Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

Background: Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement. Results In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By identifying AS isoforms from mutliexonic genes, we found that AS types were not significantly different between maize and teosinte. In addition, the two main AS types (intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species, but the average unique AS events per each alternatively spliced gene in maize (4.12) was higher than that in teosinte (2.26). Moreover, 94 genes generating 98 r...

背景：可变剪接（Alternative splicing, AS）是真核生物转录组多样性形成的重要调控机制。大量研究证据表明，可变剪接的复杂性与真核生物的演化、发育、适应性及复杂度密切相关。本研究对6份大刍草和10份玉米转录组进行测序，旨在分析玉米驯化与改良过程中的可变剪接变化及选择特征。结果：在玉米和大刍草中，共鉴定得到13593个高度保守的基因，其中包含12030个多外显子基因。通过对多外显子基因的可变剪接异构体进行鉴定，本研究发现玉米与大刍草的可变剪接类型无显著差异。此外，两种主要的可变剪接类型——内含子保留（intron retention）与可变剪接受体位点（alternative acceptor）——占两个物种的可变剪接事件的60%以上，但玉米中每个可变剪接基因的平均独特可变剪接事件数（4.12）高于大刍草（2.26）。此外，共有94个基因可产生98个……