Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

BMC Plant Biol. 2018 Nov 26;18(1):300. doi: 10.1186/s12870-018-1534-8.


Background: Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover.

Results: In this study, the red clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2194 novel isoforms from novel genes were identified. A total of 5492 alternative splicing events was identified and the majority of alter spliced events in red clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8719 including 186,517 transcripts have at least one poly(A) site. Furthermore, we identified 4333 long non-coding RNAs and 3762 fusion transcripts.

Conclusions: We analyzed full-length transcriptome of red clover with PacBio SMRT. Those new findings provided important information for improving red clover draft genome annotation and fully characterization of red clover transcriptome.

Keywords: Alternative polyadenylation; Alternative splicing; Full-length transcript; Fusion transcript; Long non-coding RNA; Red clover.

MeSH terms

  • Alternative Splicing*
  • Exons
  • Genome, Plant
  • Introns
  • Molecular Sequence Annotation
  • Protein Isoforms / genetics
  • RNA, Long Noncoding
  • RNA, Plant*
  • Sequence Analysis, RNA
  • Transcriptome
  • Trifolium / genetics*


  • Protein Isoforms
  • RNA, Long Noncoding
  • RNA, Plant