Analysis and comprehensive comparison of Pacbio and Nanopore-based RNA-sequencing in Arabidopsis transcriptome

Rapidly increased studies by third-generation sequencing [Pacific Biosciences (Pacbio) and Oxford Nanopore Technologies (ONT)] have been used in all kinds of research areas. Among them, the plant full-length single-molecule transcriptome studies were most used by Pacbio while ONT was rarely used. Therefore, in this study, we developed ONT RNA-sequencing methods in plants. We performed a detailed evaluation of reads from Pacbio and Nanopore PCR cDNA (ONT Pc) sequencing in plants (Arabidopsis), including the characteristics of raw data and identification of transcripts. We aimed to provide a valuable reference for applications of ONT in plant transcriptome analysis. Sequencing the Arabidopsis cDNA samples from overall ground parts at the same growth stage by Pacbio and Nanopore platform repectively. And then, we compared the advantages and disadvantages between Pacbio and Nanopore RNA-seq. Please note that the Sample 1 RNA-seq is to generate a transcriptome assembly and the rest of the samples are to quantify the gene expression.