The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing
The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing
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Illumina 和单分子实时 RNA 测序揭示了莲花 (Nelumbo nucifera) 中选择性剪接的复杂性和组织特异性表达情况
DOI：
10.1093/dnares/dsz010
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发表时间：
2019-06
期刊：
影响因子：
4.1
通讯作者：
Pingfang Yang
中科院分区：
文献类型：
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作者：
Yue Zhang;Tonny Maraga Nyong'A;Tao Shi;Pingfang Yang
摘要 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发挥着关键作用。然而，由于全长多剪接亚型的获得很少，因此莲花中 AS 的饱和度和复杂性仍不清楚。在这项研究中，我们应用混合组装策略，将单分子实时测序和 Illumina RNA-seq 相结合，以全面了解莲花转录组景观。我们鉴定了 211,802 个高质量的全长非嵌合读段，以及 192,690 个非冗余亚型，并更新了 Lotus 参考基因模型。此外，我们的分析从 16,543 个基因中总共鉴定了 104,288 个 AS 事件，其中替代 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 个组织中识别出 370 个组织特异性 AS 事件。组织特异性基因和亚型都可能在组织或器官发育中发挥重要作用，并且部分适合花组织中的“ABCE”模型。我们的研究中发现的大量 AS 事件和亚型变异增强了对莲花转录多样性的理解，并为进一步的功能基因组研究提供了宝贵的资源。
Abstract 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 3ʹ 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.
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DOI：
10.1007/978-1-4939-8657-6_11
发表时间：
2018-01-01
期刊：
PLANT TRANSCRIPTION FACTORS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Ichihashi, Yasunori;Fukushima, Atsushi;Shirasu, Ken
通讯作者：
Shirasu, Ken
影响因子：
16.6
作者：
Abdel-Ghany SE;Hamilton M;Jacobi JL;Ngam P;Devitt N;Schilkey F;Ben-Hur A;Reddy AS
通讯作者：
Reddy AS
甘薯谷胱甘肽 S-转移酶基因家族的鉴定和分析揭示了地上和地下组织中响应非生物胁迫的不同 GST 介导的网络
影响因子：
5.3
作者：
Ding N;Wang A;Zhang X;Wu Y;Wang R;Cui H;Huang R;Luo Y
通讯作者：
Luo Y
影响因子：
11.6
作者：
Fouquet, Romain;Martin, Federico;Settles, A. Mark
通讯作者：
Settles, A. Mark
影响因子：
12.3
作者：
Denoeud F;Aury JM;Da Silva C;Noel B;Rogier O;Delledonne M;Morgante M;Valle G;Wincker P;Scarpelli C;Jaillon O;Artiguenave F
通讯作者：
Artiguenave F