Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

Fu Yuan Zhu, Mo Xian Chen, Neng Hui Ye, Wang Min Qiao, Bei Gao, Wai Ki Law, Yuan Tian, Dong Zhang, Di Zhang, Tie Yuan Liu, Qi Juan Hu, Yun Ying Cao, Ze Zhuo Su, Jianhua ZHANG*, Ying Gao Liu

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

86 Citations (Scopus)


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.

Original languageEnglish
Article number69
JournalPlant Methods
Issue number1
Publication statusPublished - 13 Aug 2018

Scopus Subject Areas

  • Biotechnology
  • Genetics
  • Plant Science

User-Defined Keywords

  • Alternative splicing
  • BGISEQ-500
  • Differential expressed genes
  • Illumina HiSeq4000
  • Next-generation sequencing
  • Transcriptome


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