A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants
A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants
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DOI：
10.1101/2021.06.01.446647
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发表时间：
2021-06
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通讯作者：
Yaoyao Wu;Lynn C. Johnson;Baoxing Song;C. Romay;Michelle C. Stitzer;A. Siepel;E. Buckler;Armin Scheben
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作者：
Yaoyao Wu;Lynn C. Johnson;Baoxing Song;C. Romay;Michelle C. Stitzer;A. Siepel;E. Buckler;Armin Scheben
多个基因组的比对是比较基因组学的基石，但产生这些比对在技术上仍然具有挑战性，而且往往不切实际。我们基于LAST比对器开发了msa_pipeline工作流程（https：//bitbucket.org/bucklerlab/msa_pipeline），以允许以最少的用户输入对分歧的植物基因组进行实用且灵敏的多重比对。我们的工作流程只需要一组FASTA格式的基因组作为输入。该工作流以MAF格式输出多个比对，并包括帮助计算全基因组保守性分数的实用程序。由于高重复序列含量和基因组差异是植物基因组比对中的重大挑战，我们还探讨了不同的掩蔽方法和比对参数的影响，使用33个草种的基因组组装。与使用RepeatMasker的常规掩蔽相比，k-mer掩蔽方法将CDS和非编码功能区的比对率分别提高了25%和14%。我们进一步发现，默认比对参数通常表现良好，但与默认LAST设置相比，参数调整可以将非编码功能区的比对率提高52%以上。最后，通过从默认基线增加比对灵敏度，参数调整可以将可以针对保守性评分的非编码位点的数量增加超过76%。
Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) based on the LAST aligner to allow practical and sensitive multiple alignment of diverged plant genomes with minimal user inputs. Our workflow only requires a set of genomes in FASTA format as input. The workflow outputs multiple alignments in MAF format, and includes utilities to help calculate genome-wide conservation scores. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the impact of different masking approaches and alignment parameters using genome assemblies of 33 grass species. Compared to conventional masking with RepeatMasker, a k-mer masking approach increased the alignment rate of CDS and non-coding functional regions by 25% and 14% respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for non-coding functional regions by over 52% compared to default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of non-coding sites that can be scored for conservation by over 76%.