CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN, China.
University of Chinese Academy of Sciences, Beijing, China.
DNA Res. 2019 Aug 1;26(4):301-311. doi: 10.1093/dnares/dsz010.
Alternative splicing (AS) plays a critical role in regulating different physiological and developmental processes in eukaryotes, by dramatically increasing the diversity of the transcriptome and the proteome. However, the saturation and complexity of AS remain unclear in lotus due to its limitation of rare obtainment of full-length multiple-splice isoforms. In this study, we apply a hybrid assembly strategy by combining single-molecule real-time sequencing and Illumina RNA-seq to get a comprehensive insight into the lotus transcriptomic landscape. We identified 211,802 high-quality full-length non-chimeric reads, with 192,690 non-redundant isoforms, and updated the lotus reference gene model. Moreover, our analysis identified a total of 104,288 AS events from 16,543 genes, with alternative 3' splice-site being the predominant model, following by intron retention. By exploring tissue datasets, 370 tissue-specific AS events were identified among 12 tissues. Both the tissue-specific genes and isoforms might play important roles in tissue or organ development, and are suitable for 'ABCE' model partly in floral tissues. A large number of AS events and isoform variants identified in our study enhance the understanding of transcriptional diversity in lotus, and provide valuable resource for further functional genomic studies.
可变剪接（AS）在真核生物中通过显著增加转录组和蛋白质组的多样性，对不同的生理和发育过程的调控起着至关重要的作用。然而，由于难以获得全长的多剪接异构体，莲的 AS 饱和度和复杂性仍不清楚。在这项研究中，我们应用了一种混合组装策略，结合单分子实时测序和 Illumina RNA-seq，全面了解莲的转录组景观。我们鉴定了 211,802 条高质量的全长非嵌合reads，其中包含 192,690 个非冗余异构体，并更新了莲的参考基因模型。此外，我们的分析从 16,543 个基因中总共鉴定了 104,288 个 AS 事件，其中替代 3' 剪接位点是主要的模式，其次是内含子保留。通过探索组织数据集，在 12 种组织中鉴定了 370 个组织特异性 AS 事件。12 种组织中的组织特异性基因和异构体可能在组织或器官发育中发挥重要作用，并且在部分花组织中适合 'ABCE' 模型。我们研究中鉴定的大量 AS 事件和异构体变体增强了对莲转录多样性的理解，并为进一步的功能基因组研究提供了有价值的资源。
