期刊论文详细信息
Plant Methods
Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants
Wai-Ki Law1  Wang-Min Qiao1  Dong Zhang1  Yun-Ying Cao2  Ze-Zhuo Su3  Tie-Yuan Liu4  Di Zhang4  Bei Gao4  Mo-Xian Chen5  Jianhua Zhang5  Qi-Juan Hu5  Neng-Hui Ye6  Ying-Gao Liu7  Yuan Tian7  Fu-Yuan Zhu7 
[1] BGI-Shenzhen;College of Life Sciences, Nantong University;Department of Orthopaedics and Traumatology, The University of Hong Kong;School of Life Sciences, The Chinese University of Hong Kong;Shenzhen Research Institute, The Chinese University of Hong Kong;Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University;State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University;
关键词: Alternative splicing;    BGISEQ-500;    Differential expressed genes;    Illumina HiSeq4000;    Next-generation sequencing;    Transcriptome;   
DOI  :  10.1186/s13007-018-0337-0
来源: DOAJ
【 摘 要 】

Abstract Background 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. Methods 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. Results 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. Conclusion 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.

【 授权许可】

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