , biology , structural variation , genetics , gene duplication , computational biology , genome evolution , bacterial genome size , transposable element , comparative genomics , indel mutation , genomics , evolutionary biology , gene , single nucleotide polymorphism , genotype
Significance One fundamental analysis needed to interpret genome assemblies is genome alignment. Yet, accurately aligning regulatory and transposon regions outside of genes remains challenging. We introduce Anchored Wavefront alignment (AnchorWave), which implements a genome duplication informed longest path algorithm to identify collinear regions and performs base pair–resolved, end-to-end alignment for collinear blocks using an efficient two-piece affine gap cost strategy. AnchorWave improves the alignment under a number of scenarios: genomes with high similarity, large genomes with high transposable element activity, genomes with many inversions, and alignments between species with deeper evolutionary divergence and different whole-genome duplication histories. Potential use cases include genome comparison for evolutionary analysis of nongenic sequences and population genetics of taxa with large, repeat-rich genomes.