Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Abstract

Tomato ( Solanum lycopersicum ) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database ( http://proteomics.ysu.edu/altsplice ).

Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

“…These results are consistent with findings obtained for tomato and Ananas comosus var. bracteatus (Clark et al, 2019;Ma et al, 2019).…”

“…In plants, AS is a universal phenomenon with pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses (Filichkin et al, 2015;Sun and Xiao, 2015;Gallegos, 2018;Ruan et al, 2018;Szakonyi and Duque, 2018;Wang et al, 2018;Calixto et al, 2019;Park et al, 2019;Yang et al, 2019). For example, in peanut (Arachis hypogaea), Arabidopsis thaliana, soybean (Glycine max), tomato (Solanum lycopersicum) and moso bamboo (Phyllostachys edulis), approximately 37%, 61%, 63%, 65%, and 49% of multi-exon genes undergo AS events, respectively (Marquez et al, 2012;Shen et al, 2014;Ruan et al, 2018;Zhao et al, 2018;Clark et al, 2019). Furthermore, researchers have found that AS also plays important roles in male and female gametogenesis, seed germination in A. thaliana, plant-pathogen interactions in wheat (Triticum aestivum), and mineral nutrient homeostasis maintenance in rice (Oryza sativa) (Dong et al, 2018;Forsthoefel et al, 2018;Tognacca et al, 2019;Zhang H. et al, 2019).…”

Alternative Splicing and DNA Damage Response in Plants

“…Up to 95% of human and 70% of plant multi-exonic genes are alternatively spliced (Pan et al, 2008;Marquez et al, 2012;Chamala et al, 2015;Zhang et al, 2017b). Further studies report that about 50% of the genes in soybeans, 46% in rice, 40% in maize, and over 60% in tomatoes and barley undergo AS (Thatcher et al, 2014;Chamala et al, 2015;Clark et al, 2019;Rapazote-Flores et al, 2019), emphasizing its importance in crop plant development and environmental response. AS has a broad role in many aspects of plant biology, but its role in responding to DNA damage is mostly unknown and requires further investigation.…”

Characterization of Local and Systemic Impact of Whitefly (Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics

“…Despite their reduced coding capacity relative to other viruses, begomoviruses effectively manipulate multiple critical plant biological processes including plant hormone signaling pathways, cell cycle progression [ 9 , 10 ], DNA replication [ 11 ], mRNA maturation and export [ 12 , 13 ], translation [ 14 ], and the epigenetic regulation of gene expression [ 15 , 16 , 17 ]. Numerous observations have been made that provide insight into how begomoviruses mediate this range of effects on biological processes using so few proteins.…”