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

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Abstract

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.

Abstract

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.

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Data availability

We deposited the raw bam files of SMRT data in the Sequence Read Archives (SRA) of the National Center for Biotechnology Information (NCBI) under accession number SUB4116865. The Illumina RNA-Seq data was deposited in SRA under accession number SUB4113911.

Abbreviations

ORF :

Open reading frame

lncRNA :

Long non-coding RNA

SSR :

Simple sequence repeat

TF :

Transcript factor

NGST:

Next-generation high-throughput sequencing technology

SMRT :

Single molecule long reads sequencing technology

AS:

Alterative splice

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Acknowledgements

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.

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  1. Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China

    Yuehui Chao, Jianbo Yuan, Tao Guo, Lixin Xu, Zhiyuan Mu & Liebao Han

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  1. Yuehui Chao
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  2. Jianbo Yuan
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  3. Tao Guo
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  4. Lixin Xu
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  5. Zhiyuan Mu
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  6. Liebao Han
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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.

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Correspondence to Liebao Han.

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Communicated by Liebao Han.

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Chao, Y., Yuan, J., Guo, T. et al. Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing. Plant Mol Biol 99, 219–235 (2019). https://doi.org/10.1007/s11103-018-0813-y

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