Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Abstract

Sorghum bicolor is a member of grass family which is an attractive model plant for genome study due to interesting genome features like low genome size. In this research, we performed comprehensive investigation of Alternative Splicing and ontology aspects of genes those have undergone these events in sorghum bicolor. We used homology based alignments between gene rich transcripts, represented by tentative consensus (TC) transcript sequences, and genomic scaffolds to deduce the structure of genes and identify alternatively spliced transcripts in sorghum. Using homology mapping of assembled expressed sequence tags with genomics data, we identified 2,137 Alternative Splicing events in S. bicolor. Our study showed that complex events and intron retention are the main types of Alternative Splicing events in S. bicolor and highlights the prevalence of splicing site recognition for definition of introns in this plant. Annotations of the alternatively spliced genes revealed that they represent diverse biological process and molecular functions, suggesting a fundamental role for Alternative Splicing in affecting the development and physiology of S. bicolor.

Evolutionarily Conserved Alternative Splicing Across Monocots

“…Maize has the largest collection of RNA-Seq data among the nine species examined, and also has the largest number of AS events, but the percentage of multi-exon genes that undergo AS is similar to other species. The proportions of genes that undergo AS and the total number of AS events are higher than previously reported for many plant species (Campbell et al 2006;Amborella Genome Project 2013;Walters et al 2013;Panahi et al 2014;Abdel-Ghany et al 2016). Similar to previous genome-wide AS studies Thatcher et al 2014;Chamala et al 2015;Mandadi and Scholthof 2015), IntronR was the most commonly observed AS event type in monocots.…”

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

“…3B). The average intron size in Hordeum was close to Sorghum [18], whereas longer than the average intron size of Arabidopsis [28]. These data also verified the hypothesis that AS events in barley is line with the intron definition model.…”

“…In contrast, only 6.3% of expressed genes were alternatively spliced in Brachypodium distachyon [26]. In Sorghum, Arabidopsis and Oryza intron retention is shown to be the major AS event occurring for at least 35% of genes [18,27,28] which indicated different rates of AS events among Brachipodium, Arabidopsis and Oryza.…”

“…Interestingly, integrating transcription and phosphorylation networks in different species suggested a positive correlation between the species complexity and the degree of cooperation in the network [15]. TFs and miRNAs are the major commanders of networks which have the potential role in regulation a large set of gene expression [16][17][18].…”

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

“…Previously, using the homology based mapping approach and expressed sequence tags (ESTs) representing the functional transcripts, we identified a total of 941 AS genes in Brachypodium distachyon, a model temperate grass (Sablok et al, 2011;Walters et al, 2013). Previous reports on the identification and prevalence of the alternative splicing events in rice (Campbell et al, 2006;Wang and Brendel, 2006), sorghum (Panahi et al, 2014), and maize (Thatcher et al, 2014) have shown the functional diversity changes through EST/RNA-seq approaches. Recently we also reported our efforts in identification of AS genes in rice (both japonica and indica), maize, and sorgum (Min et al, 2015).…”