ACMGA: a reference-free multiple-genome alignment pipeline for plant species
Huafeng Zhou1,2, Xiaoquan Su3, Baoxing Song4,5
1College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, 266071, China.
BMC Genomics
|May 25, 2024
Summary
AnchorWave-Cactus Multiple Genome Alignment (ACMGA) pipeline improves plant genome analysis by identifying more variants than short-read sequencing. This tool enhances the detection of single nucleotide variants and long insertions/deletions, especially in repetitive regions.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- Short-read whole-genome sequencing (WGS) is common for plant genomic variation studies.
- Advancements in long-read sequencing yield high-quality plant genomes.
- Existing multiple genome alignment (MGA) tools may not be optimal for plant genomes.
Purpose of the Study:
- Develop and evaluate a novel MGA pipeline for plant genomes.
- Improve the identification of genomic variants missed by WGS.
- Enhance the alignment of repeat elements and detection of long insertions/deletions (INDELs).
Main Methods:
- Developed the AnchorWave-Cactus Multiple Genome Alignment (ACMGA) pipeline.
- Performed MGA on de novo assembled genomes of Arabidopsis and Maize using ACMGA and Cactus.
- Compared MGA results with previous short-read variant calling data.
Main Results:
- ACMGA improved alignment of repeat elements and identified long INDELs (> 50 bp).
- MGA identified more single nucleotide variants (SNVs) and long INDELs than WGS.
- ACMGA detected significantly more SNVs and INDELs in repetitive regions and overall compared to Cactus.
- ACMGA results showed higher concordance with previously published short-read variants than Cactus results.
- Both MGA pipelines identified numerous multi-allelic variants missed by WGS.
Conclusions:
- Aligning de novo assembled genomes identifies more SNVs and INDELs than short-read mapping.
- ACMGA integrates global alignment, a 2-piece-affine-gap cost strategy, and progressive MGA for effective plant MGA.
- ACMGA offers a practical solution for comprehensive plant genomic variation analysis.
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