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- Title
Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing.
- Authors
Chao, Yuehui; Yuan, Jianbo; Guo, Tao; Xu, Lixin; Mu, Zhiyuan; Han, Liebao
- 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.
- Subjects
ALFALFA yields; MESSENGER RNA; RNA sequencing; OPEN reading frames (Genetics); DATA analysis
- Publication
Plant Molecular Biology, 2019, Vol 99, Issue 3, p219
- ISSN
0167-4412
- Publication type
Article
- DOI
10.1007/s11103-018-0813-y