Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis

RNA-seq analysis reveals transcriptome reprogramming and alternative splicing during early response to salt stress in tomato root

Salt stress is one of the dominant abiotic stress conditions that cause severe damage to plant growth and, in turn, limiting crop productivity. It is therefore crucial to understand the molecular mechanism underlying plant root responses to high salinity as such knowledge will aid in efforts to develop salt-tolerant crops. Alternative splicing (AS) of precursor RNA is one of the important RNA processing steps that regulate gene expression and proteome diversity, and, consequently, many physiological and biochemical processes in plants, including responses to abiotic stresses like salt stress. In the current study, we utilized high-throughput RNA-sequencing to analyze the changes in the transcriptome and characterize AS landscape during the early response of tomato root to salt stress. Under salt stress conditions, 10,588 genes were found to be differentially expressed, including those involved in hormone signaling transduction, amino acid metabolism, and cell cycle regulation. More than 700 transcription factors (TFs), including members of the MYB, bHLH, and WRKY families, potentially regulated tomato root response to salt stress. AS events were found to be greatly enhanced under salt stress, where exon skipping was the most prevalent event. There were 3709 genes identified as differentially alternatively spliced (DAS), the most prominent of which were serine/threonine protein kinase, pentatricopeptide repeat (PPR)-containing protein, E3 ubiquitin-protein ligase. More than 100 DEGs were implicated in splicing and spliceosome assembly, which may regulate salt-responsive AS events in tomato roots. This study uncovers the stimulation of AS during tomato root response to salt stress and provides a valuable resource of salt-responsive genes for future studies to improve tomato salt tolerance.

The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane (Platanus × acerifolia)

Transcription and alternative splicing (AS) are now appreciated in plants, but few studies have examined the effects of changing ploidy on transcription and AS. In this study, we showed that artificially autododecaploid plants of London plane (Platanus × acerifolia (Aiton) Willd) had few flowers relative to their hexaploid progenitors. Transcriptome analysis based on full-length Oxford Nanopore Technologies (ONTs) and next-generation sequencing (NGS) revealed that the increased ploidy level in P. × acerifolia led to more transcribed isoforms, accompanied by an increase in the number of isoforms per gene. The functional enrichment of genes indicated that novel genes transcribed specifically in the dodecaploids may have been highly correlated with the ability to maintain genome stability. The dodecaploids showed a higher number of genes with upregulated differentially expressed genes (DEGs) compared with the hexaploid counterpart. The genome duplication of P. × acerifolia resulted mainly in the DEGs involved in basic biological pathways. It was noted that there was a greater abundance of alternative splicing (AS) events and AS genes in the dodecaploids compared with the hexaploids in P. × acerifolia. In addition, a significant difference between the structure and expression of AS events between the hexaploids and dodecaploids of Platanus was found. Of note, some DEGs and differentially spliced genes (DSGs) related to floral transition and flower development were consistent with the few flower traits in the dodecaploids of P. × acerifolia. Collectively, our findings explored the difference in transcription and AS regulation between the hexaploids and dodecaploids of P. × acerifolia and gained new insight into the molecular mechanisms underlying the few-flower phenotype of P. × acerifolia. These results contribute to uncovering the regulatory role of transcription and AS in polyploids and breeding few-flower germplasms.

Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species

To date, several transcriptomic studies during fruit development have been reported; however, no comprehensive integrated study on expression diversity, alternative splicing, and metabolomic profiling was reported in Capsicum. This study analyzed RNA-seq data and untargeted metabolomic profiling from early green (EG), mature green (MG), and breaker (Br) fruit stages from two Capsicum species, i.e., C. annuum (Cann) and C. frutescens (Cfrut) from Northeast India. A total of 117,416 and 96,802 alternatively spliced events (AltSpli-events) were identified from Cann and Cfrut, respectively. Among AltSpli-events, intron retention (IR; 32.2% Cann and 25.75% Cfrut) followed by alternative acceptor (AA; 15.4% Cann and 18.9% Cfrut) were the most abundant in Capsicum. Around 7600 genes expressed in at least one fruit stage of Cann and Cfrut were AltSpli. The study identified spliced variants of genes including transcription factors (TFs) potentially involved in fruit development/ripening (Aux/IAA 16-like, ETR, SGR1, ARF, CaGLK2, ETR, CaAGL1, MADS-RIN, FUL1, SEPALLATA1), carotenoid (PDS, CA1, CCD4, NCED3, xanthoxin dehydrogenase, CaERF82, CabHLH100, CaMYB3R-1, SGR1, CaWRKY28, CaWRKY48, CaWRKY54), and capsaicinoids or flavonoid biosynthesis (CaMYB48, CaWRKY51), which were significantly differentially spliced (DS) between consecutive Capsicum fruit stages. Also, this study observed that differentially expressed isoforms (DEiso) from 38 genes with differentially spliced events (DSE) were significantly enriched in various metabolic pathways such as starch and sucrose metabolism, amino acid metabolism, cysteine cutin suberin and wax biosynthesis, and carotenoid biosynthesis. Furthermore, the metabolomic profiling revealed that metabolites from aforementioned pathways such as carbohydrates (mainly sugars such as D-fructose, D-galactose, maltose, and sucrose), organic acids (carboxylic acids), and peptide groups significantly altered during fruit development. Taken together, our findings could help in alternative splicing-based targeted studies of candidate genes involved in fruit development and ripening in Capsicum crop.

Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures

Alternative splicing is an important mechanism for the regulation of gene expression in eukaryotes during development, cell differentiation or stress response. Alterations in the splicing profiles of genes under high temperatures that cause heat stress (HS) can impact the maintenance of cellular homeostasis and thermotolerance. Consequently, information on factors involved in HS-sensitive alternative splicing is required to formulate the principles of HS response. Serine/arginine-rich (SR) proteins have a central role in alternative splicing. We aimed for the identification and characterization of SR-coding genes in tomato (Solanum lycopersicum), a plant extensively used in HS studies. We identified 17 canonical SR and two SR-like genes. Several SR-coding genes show differential expression and altered splicing profiles in different organs as well as in response to HS. The transcriptional induction of five SR and one SR-like genes is partially dependent on the master regulator of HS response, HS transcription factor HsfA1a. Cis-elements in the promoters of these SR genes were predicted, which can be putatively recognized by HS-induced transcription factors. Further, transiently expressed SRs show reduced or steady-state protein levels in response to HS. Thus, the levels of SRs under HS are regulated by changes in transcription, alternative splicing and protein stability. We propose that the accumulation or reduction of SRs under HS can impact temperature-sensitive alternative splicing.

Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops

Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.

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

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).

Transcriptomics and Alternative Splicing Analyses Reveal Large Differences between Maize Lines B73 and Mo17 in Response to Aphid Rhopalosiphum padi Infestation

Maize (Zea mays L.) is a staple crop worldwide with extensive genetic variations. Various insects attack maize plants causing large yield loss. Here, we investigated the responses of maize B73, a susceptible line, and Mo17, a resistant line, to the aphid Rhopalosiphum padi on metabolite and transcriptome levels. R. padi feeding had no effect on the levels of the defensive metabolites benzoxazinoids (Bxs) in either line, and Mo17 contained substantially greater levels of Bxs than did B73. Profiling of the differentially expressed genes revealed that B73 and Mo17 responded to R. padi infestation specifically, and importantly, these two lines showed large gene expression differences even without R. padi herbivory. Correlation analysis identified four transcription factors (TFs) that might account for the high Bx levels in Mo17. Similarly, genome-wide alternative splicing (AS) analyses indicated that both B73 and Mo17 had temporally specific responses to R. padi infestation, and these two lines also exhibited large differences of AS regulation under normal condition, and 340 genes, including 10 TFs, were constantly differentially spliced. This study provides large-scale resource datasets for further studies on the mechanisms underlying maize-aphid interactions, and highlights the phenotypic divergence in defense against aphids among maize varieties.