Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon

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 ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼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 event...在真核生物中，可变剪接（alternative splicing, AS）可提升转录组与蛋白质组的多样性。目前学界对植物-微生物互作过程中全基因组范围可变剪接变化的程度仍知之甚少。本研究借助高通量双端RNA测序技术，构建了感染黍花叶病毒（Panicum mosaic virus）及其卫星病毒的二穗短柄草（Brachypodium distachyon）的异构体水平剪接组图谱。整体而言，我们在二穗短柄草中共检测到约44443条转录本，较参考基因组注释的转录本数量多出约30%。约28900条转录本的表达量不低于2片段/每千碱基转录本/每百万比对片段，且约42%的多外显子基因发生了可变剪接。通过对二穗短柄草、水稻（Oryza sativa）、玉米（Zea mays）、高粱（Sorghum bicolor）、拟南芥（Arabidopsis thaliana）、马铃薯（Solanum tuberosum）、蒺藜苜蓿（Medicago truncatula）以及毛果杨（Populus trichocarpa）的可变剪接模式进行比较分析，本研究发现单子叶与双子叶植物间的可变剪接类型比例具有保守性。病毒感染可在数量层面改变可变剪接事件……