Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing
Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing
复制标题
通过单分子长读长测序分析苜蓿的转录本和剪接亚型
DOI：
10.1007/s11103-018-0813-y
复制
发表时间：
2019-02-01
影响因子：
5.1
通讯作者：
Han, Liebao
中科院分区：
文献类型：
--
作者：
Chao, Yuehui;Yuan, Jianbo;Han, Liebao
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.
