Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China.
Plant Mol Biol. 2019 Feb;99(3):219-235. doi: 10.1007/s11103-018-0813-y. Epub 2019 Jan 2.
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.
利用 PacBio 单分子长读测序技术对紫花苜蓿全长转录组进行了分析。转录组数据提供了紫花苜蓿转录本的全长序列和基因亚型，这将改善基因组注释，并增强我们对紫花苜蓿基因结构的理解。作为一种重要的饲料作物，紫花苜蓿（Medicago sativa L.）在全球范围内种植。由于其基因组的复杂性和未完成的全基因组测序，紫花苜蓿中 mRNA 转录本的序列和完整结构仍不清楚。在这项研究中，我们应用单分子长读测序技术，使用 Pacific Biosciences 平台研究紫花苜蓿转录组，从幼叶、成熟叶和衰老叶中获得了 113321 个转录本。我们鉴定了 72606 个开放阅读框，包括 46616 个全长 ORFs、54 个 TF 家族中的 1670 个转录因子和 30797 个序列中的 44040 个简单序列重复。鉴定了 7568 个可变剪接事件，紫花苜蓿中大多数可变剪接事件为内含子保留。此外，我们还鉴定了 17740 个长非编码 RNA。我们的研究结果表明，在单分子水平上对紫花苜蓿转录组的全长 RNA 进行深度测序是可行的。
