Aberrant RNA splicing due to genetic incompatibilities in sunflower hybrids

Smith, Chris C. R.; Hulke, Brent S.; Kane, Nolan C.

doi:10.1111/evo.14360

Cited by 9 publications

(9 citation statements)

References 61 publications

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“…Previous studies showed how isoforms with species‐specific expression resulted in functional divergence between proteins of the same family and hence drove divergence of phenotypic traits between species (Huang et al., 2021; Smith et al., 2018; Smith et al., 2021; Thatcher et al., 2014; Zhang, Wang, et al., 2017). Also, when comparing isoforms between the two Nelumbo species, we identified 4854 N. nucifera genes and 4424 N. lutea genes that gave rise to lineage‐specific isoforms in each of their respective lineages.…”

Section: Discussionmentioning

confidence: 99%

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

et al. 2022

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Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear.Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.

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Section: Discussionmentioning

confidence: 99%

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

et al. 2022

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“…In plants, the domestication process has generated multiple examples of rapid adaptation via AS [19][20][21][22]. One example of this is the EARLY MATURITY 8 (EAM8) gene in barley [19], which is an orthologue of the circadian core component EARLY FLOWERING 3 (ELF3) in Arabidopsis thaliana.…”

Section: Alternative Splicing Isoforms As Source Of Transcriptome And...mentioning

confidence: 99%

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

Dwivedi,

Quiroz,

Reddy

et al. 2023

IJMS

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Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.

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“…Subsequent steps to filter the transcriptome, retain high confidence alternative isoforms, and test for differential splicing were the same as described previously (Smith et al, 2021). Briefly, we required alternative isoforms to align to the same genomic region, otherwise we labeled the isoforms as separate genes.…”

Section: Differential Splicingmentioning

confidence: 99%

Gene expression and alternative splicing contribute to adaptive divergence of ecotypes

Innes

Goebl

Smith

et al. 2023

Preprint

Self Cite

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Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. Alternative splicing (AS) is a post-transcriptional regulatory mechanism in eukaryotes that generates multiple different transcripts (isoforms) from a single gene and thus may provide a source of evolutionary novelty. In plants, AS a compelling potential target of natural selection because it plays important roles in both development and abiotic stress response. We investigated whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation between ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for a substantial contribution of trans-regulation. Genes that show significant differential expression and/or differential splicing are enriched for functions involving seed development, abiotic stress response, nutrient acquisition, and photosynthesis, some of which relate to known adaptive traits. Our results emphasize that alternative splicing has been underappreciated as a mechanism providing variation for natural selection to act upon at short time scales.

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Aberrant RNA splicing due to genetic incompatibilities in sunflower hybrids

Cited by 9 publications

References 61 publications

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

Gene expression and alternative splicing contribute to adaptive divergence of ecotypes

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