ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology

Abstract ParameciumDB (https://paramecium.i2bc.paris-saclay.fr) is a community model organism database for the genome and genetics of the ciliate Paramecium. ParameciumDB development relies on the GMOD (www.gmod.org) toolkit. The ParameciumDB web site has been publicly available since 2006 when the P. tetraurelia somatic genome sequence was released, revealing that a series of whole genome duplications punctuated the evolutionary history of the species. The genome is linked to available genetic data and stocks. ParameciumDB has undergone major changes in its content and website since the last update published in 2011. Genomes from multiple Paramecium species, especially from the P. aurelia complex, are now included in ParameciumDB. A new modern web interface accompanies this transition to a database for the whole Paramecium genus. Gene pages have been enriched with orthology relationships, among the Paramecium species and with a panel of model organisms across the eukaryotic tree. This update also presents expert curation of Paramecium mitochondrial genomes.

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The EcoCyc Database in 2021

Frontiers in Microbiology ◽

10.3389/fmicb.2021.711077 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ingrid M. Keseler ◽

Socorro Gama-Castro ◽

Amanda Mackie ◽

Richard Billington ◽

César Bonavides-Martínez ◽

...

Keyword(s):

Metabolic Pathways ◽

Regulation Of Gene Expression ◽

Model Organism ◽

Web Interface ◽

Model Organism Database ◽

Manual Curation ◽

Genome Viewer ◽

User Access ◽

Visualization Tools ◽

K 12

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

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Evolutionary History and Functional Characterization of the Amphibian Xenosensor CAR

Molecular Endocrinology ◽

10.1210/me.2011-1235 ◽

2012 ◽

Vol 26 (1) ◽

pp. 14-26 ◽

Cited By ~ 21

Author(s):

Marianne Mathäs ◽

Oliver Burk ◽

Huan Qiu ◽

Christian Nußhag ◽

Ute Gödtel-Armbrust ◽

...

Keyword(s):

Evolutionary History ◽

Functional Characterization ◽

Constitutive Androstane Receptor ◽

Pregnane X Receptor ◽

Constitutive Activity ◽

Whole Genome Duplications ◽

Genome Duplications ◽

History Of ◽

Land Vertebrates

Abstract The xenosensing constitutive androstane receptor (CAR) is widely considered to have arisen in early mammals via duplication of the pregnane X receptor (PXR). We report that CAR emerged together with PXR and the vitamin D receptor from an ancestral NR1I gene already in early vertebrates, as a result of whole-genome duplications. CAR genes were subsequently lost from the fish lineage, but they are conserved in all taxa of land vertebrates. This contrasts with PXR, which is found in most fish species, whereas it is lost from Sauropsida (reptiles and birds) and plays a role unrelated to xenosensing in Xenopus. This role is fulfilled in Xenopus by CAR, which exhibits low basal activity and pronounced responsiveness to activators such as drugs and steroids, altogether resembling mammalian PXR. The constitutive activity typical for mammalian CAR emerged first in Sauropsida, and it is thus common to all fully terrestrial land vertebrates (Amniota). The constitutive activity can be achieved by humanizing just two amino acids of the Xenopus CAR. Taken together, our results provide a comprehensive reconstruction of the evolutionary history of the NR1I subfamily of nuclear receptors. They identify CAR as the more conserved and remarkably plastic NR1I xenosensor in land vertebrates. Nonmammalian CAR should help to dissect the specific functions of PXR and CAR in the metabolism of xeno- and endobiotics in humans. Xenopus CAR is a first reported amphibian xenosensor, which opens the way to toxicogenomic and bioaugmentation studies in this critically endangered taxon of land vertebrates.

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Evolution of Lysine-Specific Demethylase 1 and REST Corepressor Gene Families and Their Molecular Interaction

10.21203/rs.3.rs-1106901/v1 ◽

2021 ◽

Author(s):

Montserrat Olivares ◽

Gianluca Merello ◽

Daniel Verbel ◽

Marcela Gonzalez ◽

María Andrés ◽

...

