A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants
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DOI：
10.1002/tpg2.20204
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发表时间：
2022-04
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影响因子：
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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
多基因组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。我们开发了msa_pipeline工作流（https://bitbucket.org/bucklerlab/msa_pipeline），以允许实用和敏感的多种多样的植物基因组比对，并以最小的用户输入计算保护分数。由于高重复序列含量和基因组差异是植物基因组比对的重大挑战，我们还利用33种草的基因组序列，探讨了不同掩蔽方法和参数对LAST比对器的影响。与使用RepeatMasker的传统掩蔽方法相比，基于k - mers （k长度的核苷酸序列）的掩蔽方法使编码序列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，默认对齐参数通常表现良好，但与默认LAST设置相比，参数调优可以将非编码功能区的对齐率提高52%以上。最后，通过增加默认基线的对齐灵敏度，参数调优可以将非编码位点的数量增加76%以上。总的来说，调整掩蔽和校准参数可以产生优化的多个校准，以推动植物中的生物发现。
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) to allow practical and sensitive multiple alignment of diverged plant genomes and calculation of conservation scores with minimal user inputs. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the effect of different masking approaches and parameters of the LAST aligner using genome assemblies of 33 grass species. Compared with conventional masking with RepeatMasker, a masking approach based on k‐mers (nucleotide sequences of k length) increased the alignment rate of coding sequence and noncoding 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 noncoding functional regions by over 52% compared with default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of noncoding sites that can be scored for conservation by over 76%. Overall, tuning of masking and alignment parameters can generate optimized multiple alignments to drive biological discovery in plants.