Evolutionarily Conserved Alternative Splicing Across Monocots

Abstract

One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau

“…Alternative splicing is closely associated with many abiotic stresses (salt stress, drought, flooding, temperature, etc.) 56 and contributes to the evolution of phenotypic novelty 57 . We also detected genes related to DNA repair and recombination, including nucleotide excision repair and homologous recombination.…”

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

“…Alternative splicing (AS) can increase a complexity of transcriptome and proteome via generating multiple transcripts and protein isoforms from the single gene. Up to 95% of mammalian precursor messenger RNAs (pre-mRNAs) are alternatively spliced ( Pan et al, 2008 ) whereas recent studies in higher plants suggest that AS is fairly conserved ( Mei et al, 2017a ) and is observed in approximately 42–61% of intron-containing genes ( Filichkin et al, 2010 ; Marquez et al, 2012 ). Common types of AS include intron retention (IR), exon skipping (ES), the alternative donor (alt 5′) or acceptor (alt 3′) splice site, and mutually exclusive exons ( Figure 1A ).…”

A Genomic View of Alternative Splicing of Long Non-coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families

“…A study of a drought-resistant rice breeding line found drought-specific splicing events as well as differences in the functions of genes undergoing AS (Wei et al, 2017 ). Evidence for evolutionary conservation of AS events across syntenous species suggests that the functions of AS in the stress responses of wheat and maize are likely to exist in rice as well (Mei et al, 2017a ).…”