title: Global dissection of alternative splicing in paleopolyploid soybean.
abstract: Alternative splicing (AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean (Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yanting
authors.initials: Y
authors.lastname: Shen
authors.forename: Zhengkui
authors.initials: Z
authors.lastname: Zhou
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Weiyu
authors.initials: W
authors.lastname: Li
authors.forename: Chao
authors.initials: C
authors.lastname: Fang
authors.forename: Mian
authors.initials: M
authors.lastname: Wu
authors.forename: Yanming
authors.initials: Y
authors.lastname: Ma
authors.forename: Tengfei
authors.initials: T
authors.lastname: Liu
authors.forename: Ling-An
authors.initials: LA
authors.lastname: Kong
authors.forename: De-Liang
authors.initials: DL
authors.lastname: Peng
authors.forename: Zhixi
authors.initials: Z
authors.lastname: Tian
mesh_terms: D017398:Alternative Splicing; D005091:Exons; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D013025:Glycine max / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D018749:RNA, Plant