Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max

Jing Liu, Shengcai Chen, Min Liu, Yimian Chen, Wei Fan, Seunghee Lee, Han Xiao, Dave Kudrna, Zixin Li, Xu Chen, Yaqi Peng, Kewei Tian, Bao Zhang, Rod A. Wing, Jianwei Zhang, Xuelu Wang

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Alternative splicing (AS) is a ubiquitous phenomenon among eukaryotic intron-contain-ing genes, which greatly contributes to transcriptome and proteome diversity. Here we performed the isoform sequencing (Iso-Seq) of soybean underground tissues inoculated and uninoculated with Rhizobium and obtained 200,681 full-length transcripts covering 26,183 gene loci. It was found that 80.78% of the multi-exon loci produced more than one splicing variant. Comprehensive analysis of these identified 7874 differentially splicing events with highly diverse splicing patterns during nodule development, especially in defense and transport-related processes. We further profiled genes with differential isoform usage and revealed that 2008 multi-isoform loci underwent stage-specific or simultaneous major isoform switches after Rhizobium inoculation, indicating that AS is a vital way to regulate nodule development. Moreover, we took the lead in identifying 1563 high-confi-dence long non-coding RNAs (lncRNAs) in soybean, and 157 of them are differentially expressed during nodule development. Therefore, our study uncovers the landscape of AS during the soy-bean-Rhizobium interaction and provides systematic transcriptomic data for future study of multiple novel directions in soybean.

Original languageEnglish (US)
Article number7371
JournalInternational journal of molecular sciences
Issue number13
StatePublished - Jul 1 2022


  • Iso-Seq
  • differentially splicing event
  • long non-coding RNA
  • major isoform switch
  • nodule development
  • soybean

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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