Increased gene dosage and mRNA expression from chromosomal duplications in <i>Caenorhabditis elegans</i>

Ragipani, Bhavana; Albritton, Sarah Elizabeth; Morao, Ana Karina; Mesquita, Diogo; Kramer, Maxwell; Ercan, Sevinç

doi:10.1093/g3journal/jkac151

Cited by 3 publications

(2 citation statements)

References 56 publications

(71 reference statements)

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“…However, dosage compensation of individual autosomal genes is less well understood. Systematic transcriptional analysis suggests the degree of compensation can vary substantially at the level of individual genes, though the vast majority show no or only partial compensation (Malone et al, 2012; Ragipani et al, 2022).…”

Section: Resultsmentioning

confidence: 99%

Nonlinear readout of spatial cues underlies robustness of asymmetric cell division

Rodrigues,

Bland,

et al. 2023

Preprint

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A key challenge in the development of an organism is to maintain robust phenotypic outcomes in the face of perturbation. Yet, how such robust outcomes are encoded by developmental networks remains poorly explored. Here we use theC. eleganszygote as a model to understand sources of developmental robustness during PAR polarity-dependent asymmetric cell division. By quantitatively linking alterations in protein dosage to phenotype in individual embryos, we show that spatial information in the zygote is read out in a highly nonlinear fashion and, as a result, phenotypes are highly canalized against substantial variation in input signals. Specifically, our data point towards an intrinsic robustness of the conserved PAR polarity network that renders polarity axis specification resistant to variations in both the strength of upstream symmetry-breaking cues and PAR protein dosage. At the same time, we find that downstream pathways involved in cell size and fate asymmetry are similarly robust to dosage-dependent changes in the local concentrations of PAR proteins, implying non-trivial complexity in translating PAR signals into pathway outputs. We propose that “quantitative decoupling” of symmetry-breaking, polarity, and asymmetric division modules acts to suppress the accumulation of error as embryos move along this developmental trajectory, thereby ensuring that asymmetric division is robust to perturbation. Such modular organization of developmental networks is likely to be a general mechanism to achieve robust developmental outcomes.

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Section: Resultsmentioning

confidence: 99%

Nonlinear readout of spatial cues underlies robustness of asymmetric cell division

Rodrigues,

Bland,

et al. 2023

Preprint

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“…These novel functions can be retained if they confer a fitness benefit that makes an organism better adapted to its environment (Pearce et al 2017). In addition to providing fuel for evolutionary novelties, an increase in gene dosage can lead to higher expression levels of a gene family, thus increasing the likelihood of translation of those proteins (Ragipani et al 2022). Along with this, changes in gene expression at particular loci can facilitate an organism’s adaptation to its surroundings (López-Maury et al 2008; Nourmohammad et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics and the salivary transcriptome of the redbanded stink bug shed light on its high damage potential to soybean

Walt,

King,

Towles

et al. 2023

Preprint

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The redbanded stink bug,Piezodorus guildinii(Westwood) (Hemiptera: Pentatomidae), is a significant soybean pest in the Americas, inflicting more physical damage on soybean than other native stink bugs. Studies suggest that its heightened impact is attributed to the aggressive digestive properties of its saliva. Despite its agricultural importance, the factors driving its greater ability to degrade plant tissues have remained unexplored in a genomic evolutionary context. In this study, we hypothesized that lineage-specific gene family expansions have increased the dosage of digestive genes expressed in the salivary glands. To investigate this, we annotated a previously published genome assembly of the redbanded stink bug and performed a comparative genomic analysis on 11 hemipteran species and reconstructed patterns of gene duplication, gain, and loss in the redbanded stink bug. We also performed RNA-seq on the redbanded stink bug’s salivary tissues, along with the rest of the body without salivary glands. We identified hundreds of differentially expressed salivary genes, including a subset lost in other stink bug lineages but retained and expressed in the redbanded stink bug’s salivary glands. These genes were significantly enriched with protein families involved in proteolysis, potentially explaining the redbanded stink bug’s heightened damage to soybeans. Contrary to our hypothesis, we found no support for an increased dosage of digestive genes in the salivary glands of the redbanded stink bug. Nonetheless, these results provide insight into the evolution of this important crop pest, establishing a link between its genomic history and its agriculturally important physiology.SIGNIFICANCE STATEMENTThe redbanded stink bug, an important soybean pest in the Americas, inflicts greater damage to soybean due to higher salivary digestion. We employed comparative genomics and analyses of the salivary transcriptome to explore this and found that the differential retention of ancestral salivary genes may explain this phenomenon better than gene gains or duplications in the redbanded stink bug genome. We identify a distinct set of genes in the salivary gland that were differentially retained and expressed in the redbanded stink bug lineage, demonstrating enrichment in proteolytic function. This discovery offers a potential explanation for the redbanded stink bug’s elevated damage to soybean crops.

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Comparative Genomics and the Salivary Transcriptome of the Redbanded Stink Bug Shed Light on Its High Damage Potential to Soybean

Walt,

King,

Towles

et al. 2024

Genome Biology and Evolution

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The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae), is a significant soybean pest in the Americas, which inflicts more physical damage on soybean than other native stink bugs. Studies suggest that its heightened impact is attributed to the aggressive digestive properties of its saliva. Despite its agricultural importance, the factors driving its greater ability to degrade plant tissues have remained unexplored in a genomic evolutionary context. In this study, we hypothesized that lineage-specific gene family expansions have increased the copy number of digestive genes expressed in the salivary glands. To investigate this, we annotated a previously published genome assembly of the redbanded stink bug, performed a comparative genomic analysis on 11 hemipteran species, and reconstructed patterns of gene duplication, gain, and loss in the redbanded stink bug. We also performed RNA-seq on the redbanded stink bug's salivary tissues, along with the rest of the body without salivary glands. We identified hundreds of differentially expressed salivary genes, including a subset lost in other stink bug lineages, but retained and expressed in the redbanded stink bug's salivary glands. These genes were significantly enriched with protein families involved in proteolysis, potentially explaining the redbanded stink bug's heightened damage to soybeans. Contrary to our hypothesis, we found no support for an enrichment of duplicated digestive genes that are also differentially expressed in the salivary glands of the redbanded stink bug. Nonetheless, these results provide insight into the evolution of this important crop pest, establishing a link between its genomic history and its agriculturally important physiology.

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Increased gene dosage and mRNA expression from chromosomal duplications in Caenorhabditis elegans

Cited by 3 publications

References 56 publications

Nonlinear readout of spatial cues underlies robustness of asymmetric cell division

Nonlinear readout of spatial cues underlies robustness of asymmetric cell division

Comparative genomics and the salivary transcriptome of the redbanded stink bug shed light on its high damage potential to soybean

Comparative Genomics and the Salivary Transcriptome of the Redbanded Stink Bug Shed Light on Its High Damage Potential to Soybean

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