Introgressions lead to reference bias in wheat RNA-Seq analysis

Introgressions lead to reference bias in wheat RNA-Seq analysis
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基因渗入导致小麦 RNA-Seq 分析中的参考偏差

DOI：
10.1101/2023.10.04.560829
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发表时间：
2023
期刊：
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影响因子：
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通讯作者：
Coombes B
Coombes B
中科院分区：
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文献类型：
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作者：
Coombes B

文献摘要

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背景RNA-seq是基因组学中的一项基本技术，然而参考偏差，即来自非参考等位基因的转录本被较不准确地量化，可能会破坏RNA-seq定量的准确性，从而影响下游的结论。尽管有证据表明，RNA-seq分析中的参照偏差通常是野生相对导入的复杂马赛克，从而引入了高度分化的基因块，但在复杂多倍体基因组中，参考偏差尚未得到探索。结果我们以六倍体小麦为模型复杂多倍体，使用模拟和实验数据表明，小麦RNA-seq排列存在广泛的参照偏差，这在很大程度上是由发散的导入基因驱动的。这导致了对基因表达的低估和对同源基因表达平衡的错误评估。通过将来自10个小麦基因组组合的基因模型整合到全转录组参考中，我们提出了一种新的方法来减少参考偏差，该方法可以很容易地随着新的基因组和转录组数据的获得而被扩展以捕捉更多的变异。结论本研究表明在小麦RNA-SEQ分析中引入导入会导致参考偏差。使用非样本参考基因组进行RNA-SEQ比对的研究人员应谨慎行事，并应考虑新的方法，如本文提出的方法。
BackgroundRNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes.ResultsHere we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available.ConclusionsThis study shows that the presence of introgressions can lead to reference bias in wheat RNA-seq analysis. Caution should be exercised by researchers using non-sample reference genomes for RNA-seq alignment and novel methods, such as the one presented here, should be considered.