Identification and Analysis of Alternative Splicing in Soybean Plants

Abstract

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.

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

“…TE insertion is probably an important mechanism for IR-type AS in maize. The AS levels of 3864 genes were significantly different between maize and teosinte, of which 151 AS levelaltered genes involved in transcriptional regulation and in stress responses were located in the regions that were targets of selection during maize genetic improvement [177].…”

“…Over 11,000 novel splice isoforms, alternative polyadenylation (APA) of ~11,000 expressed genes and more than 2100 novel genes were reported in sorghum [30,178], whereas 15,102 fiber-specific AS were reported in cotton [99]. To date, a large number of AS events associated with various development stages and molecular functions have been reported in soybean-294,164 AS events across multiple experiments [177]; 1278 AS events associated with nitrate stress in root hairs [179]; and 154,469 AS events in 23,764 genes across development stages [180]. The intron retention form of AS events was predominant in most of the research reported here followed by alternative acceptor sites, alternative donor sites, and exon skipping.…”