scholarly journals The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Nature Plants ◽  
2016 ◽  
Vol 2 (11) ◽  
Author(s):  
Xiangchao Gan ◽  
Angela Hay ◽  
Michiel Kwantes ◽  
Georg Haberer ◽  
Asis Hallab ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Human Genetics ◽  
Morphological Evolution ◽  
Morphological Diversity ◽  
Close Relative ◽  
Gene Duplications ◽  
Tandem Gene Duplication ◽  
Genome Wide ◽  
Differential Gene

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

scholarly journals CopR, a global regulator of transcription to maintain copper homeostasis in Pyrococcus furiosus

2020 ◽  
Author(s):  
Felix Grünberger ◽  
Robert Reichelt ◽  
Ingrid Waege ◽  
Verena Ned ◽  
Korbinian Bronner ◽  
...  
Keyword(s):  
Essential Role ◽  
Pyrococcus Furiosus ◽  
Copper Homeostasis ◽  
Negative Stain ◽  
Cellular Life ◽  
Transmission Electron ◽  
Genome Wide ◽  
Binding Data ◽  
Differential Gene

AbstractAlthough copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analysed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process.To this end, we employed biochemical and biophysical methods to characterise the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the complex regulatory network that enables Pyrococcus to respond to increased copper concentrations.

scholarly journals Evolution of the potassium channel gene Kcnj13 underlies colour pattern diversification in Danio fish

2020 ◽  
Author(s):  
Marco Podobnik ◽  
Hans Georg Frohnhöfer ◽  
Christopher M. Dooley ◽  
Anastasia Eskova ◽  
Christiane Nüsslein-Volhard ◽  
...  
Keyword(s):  
Potassium Channel ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Colour Pattern ◽  
Minor Role ◽  
Cell Contact ◽  
Leading Role ◽  
Vertical Bars ◽  
Colour Patterns

AbstractThe genetic basis of morphological variation provides a major topic in evolutionary biology1-6. Colour patterns in fish are among the most diverse of all vertebrates. Species of the genus Danio display strikingly different colour patterns ranging from horizontal stripes, to vertical bars or spots7-10. Stripe formation in zebrafish, Danio rerio, oriented by the horizontal myoseptum, is a self-organizing process based on cell-contact-mediated interactions between three types of chromatophores with a leading role of iridophores11-14. We investigated genes known to regulate chromatophore interactions in zebrafish as candidates that might have evolved to produce a pattern of vertical bars in its sibling species, Danio aesculapii8,10. Using gene editing15-17 we generated several mutants in D. aesculapii that demonstrate a lower complexity in the interactions between chromatophores in this species, as well as a minor role of iridophores in patterning. Complementation tests in interspecific hybrids18,19 identified obelix/Kcnj13, which encodes an inwardly rectifying potassium channel (Kir7.1)20, as a gene evolved between D. rerio and D. aesculapii as well as in two of seven more Danio species tested. Our results demonstrate that the CRISPR/Cas9-system allows straightforward genetic tests also in non-model vertebrates to identify genes that underlie morphological evolution.

scholarly journals CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus

2021 ◽  
Vol 11 ◽  
Author(s):  
Felix Grünberger ◽  
Robert Reichelt ◽  
Ingrid Waege ◽  
Verena Ned ◽  
Korbinian Bronner ◽  
...  
Keyword(s):  
Essential Role ◽  
Pyrococcus Furiosus ◽  
Copper Homeostasis ◽  
Negative Stain ◽  
Cellular Life ◽  
Transmission Electron ◽  
Genome Wide ◽  
Binding Data ◽  
Differential Gene

Although copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analyzed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process. To this end, we employed biochemical and biophysical methods to characterize the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the regulatory network that enables Pyrococcus to respond to increased copper concentrations.

scholarly journals Genome-wide disruption of DNA methylation by 5-aza-2’-deoxycytidine in the parasitoid wasp Nasonia vitripennis

2018 ◽  
Author(s):  
Nicola Cook ◽  
Darren J Parker ◽  
Frances Turner ◽  
Eran Tauber ◽  
Bart A Pannebakker ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Evolutionary Biology ◽  
Sex Allocation ◽  
Phenotypic Expression ◽  
Parasitoid Wasp ◽  
Nasonia Vitripennis ◽  
Genomic Conflict ◽  
Genome Wide ◽  
A Genome