Keyword(s):

Catalytic Activity ◽

Molecular Biology ◽

Gene Families ◽

Whole Genome ◽

Model Species ◽

Whole Genome Duplications ◽

Lysine Specific Demethylase ◽

Genome Duplications ◽

History Of ◽

The Common

Abstract Lysine-specific demethylase 1A (LSD1) binds to RCOR gene family of corepressors to erase transcriptionally active marks on histones. Functional diversity in these complexes depends on the type of RCOR included, which modulates the complex´s catalytic activity. We studied the duplicative history of RCOR and LSD gene families, and analyzed the evolution of their interaction. We found that RCOR genes are the product of the two rounds of whole-genome duplications that occurred early in vertebrate evolution. In contrast, the origin of the LSD genes traces back before to the divergence of animals and plants. Coimmunoprecipitation experiments using resurrected RCOR and LSD1 proteins of the jawed vertebrate ancestor, and the common hop, date the origin of LSD1-RCOR interaction to the ancestor of animals, fungi, and plants. Overall, we trace LSD1-RCOR complex evolution and propose that animal, fungi, and plant non-model species offer advantages in addressing questions about the molecular biology of this epigenetic complex.

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Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe

Molecular Biology and Evolution ◽

10.1093/molbev/msaa327 ◽

2020 ◽

Author(s):

Xinyi Guo ◽

Terezie Mandáková ◽

Karolína Trachtová ◽

Barış Özüdoğru ◽

Jianquan Liu ◽

...

Keyword(s):

Genome Evolution ◽

Reticulate Evolution ◽

Land Plant ◽

Whole Genome ◽

Plant Family ◽

Whole Genome Duplications ◽

Genome Duplications ◽

History Of ◽

Single Genus ◽

Genomic Relatedness

Abstract Pervasive hybridization and whole genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. While frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (c. 60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring post-polyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.

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Universal trends of post-duplication evolution revealed by the genomes of 13 Paramecium species sharing an ancestral whole-genome duplication

10.1101/573576 ◽

2019 ◽

Cited By ~ 2

Author(s):

Jean-Francois Gout ◽

Parul Johri ◽

Olivier Arnaiz ◽

Thomas G. Doak ◽

Simran Bhullar ◽

...

Keyword(s):

Gene Loss ◽

Genome Duplication ◽

Model Organism ◽

Whole Genome ◽

Segmental Duplications ◽

Gene Repertoire ◽

Paramecium Tetraurelia ◽

Selective Pressures ◽

Whole Genome Duplications ◽

Genome Duplications

AbstractWhole-Genome Duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD-derived paralogs are maintained over long evolutionary periods and the relative contributions of different selective pressures to their maintenance is still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the P. aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and one additional outgroup, allowing us to track post-WGD evolution in 13 species that share a common ancestral WGD. We found similar biases in gene retention compatible with dosage constraints playing a major role opposing post-WGD gene loss across all 13 species. Interestingly we found that post-WGD gene loss was slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. We also report a lack of recent segmental duplications in Paramecium, which we interpret as additional evidence for strong selective pressures against individual genes dosage changes. Finally, we hope that this exceptional dataset of 13 species sharing an ancestral WGD and two closely related outgroup species will be a useful resource for future studies and will help establish Paramecium as a major model organism in the study of post-WGD evolution.

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Evolutionary history of an Alpine archaeognath (Machilis pallida) – insights from different variant types

10.1101/2021.09.17.460766 ◽

2021 ◽

Author(s):

Marlene Haider ◽

Martin P. Schilling ◽

Markus H. Moest ◽

Florian M. Steiner ◽

Birgit C. Schlick-Steiner ◽

...

Keyword(s):

Genome Organization ◽

Evolutionary Biology ◽

Evolutionary History ◽

De Novo ◽

Model Organisms ◽

De Novo Transcriptome ◽

History Of ◽

The Alps ◽

Nuclear Variation ◽

Genetic Signatures

AbstractReconstruction of species histories is a central aspect of evolutionary biology. Patterns of genetic variation within and among populations can be leveraged to elucidate evolutionary processes and demographic histories. However, interpreting genetic signatures and unraveling the contributing processes can be challenging, in particular for non-model organisms with complex reproductive modes and genome organization. One way forward is the combined consideration of patterns revealed by different molecular markers (nuclear vs. mitochondrial) and types of variants (common vs. rare) that differ in their age, mode and rate of evolution. Here, we applied this approach to Machilis pallida (Archaeognatha), an Alpine jumping bristletail considered parthenogenetic and triploid. We generated de-novo transcriptome and mitochondrial assemblies to obtain high-density data to investigate patterns of mitochondrial and common and rare nuclear variation in 17 M. pallida individuals sampled across the Alps from all known populations. We find that the different variant types capture distinct aspects of the evolutionary history and discuss the observed patterns in the context of parthenogenesis, polyploidy and survival during glaciation. This study highlights the potential of different variant types to unravel complex evolutionary scenarios and the suitability of M. pallida and the genus Machilis as a study system for the evolution of sexual strategies and polyploidization during environmental change. We also emphasize the need for further research which will be stimulated and facilitated by these newly generated resources and insights.

