A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

Area of Science:

• Comparative genomics
• Bioinformatics
• Plant science

Background:

• Multiple genome alignments are crucial for comparative genomics but are technically challenging.
• High repeat content and genomic divergence in plants complicate alignment.

Purpose of the Study:

• To develop a practical workflow (msa_pipeline) for sensitive multiple alignment of diverged plant genomes.
• To evaluate the impact of masking strategies and LAST aligner parameters on alignment efficiency.

Main Methods:

• Developed the msa_pipeline workflow for plant genome alignment.
• Compared RepeatMasker with k-mer-based masking.
• Assessed LAST aligner parameter effects on 33 grass species genome assemblies.

Main Results:

• K-mer masking improved coding and noncoding region alignment rates by 25% and 14%, respectively.
• Parameter tuning increased noncoding region alignment rates by over 52%.
• Increased alignment sensitivity boosted scorable noncoding sites by over 76%.

Conclusions:

• Optimized masking and alignment parameters enhance multiple genome alignment sensitivity and scope in plants.
• The msa_pipeline workflow facilitates practical and sensitive plant genome alignment.
• Improved alignments enable more robust biological discovery in plant comparative genomics.