AbstractDNA methylation of cytosine residues across the genome influences how genes and phenotypes are regulated in a wide range of organisms. As such, understanding the role of DNA methylation and other epigenetic mechanisms has become very much a part of mapping genotype to phenotype, a major question in evolutionary biology. Ideally, we would like to manipulate DNA methylation patterns on a genome-wide scale, to help us to elucidate the role that epigenetic modifications play in phenotypic expression. Recently, the demethylating agent 5-aza-2’-deoxycytidine (5-aza-dC; commonly used in the epigenetic treatment of certain cancers), has been deployed to explore the epigenetic regulation of a number of traits of interest to evolutionary ecologists, including facultative sex allocation in the parasitoid wasp Nasonia vitripennis. In a recent study, we showed that treatment with 5-aza-dC did not ablate the facultative sex allocation response in Nasonia, but shifted the patterns of sex allocation in a way predicted by genomic conflict theory. This was the first (albeit indirect) experimental evidence for genomic conflict over sex allocation facilitated by DNA methylation. However, that work lacked direct evidence of the effects of 5-aza-dC on DNA methylation, and indeed the effect of the chemical has since been questioned in Nasonia. Here, using whole-genome bisulphite sequencing of more than 4 million CpGs, across more than 11,000 genes, we demonstrate unequivocally that 5-aza-dC disrupts methylation on a large scale across the Nasonia vitripennis genome. We show that the disruption can lead to both hypo- and hyper-methylation, may vary across tissues and time of sampling, and that the effects of 5-aza-dC are context- and sequence specific. We conclude that 5-aza-dC does indeed have the potential to be repurposed as a tool for studying the role of DNA methylation in evolutionary ecology, whilst many details of its action remain to be discovered.Author SummaryShedding light on the mechanistic basis of phenotypes is a major aim in the field of evolutionary biology. If we understand how phenotypes are controlled at the molecular level, we can begin to understand how evolution has shaped that phenotype and conversely, how genetic architecture may constrain trait evolution. Epigenetic markers (such as DNA methylation) also influence phenotypic expression by regulating how and when genes are expressed. Recently, 5-aza-2’-deoxycytidine (5-aza-dC), a hypomethylating agent used in the treatment of certain cancers, has been used to explore the epigenetic regulation of traits of interest to evolutionary ecologists. Previously, we used 5-aza-dC to validate a role for DNA methylation in facultative sex allocation behaviour in the parasitoid wasp Nasonia vitripennis. However, the direct effects of the chemical were not examined at that point and its efficacy in insects was questioned. Here, we demonstrate that 5-aza-dC disrupts DNA methylation on a genome-wide scale in a context- and sequence-specific manner and results in both hypo- and hyper-methylation. Our work demonstrates that 5-aza-dC has the potential to be repurposed as a tool for studying the role of DNA methylation in phenotypic expression.

Canalization and Robustness in Human Genetics and Disease

2020 ◽  
Vol 54 (1) ◽  
pp. 189-211 ◽  
Author(s):  
Greg Gibson ◽  
Kristine A. Lacek
Keyword(s):  
Human Genetics ◽  
Empirical Evaluation ◽  
Disease Prevalence ◽  
Adult Onset ◽  
Common Variants ◽  
Genotype By Environment ◽  
Genome Wide ◽  
Strong Inference ◽  
Number Of Individuals

Canalization refers to the evolution of populations such that the number of individuals who deviate from the optimum trait, or experience disease, is minimized. In the presence of rapid cultural, environmental, or genetic change, the reverse process of decanalization may contribute to observed increases in disease prevalence. This review starts by defining relevant concepts, drawing distinctions between the canalization of populations and robustness of individuals. It then considers evidence pertaining to three continuous traits and six domains of disease. In each case, existing genetic evidence for genotype-by-environment interactions is insufficient to support a strong inference of decanalization, but we argue that the advent of genome-wide polygenic risk assessment now makes an empirical evaluation of the role of canalization in preventing disease possible. Finally, the contributions of both rare and common variants to congenital abnormality and adult onset disease are considered in light of a new kerplunk model of genetic effects.

scholarly journals New genes from old: asymmetric divergence of gene duplicates and the evolution of development

2017 ◽  
Vol 372 (1713) ◽  
pp. 20150480 ◽  
Author(s):  
Peter W. H. Holland ◽  
Ferdinand Marlétaz ◽  
Ignacio Maeso ◽  
Thomas L. Dunwell ◽  
Jordi Paps
Keyword(s):  
Gene Duplication ◽  
Homeobox Genes ◽  
Morphological Diversity ◽  
Gene Duplications ◽  
Tandem Gene Duplication ◽  
Sequence Change ◽  
New Genes ◽  
Gene Duplicates ◽  
Evo Devo ◽  
Animal Genomes

Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such ‘asymmetric evolution’ seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

scholarly journals Analysis of the Placental Tissue Transcriptome of Normal and Preeclampsia Complicated Pregnancies

Acta Naturae ◽  
2014 ◽  
Vol 6 (2) ◽  
pp. 71-83 ◽  
Author(s):  
E. A. Trifonova ◽  
T. V. Gabidulina ◽  
N. I. Ershov ◽  
V. N. Serebrova ◽  
A. Yu. Vorozhishcheva ◽  
...  
Keyword(s):  
Intracellular Signaling ◽  
Molecular Mechanisms ◽  
Ischemia Reperfusion ◽  
Placental Tissue ◽  
Immunological Tolerance ◽  
Leading Role ◽  
New Genes ◽  
Genome Wide ◽  
Differential Gene

