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.

中文翻译：

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Illumina和单分子实时RNA测序揭示了莲花（Nelumbo nucifera）的选择性剪接和组织特异性表达的复杂性。

选择性剪接（AS）通过显着增加转录组和蛋白质组的多样性，在调节真核生物的不同生理和发育过程中起关键作用。然而，由于其罕见的全长多重剪接同工型的局限性，莲花中AS的饱和度和复杂性仍不清楚。在这项研究中，我们通过结合单分子实时测序和Illumina RNA-seq来应用混合装配策略，以全面了解莲花转录组的情况。我们鉴定了211,802个高质量的全长非嵌合读物，以及192,690个非冗余同工型，并更新了Lotus参考基因模型。此外，我们的分析从16,543个基因中识别出104,288个AS事件，其中3'剪接位点是主要模型，其次是内含子保留。通过探索组织数据集，在12个组织中鉴定出370个组织特异性AS事件。组织特异性基因和同工型都可能在组织或器官发育中起重要作用，并且部分适合于花卉组织中的“ ABCE”模型。在我们的研究中发现的大量AS事件和同种型变异体增强了对莲花转录多样性的了解，并为进一步的功能基因组研究提供了宝贵的资源。