scholarly journals Origin and evolutionary landscape of Nr2f transcription factors across Metazoa

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0254282
Author(s):  
Ugo Coppola ◽  
Joshua S. Waxman
Keyword(s):  
Transcription Factors ◽  
Evolutionary History ◽  
Gene Evolution ◽  
Domain Architecture ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Syntenic Conservation ◽  
Exon Structure ◽  
Structure Domain ◽  
Nuclear Receptor Subfamily

Background Nuclear Receptor Subfamily 2 Group F (Nr2f) orphan nuclear hormone transcription factors (TFs) are fundamental regulators of many developmental processes in invertebrates and vertebrates. Despite the importance of these TFs throughout metazoan development, previous work has not clearly outlined their evolutionary history. Results We integrated molecular phylogeny with comparisons of intron/exon structure, domain architecture, and syntenic conservation to define critical evolutionary events that distinguish the Nr2f gene family in Metazoa. Our data indicate that a single ancestral eumetazoan Nr2f gene predated six main Bilateria subfamilies, which include single Nr2f homologs, here referred to as Nr2f1/2/5/6, that are present in invertebrate protostomes and deuterostomes, Nr2f1/2 homologs in agnathans, and Nr2f1, Nr2f2, Nr2f5, and Nr2f6 orthologs that are found in gnathostomes. Four cnidarian Nr2f1/2/5/6 and three agnathan Nr2f1/2 members are each due to independent expansions, while the vertebrate Nr2f1/Nr2f2 and Nr2f5/Nr2f6 members each form paralogous groups that arose from the established series of whole-genome duplications (WGDs). Nr2f6 members are the most divergent Nr2f subfamily in gnathostomes. Interestingly, in contrast to the other gnathostome Nr2f subfamilies, Nr2f5 has been independently lost in numerous vertebrate lineages. Furthermore, our analysis shows there are differential expansions and losses of Nr2f genes in teleosts following their additional rounds of WGDs. Conclusion Overall, our analysis of Nr2f gene evolution helps to reveal the origins and previously unrecognized relationships of this ancient TF family, which may allow for greater insights into the conservation of Nr2f functions that shape Metazoan body plans.

scholarly journals Origin and evolutionary landscape of Nr2f transcription factors across Metazoa

2021 ◽  
Author(s):  
Ugo Coppola ◽  
Joshua S. Waxman
Keyword(s):  
Transcription Factors ◽  
Domain Architecture ◽  
Genomic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Evolutionary Genomic ◽  
Syntenic Conservation ◽  
Exon Structure ◽  
Structure Domain ◽  
Nuclear Receptor Subfamily

Background:  Nuclear Receptor Subfamily 2 Group F (Nr2f) orphan nuclear hormone transcription factors (TFs) are fundamental regulators of many developmental processes in invertebrates and vertebrates. Despite the importance of these TFs throughout metazoan development, previous work has not clearly outlined their evolutionary history. Results:  We integrated molecular phylogeny with comparisons of intron/exon structure, domain architecture, and syntenic conservation to define critical evolutionary events that distinguish the  Nr2f  gene family in Metazoa. Our data indicate that a single ancestral pre-metazoan  Nr2f  gene, we have termed  Nr2f1/2/5/6,  predated six main Bilateria subfamilies, which include a single  Nr2f1/2/5  homolog that is present throughout protostomes and invertebrate deuterostomes,  Nr2f1/2 homologs in agnathans, and  Nr2f1 ,  Nr2f2 ,  Nr2f5 ,  Nr2f6  orthologs that are found in gnathostomes. The three  Nr2f1/2 members in agnathans are due to independent expansions not found in gnathostomes, while the vertebrate  Nr2f1 ,  Nr2f2 ,  Nr2f5  members arose from whole-genome duplications (WGDs). However,  Nr2f6  members are the most divergent subfamily, likely originating from an ancient duplication, and are only retained by gnathostomes. Interestingly,  Nr2f5  TFs have been independently lost in both cartilaginous fish and amniotes, such as humans. Furthermore, our analysis shows there are differential expansions and losses of  Nr2f  genes in teleosts following their additional rounds of WGDs. Conclusion:  Overall, our evolutionary genomic analysis of Nr2f proteins helps to reveal the origins and previously unrecognized relationships of this ancient transcription factor family, which may allow for greater insights into the conservation of Nr2f functions that shape Metazoan body plans.

scholarly journals Evolutionary History and Functional Characterization of the Amphibian Xenosensor CAR

2012 ◽  
Vol 26 (1) ◽  
pp. 14-26 ◽  
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.

scholarly journals The Aquilegia genome reveals a hybrid origin of core eudicots

2018 ◽  
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.

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 Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ming Ma ◽  
Qiming Chen ◽  
Huizhen Dong ◽  
Shaoling Zhang ◽  
Xiaosan Huang
Keyword(s):  
Transcription Factors ◽  
Expression Analysis ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Whole Genome ◽  
Virus Induced Gene Silencing ◽  
Abiotic Stress Response ◽  
Whole Genome Duplications ◽  
Genome Duplications

Abstract Background Transcription factors (TFs) are involved in many important biological processes, including cell stretching, histological differentiation, metabolic activity, seed storage, gene regulation, and response to abiotic and biotic stresses. Little is known about the functions, evolutionary history, and expression patterns of basic region-leucine zipper TF family genes in pear, despite the release of the genome of Chinese white pears (“Dangshansuli”). Results Overall, 92 bZIP genes were identified in the pear genome (Pyrus breschneideri). Of these, 83 were randomly distributed on all 17 chromosomes except chromosome 4, and the other 9 genes were located on loose scaffolding. The genes were divided into 14 subgroups. Whole-genome duplications, dispersed duplication, and purifying selection for whole-genome duplications are the main reasons for the expansion of the PbrbZIP gene family. The analysis of functional annotation enrichment indicated that most of the functions of PbrbZIP genes were enriched in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways involved in the abiotic stress response. Next, expression analysis and virus-induced gene silencing results indicated that PbrbZIP genes might play critical roles in response to drought and cold stresses, especially for the genes from subgroups A, C, G, I, and S. Conclusions Ninety-two PbrbZIP genes were identified from the pear genome and classified into 14 subgroups. PbrbZIP genes were mainly expanded from whole-genome duplications and dispersed duplications and retained by purifying selection. PbrbZIP genes were induced by cold and drought stresses and played important roles in drought and cold tolerance. These results provided useful information for further increasing the tolerance of pears to stresses and a foundation to study the cold and drought tolerance mechanism of PbrbZIP genes.

scholarly journals Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

2014 ◽  
Vol 112 (5) ◽  
pp. 1493-1498 ◽  
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.

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 The Aquilegia genome reveals a hybrid origin of core eudicots

2019 ◽  
Vol 20 (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

Abstract Background Whole-genome duplications (WGDs) 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. Results Within-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. Conclusions Novel 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.

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

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