Genomic expression dominance in allopolyploids

The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage‐specific adaptive evolution of protein‐coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post‐transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA‐dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.

show abstract

“…13 Ma and show ca. 22% DE, Jiang et al., 2013; e.g., Gossypium species diverged 5–10 Ma and show up to 53% DE, Rapp, Udall, & Wendel, 2009). …”

Section: Discussionmentioning

confidence: 99%

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Both of these findings represented the expression dominance of one genome over the other, but they are different phenomena: one is in terms of which homoeologous gene copy is most expressed and the other is in terms of the overall expression of all gene copies at a locus (see Figure 1). There has been some confusion in the literature since this discovery, as both phenomena have been referred to as 'genome dominance' (for example, Rapp et al, 2009;Schnable et al, 2011). To clarify this, the Yoo et al (2013) paper in this issue suggests that 'expression-level dominance' should be used to refer to patterns of overall gene expression (termed 'genome dominance' in Rapp et al, 2009), and 'homoeolog expression bias' should be used to refer to patterns in the ratio of homoeologous expression (referred to as 'genome dominance' in Schnable et al, 2011).…”

mentioning

confidence: 99%

“…The microarrays measuring total expression of each locus showed a new phenomenon: the expression level of each locus in allopolyploid genomes was often similar to the level found at that locus in one and not the other parental diploid species (Rapp et al, 2009). Both of these findings represented the expression dominance of one genome over the other, but they are different phenomena: one is in terms of which homoeologous gene copy is most expressed and the other is in terms of the overall expression of all gene copies at a locus (see Figure 1).…”

mentioning

confidence: 99%

“…Taking cotton as their study system over the past decade, the Wendel lab have applied a portfolio of newly emerging technologies to characterise patterns of gene expression in wild and cultivated species of diploid and allopolyploid cotton. Starting with singlestranded conformation polymorphism analysis (Adams et al, 2003), they moved on to two generations of Nimblegen microarrays (Udall et al, 2006(Udall et al, , 2007Flagel et al, 2008;Hovav et al, 2008;Rapp et al, 2009), Sequenom MassARRAYs (Chaudhary et al, 2009), proteomics (Hu et al, 2011), and as reported by Yoo et al (2013), high coverage Illumina sequencing.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Unravelling gene expression of complex crop genomes

Buggs¹

2012

Heredity

View full text Add to dashboard Cite

“…Hybridization between two species can result in extensive changes in gene expression, and that has been a topic of considerable interest with numerous studies having been published in the last few years. Both up-and downregulation of gene expression levels compared with their parents have been shown in various diploid, triploid, allotetraploid, and allohexaploid hybrids (e.g., Hegarty et al 2006Hegarty et al , 2009Wang et al 2006a;Rapp et al 2009). Other studies that assayed expression levels of individual alleles in a diploid hybrid or homeologs in an allopolyploid revealed allelic expression biases and silencing of one allele (e.g., Springer and Stupar 2007b;Flagel et al 2008;Hovav et al 2008;Zhang and Borevitz 2009).…”

mentioning

confidence: 99%

An Interspecific Plant Hybrid Shows Novel Changes in Parental Splice Forms of Genes for Splicing Factors

Scascitelli

Cognet²,

Adams

2010

Genetics

View full text Add to dashboard Cite

Interspecific hybridization plays an important role in plant adaptive evolution and speciation, and the process often results in phenotypic novelty. Hybrids can show changes in genome structure and gene expression compared with their parents including chromosomal rearrangments, changes in cytosine methylation, up-and downregulation of gene expression, and gene silencing. Alternative splicing (AS) is a fundamental aspect of the expression of many genes. However alternative splicing patterns have not been examined in multiple genes in an interspecific plant hybrid compared with its parents. Here we studied alternative splicing patterns in an interspecific Populus hybrid and its parents by assaying 40 genes using reverse transcription PCR. Most of the genes showed identical alternative splicing patterns between the parents and the hybrid. We found new alternative splicing variants present in the hybrid in two SR genes involved in the regulation of splicing and alternative splicing. The novel alternative splicing patterns included changes in donor and acceptor sites to create a new exon in one allele of PtRSZ22 in the hybrid and retention of an intron in both alleles of PtSR34a.1 in the hybrid, with effects on the function of the corresponding truncated proteins, if present. Our results suggest that novel alternative splicing patterns are present in a small percentage of genes in hybrids, but they could make a considerable impact on the expression of some genes. Changes in alternative splicing are likely to be an important component of the genetic changes that occur upon interspecific hybridization.

show abstract

Genomic expression dominance in allopolyploids

Abstract: Background: Allopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).

Cited by 254 publications

References 41 publications

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

Unravelling gene expression of complex crop genomes

An Interspecific Plant Hybrid Shows Novel Changes in Parental Splice Forms of Genes for Splicing Factors

Contact Info

Product

Resources

About