Genomic Forces Play Important Roles in Soybean Alternative Splicing

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.

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, Dr.TIAN Zhixi and his colleague at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, found that more than 63% of multiexonic genes underwent AS in soybean. 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, this 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.

This work has been published online on Plant Cell (DOI：10.1105/tpc.114.122739) with SHEN Yanting as the first author and Dr. ZHOU Zhengkui as co-first author.