Plant Molecular Biology

, Volume 99, Issue 3, pp 219–235 | Cite as

Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing

  • Yuehui Chao
  • Jianbo Yuan
  • Tao Guo
  • Lixin Xu
  • Zhiyuan Mu
  • Liebao HanEmail author


Key message

The full-length transcriptome of alfalfa was analyzed with PacBio single-molecule long-read sequencing technology. The transcriptome data provided full-length sequences and gene isoforms of transcripts in alfalfa, which will improve genome annotation and enhance our understanding of the gene structure of alfalfa.


As an important forage, alfalfa (Medicago sativa L.) is world-wide planted. For its complexity of genome and unfinished whole genome sequencing, the sequences and complete structure of mRNA transcripts remain unclear in alfalfa. In this study, single-molecule long-read sequencing was applied to investigate the alfalfa transcriptome using the Pacific Biosciences platform, and a total of 113,321 transcripts were obtained from young, mature and senescent leaves. We identified 72,606 open reading frames including 46,616 full-length ORFs, 1670 transcription factors from 54 TF families and 44,040 simple sequence repeats from 30,797 sequences. A total of 7568 alternative splicing events was identified and the majority of alternative splicing events in alfalfa was intron retention. In addition, we identified 17,740 long non-coding RNAs. Our results show the feasibility of deep sequencing full-length RNA from alfalfa transcriptome on a single-molecule level.


Medicago sativa L. Transcripts and splice isoforms Single-molecule long-read sequencing lncRNA 



Open reading frame


Long non-coding RNA


Simple sequence repeat


Transcript factor


Next-generation high-throughput sequencing technology


Single molecule long reads sequencing technology


Alterative splice



The program was supported by the National Natural Science Foundation of China (Grant Nos. 31601989 and 31672477). We acknowledge Jingjing Sui, Huaigen Xin and Dandan Chen from Biomarker Corporation (Beijing, China) for the facilities and expertise of the PacBio platform for libraries construction and sequencing.

Author contributions

YC and LH conceived and designed the research. YC, JY and TG conducted experiments. ZM and LX analyzed data. YC and LH wrote the manuscript. All authors read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Turfgrass Research Institute, Beijing Forestry UniversityBeijingChina

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