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The Aquilegia genome reveals a hybrid origin of core eudicots

10.1101/407973 ◽

2018 ◽

Cited By ~ 1

Author(s):

Gökçe Aköz ◽

Magnus Nordborg

Keyword(s):

Evolutionary History ◽

Genetic Material ◽

Diploid Species ◽

Hybrid Origin ◽

The Core ◽

Whole Genome Duplications ◽

Core Eudicots ◽

Eventual Return ◽

Genome Duplications ◽

History Of

AbstractBackgroundWhole-genome duplications (WGD) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots.ResultsWithin-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization, and that core eudicots thus have a hybrid origin.ConclusionsNovel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.

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Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales

10.1101/789040 ◽

2019 ◽

Cited By ~ 4

Author(s):

Makenzie E. Mabry ◽

Julia M. Brose ◽

Paul D. Blischak ◽

Brittany Sutherland ◽

Wade T. Dismukes ◽

...

Keyword(s):

Evolutionary History ◽

Whole Genome ◽

Genome Survey ◽

Whole Genome Duplications ◽

The Family ◽

Genome Duplications ◽

Duplication Events ◽

History Of ◽

Inference Methods ◽

Ideal Group

ABSTRACTWhole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. However, while its sister family, Cleomaceae, has also been characterized by a WGD, its placement, as well as that of other WGD events in other families in the order, remains unclear. Using phylo-transcriptomics from 74 taxa and genome survey sequencing for 66 of those taxa, we infer nuclear and chloroplast phylogenies to assess relationships among the major families of the Brassicales and within the Brassicaceae. We then use multiple methods of WGD inference to assess placement of WGD events. We not only present well-supported chloroplast and nuclear phylogenies for the Brassicales, but we also putatively place Th-α and provide evidence for previously unknown events, including one shared by at least two members of the Resedaceae, which we name Rs-α. Given its economic importance and many genomic resources, the Brassicales are an ideal group to continue assessing WGD inference methods. We add to the current conversation on WGD inference difficulties, by demonstrating that sampling is especially important for WGD identification.

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Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1417803112 ◽

2014 ◽

Vol 112 (5) ◽

pp. 1493-1498 ◽

Cited By ~ 83

Author(s):

Fabio Cortesi ◽

Zuzana Musilová ◽

Sara M. Stieb ◽

Nathan S. Hart ◽

Ulrike E. Siebeck ◽

...

Keyword(s):

Gene Family ◽

Gene Evolution ◽

Single Gene ◽

Gene Family Evolution ◽

Raw Material ◽

Opsin Gene ◽

Evolutionary Mechanisms ◽

Whole Genome Duplications ◽

Genome Duplications ◽

History Of

Single-gene and whole-genome duplications are important evolutionary mechanisms that contribute to biological diversification by launching new genetic raw material. For example, the evolution of animal vision is tightly linked to the expansion of the opsin gene family encoding light-absorbing visual pigments. In teleost fishes, the most species-rich vertebrate group, opsins are particularly diverse and key to the successful colonization of habitats ranging from the bioluminescence-biased but basically dark deep sea to clear mountain streams. In this study, we report a previously unnoticed duplication of the violet-blue short wavelength-sensitive 2 (SWS2) opsin, which coincides with the radiation of highly diverse percomorph fishes, permitting us to reinterpret the evolution of this gene family. The inspection of close to 100 fish genomes revealed that, triggered by frequent gene conversion between duplicates, the evolutionary history of SWS2 is rather complex and difficult to predict. Coincidentally, we also report potential cases of gene resurrection in vertebrate opsins, whereby pseudogenized genes were found to convert with their functional paralogs. We then identify multiple novel amino acid substitutions that are likely to have contributed to the adaptive differentiation between SWS2 copies. Finally, using the dusky dottyback Pseudochromis fuscus, we show that the newly discovered SWS2A duplicates can contribute to visual adaptation in two ways: by gaining sensitivities to different wavelengths of light and by being differentially expressed between ontogenetic stages. Thus, our study highlights the importance of comparative approaches in gaining a comprehensive view of the dynamics underlying gene family evolution and ultimately, animal diversification.

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