BackgroundThe 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.MethodsTo 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.ResultsThe 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (10.1186/s13007-018-0337-0) contains supplementary material, which is available to authorized users.

Summary In rice (Oryza sativa), OsF2H and OsFNSII direct flavanones to independent pathways that form soluble flavone C‐glycosides and tricin‐type metabolites (both soluble and lignin‐bound), respectively. Production of soluble tricin metabolites requires CYP75B4 as a chrysoeriol 5′‐hydroxylase. Meanwhile, the close homologue CYP75B3 is a canonical flavonoid 3′‐hydroxylase (F3′H). However, their precise roles in the biosynthesis of soluble flavone C‐glycosides and tricin–lignins in cell walls remain unknown. We examined CYP75B3 and CYP75B4 expression in vegetative tissues, analyzed extractable flavonoid profiles, cell wall structure and digestibility of their mutants, and investigated catalytic activities of CYP75B4 orthologues in grasses. CYP75B3 and CYP75B4 showed co‐expression patterns with OsF2H and OsFNSII, respectively. CYP75B3 is the sole F3′H in flavone C‐glycosides biosynthesis, whereas CYP75B4 alone provides sufficient 3′,5′‐hydroxylation for tricin–lignin deposition. CYP75B4 mutation results in production of apigenin‐incorporated lignin and enhancement of cell wall digestibility. Moreover, tricin pathway‐specific 3′,5′‐hydroxylation activities are conserved in sorghum CYP75B97 and switchgrass CYP75B11. CYP75B3 and CYP75B4 represent two different pathway‐specific enzymes recruited together with OsF2H and OsFNSII, respectively. Interestingly, the OsF2H‐CYP75B3 and OsFNSII‐CYP75B4 pairs appear to be conserved in grasses. Finally, manipulation of tricin biosynthesis through CYP75B4 orthologues can be a promising strategy to improve digestibility of grass biomass for biofuel and biomaterial production.

Using RNA sequencing and qualitative and quantitative proteomics, we unravel alternative spliced isoforms and new ‘frame’ proteins during hypoxic germination in rice.