Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry
Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry
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通过比较分析草莓中基于 SMRT 和 Illumina 的 RNA-seq 来全面鉴定选择性剪接
DOI：
10.1111/tpj.13462
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发表时间：
2017-04-01
期刊：
影响因子：
7.2
通讯作者：
Kang, Chunying
中科院分区：
文献类型：
--
作者：
Li, Yongping;Dai, Cheng;Kang, Chunying
选择性剪接（alternative splicing，AS）是一种重要的转录后调控机制，但目前对AS在果树中的作用知之甚少。在这里，AS在野生草莓Fragaria vesca基因组中进行了全局分析，其中RNA-seq数据来自果实发育的不同阶段。在单分子实时（SMRT）和Illumina RNA-seq平台之间表征和比较AS景观。虽然SMRT具有较低的测序深度，但与Illumina（33.48%）相比，它鉴定出更多经历AS的基因（检测到的多外显子基因的57.67%），说明SMRT在AS鉴定中的功效。我们研究了不同模式的AS在果实发育的背景下，内含子保留（IR）的百分比显着降低，而替代受体位点（AA）显着增加受精后相比，受精前。将所有已鉴定的转录本合并，共检测到66.43%的草莓多外显子基因发生AS，其中一些导致基因产物中保守结构域的增加或丢失。这项工作表明，SMRT测序是非常强大的AS发现，并提供了丰富的数据资源，为以后的功能研究的不同亚型。此外，AS模式的转变可能导致坐果期基因表达的快速变化。意义声明选择性剪接是一种关键的转录后调控机制，但对它在果树中的作用知之甚少。在这里，我们使用来自草莓果实的转录组数据全面分析了选择性剪接，并表明单分子真实的时间（SMRT）RNA-seq数据在发现选择性剪接变体方面非常有效。
Alternative splicing (AS) is a key post-transcriptional regulatory mechanism, yet little information is known about its roles in fruit crops. Here, AS was globally analyzed in the wild strawberry Fragaria vesca genome with RNA-seq data derived from different stages of fruit development. The AS landscape was characterized and compared between the single-molecule, real-time (SMRT) and Illumina RNA-seq platform. While SMRT has a lower sequencing depth, it identifies more genes undergoing AS (57.67% of detected multiexon genes) when it is compared with Illumina (33.48%), illustrating the efficacy of SMRT in AS identification. We investigated different modes of AS in the context of fruit development; the percentage of intron retention (IR) is markedly reduced whereas that of alternative acceptor sites (AA) is significantly increased post-fertilization when compared with pre-fertilization. When all the identified transcripts were combined, a total of 66.43% detected multiexon genes in strawberry undergo AS, some of which lead to a gain or loss of conserved domains in the gene products. The work demonstrates that SMRT sequencing is highly powerful in AS discovery and provides a rich data resource for later functional studies of different isoforms. Further, shifting AS modes may contribute to rapid changes of gene expression during fruit set.Significance Statement Alternative splicing is a key post-transcriptional regulatory mechanism, yet little is known about its roles in fruit crops. Here we globally analyzed alternative splicing using transcriptome data from strawberry fruits, and show that single molecule real time (SMRT) RNA-seq data is highly efficient in uncovering alternatively spliced variants.