Preeclampsia is one of the most severe gestational complications which is one of the leading causes of maternal and perinatal morbidity and mortality. A growth in the incidence of severe and combined forms of the pathology has been observed in recent years. According to modern concepts, inadequate cytotrophoblast invasion into the spiral arteries of the uterus and development of the ischemia-reperfusion syndrome in the placental tissue play the leading role in the development of preeclampsia, which is characterized by multipleorgan failure. In this regard, our work was aimed at studying the patterns of placental tissue transcriptome that are specific to females with PE and with physiological pregnancy, as well as identifying the potential promising biomarkers and molecular mechanisms of this pathology. We have identified 63 genes whose expression proved to differ significantly in the placental tissue of females with PE and with physiological pregnancy. A cluster of differentially expressed genes (DEG) whose expression level is increased in patients with preeclampsia includes not only the known candidate genes that have been identified in many other genome-wide studies (e.g., LEP, BHLHB2, SIGLEC6, RDH13, BCL6), but also new genes (ANKRD37, SYDE1, CYBA, ITGB2, etc.), which can be considered as new biological markers of preeclampsia and are of further interest. The results of a functional annotation of DEG show that the development of preeclampsia may be related to a stress response, immune processes, the regulation of cell-cell interactions, intracellular signaling cascades, etc. In addition, the features of the differential gene expression depending on preeclampsia severity were revealed. We have found evidence of the important role of the molecular mechanisms responsible for the failure of immunological tolerance and initiation of the pro-inflammatory cascade in the development of severe preeclampsia. The results obtained elaborate the concept of the pathophysiology of preeclampsia and contain the information necessary to work out measures for targeted therapy of this disease.

scholarly journals Local adaptation fuels cryptic speciation in terrestrial annelids

2019 ◽  
Author(s):  
Daniel Fernández Marchán ◽  
Marta Novo ◽  
Nuria Sánchez ◽  
Jorge Domínguez ◽  
Darío J. Díaz Cosín ◽  
...  
Keyword(s):  
Geometric Morphometrics ◽  
Cryptic Species ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Phylogenetic Signal ◽  
Regulation Of Transcription ◽  
Cryptic Speciation ◽  
Evolutionary Forces ◽  
Genome Wide

AbstractUncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

scholarly journals The preeminent role of directional selection in generating extreme morphological change in Glyptodonts (Cingulata; Xenarthra)

2021 ◽  
Author(s):  
Fabio Andrade Machado ◽  
Gabriel Marroig ◽  
Alex Hubbe
Keyword(s):  
Morphological Evolution ◽  
Morphological Diversity ◽  
Directional Selection ◽  
Stabilizing Selection ◽  
Specialist Herbivore ◽  
Rates Of Evolution ◽  
Morphological Modification ◽  
Empirical Tests ◽  
Adaptive Zone

The prevalence of stasis on paleontological and comparative data has been classically taken as evidence of the strong role of stabilizing selection in shaping morphological evolution. When confronted against biologically informed predictions, empirical rates of evolution tend to fall below what is expected under genetic drift, suggesting that the signal for directional selection is erased at longer time scales. However, empirical tests of these claims are few and tend to focus on univariate traits, ignoring the potential roles of trait covariances in constraining evolution. Here we investigated the multivariate rates of morphological evolution in a fossil lineage that underwent extreme morphological modification, the glyptodonts. Contrary to what was expected, biologically informed models of evolution suggest a preeminent role of directional selection on the divergence of glyptodonts from living armadillos. Furthermore, the reconstruction of selection patterns shows that traits selected to generate a glytodont morphology are markedly different from those necessary to explain the extant armadillos' morphological diversity. Changes in both direction and magnitude of selection are probably tied to the invasion of a specialist-herbivore adaptive zone by glyptodonts. These results suggest that directional selection might have played a more important role in the evolution of extreme morphologies than previously imagined.

scholarly journals Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

2011 ◽  
Vol 279 (1732) ◽  
pp. 1277-1286 ◽  
Author(s):  
Bruce E. Deagle ◽  
Felicity C. Jones ◽  
Yingguang F. Chan ◽  
Devin M. Absher ◽  
David M. Kingsley ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Population Genomics ◽  
Haida Gwaii ◽  
Single Nucleotide ◽  
Genome Scans ◽  
Genetic Changes ◽  
Genome Wide ◽  
Outlier Loci ◽  
Genomic Regions

Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream–lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F ST between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream–lake outlier regions match those previously identified in marine–freshwater and benthic–limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream–lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.

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