Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants.
Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants.
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BGISEQ-500 和 Illumina HiSeq4000 测序平台在植物转录组分析中的性能比较
DOI：
10.1186/s13007-018-0337-0
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发表时间：
2018
期刊：
影响因子：
5.1
通讯作者：
Liu YG
中科院分区：
文献类型：
--
作者：
Zhu FY;Chen MX;Ye NH;Qiao WM;Gao B;Law WK;Tian Y;Zhang D;Zhang D;Liu TY;Hu QJ;Cao YY;Su ZZ;Zhang J;Liu YG
下一代测序（NGS）技术极大地促进了基因组和转录组研究，对拓展当前关于基因组和转录组的知识做出了重大贡献。然而，测序平台、方案和分析流程的不断演变，使得研究界专注于跨平台评估和标准化。作为中国的NGS先驱，华大基因（BGI）自2016年起推出了自己的NGS平台——BGISEQ - 500。该平台在大规模DNA测序和小RNA分析方面的能力已经得到评估。然而，BGISEQ - 500平台在转录组分析方面的比较性能仍有待阐明。Illumina系列是中国测序市场的领先测序平台，可作为评估新平台的较好参照。
为此，我们描述了一项针对拟南芥野生型（Col 0）转录组分析的BGISEQ - 500和Illumina HiSeq4000之间的跨平台比较研究。使用上述平台，在生物学重复实验中对RNA测序和转录组数据处理的关键参数进行了评估。
BGISEQ - 500和Illumina HiSeq4000这两个平台的结果在基因定量、差异表达基因的鉴定以及可变剪接事件方面，平台间（相关性，0.88 - 0.93）和平台内（相关性，0.95 - 0.98）比较都具有高度一致性。然而，两个平台在单核苷酸多态性和插入缺失分析方面得出的结果差异很大。
本案例研究提供了一个全面的参考数据集，以验证BGISEQ - 500的能力，使其能够确立为植物转录组分析中一个具有竞争力且可靠的平台。
本文的网络版（10.1186/s13007 - 018 - 0337 - 0）包含补充材料，授权用户可获取。
The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016. The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated. However, the comparative performance of BGISEQ-500 platform in transcriptome analysis remains yet to be elucidated. The Illumina series, a leading sequencing platform in China’s sequencing market, would be a preferable reference to evaluate new platforms. To this end, we describe a cross-platform comparative study between BGISEQ-500 and Illumina HiSeq4000 for analysis of Arabidopsis thaliana WT (Col 0) transcriptome. The key parameters in RNA sequencing and transcriptomic data processing were assessed in biological replicate experiments, using aforesaid platforms. The results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter- (correlation, 0.88–0.93) and intra-platform (correlation, 0.95–0.98) comparison for gene quantification, identification of differentially expressed genes and alternative splicing events. However, the two platforms yielded highly variable interpretation results for single nucleotide polymorphism and insertion–deletion analysis. The present case study provides a comprehensive reference dataset to validate the capability of BGISEQ-500 enabling it to be established as a competitive and reliable platform in plant transcriptome analysis. The online version of this article (10.1186/s13007-018-0337-0) contains supplementary material, which is available to authorized users.
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影响因子：
5.7
作者：
Fehlmann T;Reinheimer S;Geng C;Su X;Drmanac S;Alexeev A;Zhang C;Backes C;Ludwig N;Hart M;An D;Zhu Z;Xu C;Chen A;Ni M;Liu J;Li Y;Poulter M;Li Y;Stähler C;Drmanac R;Xu X;Meese E;Keller A
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Keller A
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影响因子：
5.6
作者：
Chen H;Lin L;Ali F;Xie M;Zhang G;Su W
通讯作者：
Su W
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
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通讯作者：
Dudoit S
影响因子：
48
作者：
Katz, Yarden;Wang, Eric T.;Airoldi, Edoardo M.;Burge, Christopher B.
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