The value of genotype-specific reference for transcriptome analyses in barley.
The value of genotype-specific reference for transcriptome analyses in barley.
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DOI：
10.26508/lsa.202101255
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发表时间：
2022-08
影响因子：
4.4
通讯作者：
Zhang, Runxuan
中科院分区：
文献类型：
--
作者：
Guo, Wenbin;Coulter, Max;Waugh, Robbie;Zhang, Runxuan
我们在这项研究中证明，使用一个共同的参考基因组可能会导致基因型特定的信息在组装的参考转录数据集（RTD）和错误的，不完整的，或误导性的转录组学分析结果在大麦的产生损失。越来越明显的是，虽然一个物种内的不同基因型共享“核心”基因，但它们也包含可变数量的“特定”基因和不同结构的“核心”基因，这些基因只存在于一个子集的个体中。因此，使用共同的参考基因组可能会导致组装的参考转录本数据集（RTD）中基因型特异性信息的丢失，并产生错误、不完整或误导性的转录组学分析结果。在这项研究中，我们组装基因型特异性RTD（sRTD）和共同的参考为基础的RTD（cRTD）从RNA-seq数据的栽培Barke和Morex大麦，分别。我们的定量评估表明，sRTD具有显著更高的转录物和可变剪接事件的多样性，而cRTD错过了sRTD中存在的40%的转录物，并且它仅具有约70%的准确转录物组装。我们发现，sRTD是更准确的转录定量以及差异表达分析。然而，基因水平的定量受影响较小，这可能是一个合理的妥协时，高质量的基因型特异性参考是不可用的。
We demonstrate in this study that using a common reference genome may lead to loss of genotype-specific information in the assembled Reference Transcript Dataset (RTD) and the generation of erroneous, incomplete, or misleading transcriptomics analysis results in barley. It is increasingly apparent that although different genotypes within a species share “core” genes, they also contain variable numbers of “specific” genes and different structures of “core” genes that are only present in a subset of individuals. Using a common reference genome may thus lead to a loss of genotype-specific information in the assembled Reference Transcript Dataset (RTD) and the generation of erroneous, incomplete or misleading transcriptomics analysis results. In this study, we assembled genotype-specific RTD (sRTD) and common reference–based RTD (cRTD) from RNA-seq data of cultivated Barke and Morex barley, respectively. Our quantitative evaluation showed that the sRTD has a significantly higher diversity of transcripts and alternative splicing events, whereas the cRTD missed 40% of transcripts present in the sRTD and it only has ∼70% accurate transcript assemblies. We found that the sRTD is more accurate for transcript quantification as well as differential expression analysis. However, gene-level quantification is less affected, which may be a reasonable compromise when a high-quality genotype-specific reference is not available.
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影响因子：
4.6
作者：
Jin M;Liu H;He C;Fu J;Xiao Y;Wang Y;Xie W;Wang G;Yan J
通讯作者：
Yan J
影响因子：
4.6
作者：
Hsieh, Ping-Han;Oyang, Yen-Jen;Chen, Chien-Yu
通讯作者：
Chen, Chien-Yu
影响因子：
16.6
作者：
Golicz, Agnieszka A.;Bayer, Philipp E.;Barker, Guy C.;Edger, Patrick P.;Kim, HyeRan;Martinez, Paula A.;Chan, Chon Kit Kenneth;Severn-Ellis, Anita;McCombie, W. Richard;Parkin, Isobel A. P.;Paterson, Andrew H.;Pires, J. Chris;Sharpe, Andrew G.;Tang, Haibao;Teakle, Graham R.;Town, Christopher D.;Batley, Jacqueline;Edwards, David
通讯作者：
Edwards, David
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
7.7
作者：
Baeza-Centurion P;Miñana B;Valcárcel J;Lehner B
通讯作者：
Lehner B