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

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.

scholarly journals Evolutionary history of the vertebrate Piwi gene family

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12451
Author(s):  
Javier Gutierrez ◽  
Roy Platt ◽  
Juan C. Opazo ◽  
David A. Ray ◽  
Federico Hoffmann ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Regulatory Proteins ◽  
Vertebrate Evolution ◽  
Transcriptional Gene Silencing ◽  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
History Of ◽  
Argonaute Family ◽  
The Common

PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.

scholarly journals Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications

2020 ◽  
Vol 37 (11) ◽  
pp. 3324-3337
Author(s):  
Elise Parey ◽  
Alexandra Louis ◽  
Cédric Cabau ◽  
Yann Guiguen ◽  
Hugues Roest Crollius ◽  
...  
Keyword(s):  
Gene Families ◽  
Sequence Evolution ◽  
Whole Genome ◽  
Gene Trees ◽  
Ensembl Database ◽  
Whole Genome Duplications ◽  
Gene Copies ◽  
Genome Duplications ◽  
Phenotypic Robustness ◽  
New Gene

Abstract Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

scholarly journals Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

2020 ◽  
Author(s):  
Elise Parey ◽  
Alexandra Louis ◽  
Cédric Cabau ◽  
Yann Guiguen ◽  
Hugues Roest Crollius ◽  
...  
Keyword(s):  
Gene Families ◽  
Sequence Evolution ◽  
Whole Genome ◽  
Gene Trees ◽  
Ensembl Database ◽  
Whole Genome Duplications ◽  
Gene Copies ◽  
Genome Duplications ◽  
Phenotypic Robustness ◽  
New Gene

AbstractWhole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-million-year-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,391) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

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

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.

scholarly journals Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

2020 ◽  
Author(s):  
Amber Harper ◽  
Luis Baudouin Gonzalez ◽  
Anna Schönauer ◽  
Michael Seiter ◽  
Michaela Holzem ◽  
...  
Keyword(s):  
Genetic Material ◽  
Gene Families ◽  
Comparative Approach ◽  
Whole Genome ◽  
Developmental Gene ◽  
Spider Species ◽  
Transcriptomic Data ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Horseshoe Crabs

AbstractWhole genome duplications (WGD) have occurred multiple times in the evolution of animals, including in the lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic genomic events initially produce a wealth of new genetic material, which is generally followed by extensive gene loss. It appears that developmental genes such as homeobox genes, signalling pathway components and microRNAs, however, tend to be more frequently retained in duplicate following WGD (ohnologs). These not only provide the best evidence for the occurrence of WGD, but an opportunity to study its evolutionary implications. Although these genes are relatively well studied in the context of vertebrate WGD, genomic and transcriptomic data for independent comparison in other groups are scarce, with patchy sampling of only two of the five extant arachnopulmonate orders. To improve our knowledge of developmental gene repertoires, and their evolution since the arachnopulmonate WGD, we sequenced embryonic transcriptomes from two additional spider species and two whip spider species and surveyed them for three important gene families: Hox, Wnt and frizzled. We report extensive retention of ohnologs in all four species, further supporting the arachnopulmonate WGD hypothesis. Thanks to improved sampling we were able to identify patterns of likely ohnolog retention and loss within spiders, including apparent differences between major clades. The two amblypygid species have larger ohnolog repertoires of these genes than both spiders and scorpions; including the first reported duplicated Wnt1/wg, the first Wnt10 recovered in an arachnid, and broad retention of frizzled genes. These insights shed light on the evolution of the enigmatic whip spiders, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

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

2019 ◽  
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.

scholarly journals Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications

2014 ◽  
Vol 202 (3) ◽  
pp. 986-1000 ◽  
Author(s):  
Cyril Jourda ◽  
Céline Cardi ◽  
Didier Mbéguié-A-Mbéguié ◽  
Stéphanie Bocs ◽  
Olivier Garsmeur ◽  
...  
Keyword(s):  
Gene Families ◽  
Ethylene Biosynthesis ◽  
Musa Acuminata ◽  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications

scholarly journals Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

2021 ◽  
Author(s):  
Amber Harper ◽  
Luis Baudouin Gonzalez ◽  
Anna Schönauer ◽  
Ralf Janssen ◽  
Michael Seiter ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Material ◽  
Gene Families ◽  
Comparative Approach ◽  
Whole Genome ◽  
Animal Evolution ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Horseshoe Crabs

Abstract Whole genome duplications have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signalling pathway components and microRNAs are frequently retained as duplicates (so called ohnologs) following whole-genome duplication. These not only provide the best evidence for whole-genome duplication, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate whole-genome duplication, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt and frizzled, across these and twelve existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate whole-genome duplication. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with inter-order variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

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