Alternative splicing (AS) increases the diversities of transcriptomes and proteomes in plants. The work reports identification and analysis of genes and their transcripts with a focus on AS in soybean plants by integrating mapping information of over 1.5 million of mRNAs and expressed sequence tags (ESTs) with more than 6 billons of mapped reads collected from 90 RNA-seq datasets obtained from multiple experiments. A total of 294,164 AS events were detected and categorized into basic events (151,710, 51.57%) and complex events (142,454, 48.43%). The basic AS events include intron retention (18.52%), alternative acceptor sites (16.33%), alternative donor site (8.99%), and exon skipping (7.73%). The AS rate in intron containing genes was estimated to be ~56.3% in soybean based on the current analysis. In addition, a total of 41,453 new genomic loci, which were not previously annotated in the genome, were detected by mapping transcripts to the genome. The annotated data can be accessed through a public database for searching and downloading. This work provides a resource for further detailed functional analysis of gene products in soybean plants.

Soybean [Glycine max] is an important oil and food plant for both humans and animals. Recent development in RNA sequencing (RNA-seq) technology provides a cost effective approach to analyzing transcriptomes of plants at different developmental stages and in responses to different biotic and abiotic challenges. Currently there are over 5 000 RNA-seq datasets in soybean plants publicly available at SRA database in the National Center for Biotechnology Information (NCBI). Such a large number of RNA-seq datasets provide soybean researchers an opportunity as well as a challenge for fully exploring the data to understand soybean biology. A number of research articles have been published on applications of RNA-seq in transcriptome analysis of soybean plants, covering a wide range of topics including growth and development, plant mineral nutrients, responses to environmental stresses, pathogens and pests. In this work we compile and review recent advances of RNA-seq transcriptome analyses including profiling of differential gene expression, gene alternative splicing, and gene regulatory networks in soybean plants, with key findings excerpted from each individual published article.