Homeolog expression quantification methods for allopolyploids
Homeolog expression quantification methods for allopolyploids
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DOI：
10.1093/bib/bby121
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发表时间：
2020-03-01
影响因子：
9.5
通讯作者：
Sese, Jun
中科院分区：
文献类型：
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作者：
Kuo, Tony C. Y.;Hatakeyama, Masaomi;Sese, Jun
杂交或异源多倍化导致的基因组复制发生在动物、真菌和植物中，并且在农作物中尤其常见。由于多倍体基因组组装的进展，人们对异源多倍体的研究越来越感兴趣。然而，重复基因拷贝（同源基因）的高度序列相似性带来了许多挑战。在这里，我们将目前用于二倍体物种的标准 RNA-seq 表达定量方法与将读数分别映射到每个亚基因组的亚基因组分类方法进行了比较。我们使用之前和新的 RNA-seq 数据检查了映射误差，其中通过实验添加亚基因组（合成异源四倍体拟南芥）或减少亚基因组（异源六倍体小麦与提取的异源四倍体）作为基本事实。这两个物种的错误率非常相似。标准方法显示出较高的错误率（使用 Kallisto 伪比对时>10%），而亚基因组分类方法显示出低得多的错误率（
Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (