Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon
Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon
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DOI：
10.1105/tpc.114.133991
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发表时间：
2015-01-01
期刊：
影响因子：
11.6
通讯作者：
Scholthof, Karen-Beth G.
中科院分区：
文献类型：
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作者：
Mandadi, Kranthi K.;Scholthof, Karen-Beth G.
在真核生物中，选择性剪接（AS）促进转录组和蛋白质组的多样性。在植物与微生物相互作用过程中，全基因组AS变化的程度在很大程度上是未知的。在这里，我们使用高通量，配对端RNA测序，生成了短掌叶花叶病毒及其卫星病毒感染短掌叶花叶病毒的同工型剪接体图谱。总的来说，我们在双双体中检测到类似的44,443个转录本，比参考基因组中注释的转录本多出30%。类似28900个转录本的表达量为>= 2个片段/千个碱基的转录本/百万个映射片段，类似42%的多外显子基因被选择性剪接。对长叶白杨、水稻（Oryza sativa）、玉米（Zea mays）、高粱（sorghum bicolor）、拟南芥（Arabidopsis thaliana）、马铃薯（Solanum tuberosum）、苜蓿（Medicago truncatula）和杨树（Populus trichocarpa）的AS类型进行比较分析，发现单子叶和双子叶之间AS类型的保守比例。病毒感染定量地改变了短柄草的AS事件，但对AS比率影响不大。我们发现了bbbb100免疫相关基因编码受体样激酶、NB-LRR抗性蛋白、转录因子、RNA沉默和剪接相关蛋白的AS事件。SCL33是一种富含丝氨酸/精氨酸的剪接因子，其克隆和分子特征鉴定发现了多种新的内含子保留剪接变体，这些变体在病毒感染期间受到发育调控和调节。与遥远的拟南芥SCL33同源植物相比，B.远端子SCL33剪接模式也非常保守。这一分析结果为了解单子房和双子房间的AS景观提供了新的见解，并揭示了植物防御相关基因中的AS事件。
In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected similar to 44,443 transcripts in B. distachyon, similar to 30% more than those annotated in the reference genome. Expression of similar to 28,900 transcripts was >= 2 fragments per kilobase of transcript per million mapped fragments, and similar to 42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for > 100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes.