scholarly journals Connexins during 500 Million Years—From Cyclostomes to Mammals

2021 ◽  
Vol 22 (4) ◽  
pp. 1584
Author(s):  
Svein-Ole Mikalsen ◽  
Sunnvør í Kongsstovu ◽  
Marni Tausen
Keyword(s):  
Gene Family ◽  
Lower Number ◽  
Gene Duplications ◽  
Phylogenetic Affinity ◽  
Connexin Gene ◽  
Genome Duplications ◽  
Alpha Beta ◽  
Few Data

It was previously shown that the connexin gene family had relatively similar subfamily structures in several vertebrate groups. Still, many details were left unclear. There are essentially no data between tunicates, which have connexins that cannot be divided into the classic subfamilies, and teleosts, where the subfamilies are easily recognized. There are also relatively few data for the groups that diverged between the teleosts and mammals. As many of the previously analyzed genomes have been improved, and many more genomes are available, we reanalyzed the connexin gene family and included species from all major vertebrate groups. The major results can be summarized as follows: (i) The same connexin subfamily structures are found in all Gnathostomata (jawed vertebrates), with some variations due to genome duplications, gene duplications and gene losses. (ii) In contrast to previous findings, birds do not have a lower number of connexins than other tetrapods. (iii) The cyclostomes (lampreys and hagfishes) possess genes in the alpha, beta, gamma and delta subfamilies, but only some of the genes show a phylogenetic affinity to specific genes in jawed vertebrates. Thus, two major evolutionary transformations have occurred in this gene family, from tunicates to cyclostomes and from cyclostomes to jawed vertebrates.

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.

scholarly journals Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes

2001 ◽  
Vol 11 (5) ◽  
pp. 771-780 ◽  
Author(s):  
Austin L. Hughes ◽  
Jack da Silva ◽  
Robert Friedman
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Gene Duplications ◽  
Human Chromosomes ◽  
Time Period ◽  
Genome Duplications

The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the fourHox-bearing chromosomes (the chromosomes bearing theHox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the humanHox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hoxclusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

scholarly journals Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

GigaScience ◽  
2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Zheng Li ◽  
Michael S Barker
Keyword(s):  
Gene Family ◽  
False Positive Rate ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Plant Genome ◽  
Total Evidence ◽  
Whole Genome ◽  
Green Plants ◽  
Whole Genome Duplications ◽  
Genome Duplications

Abstract Background Polyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project. Results In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset. Conclusions We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.

scholarly journals Polyploidy and the Evolution of Complex Traits

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lukasz Huminiecki ◽  
Gavin C. Conant
Keyword(s):  
Complex Traits ◽  
Genome Duplication ◽  
Single Gene ◽  
Whole Genome ◽  
Gene Duplications ◽  
Evolutionary Potential ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Modern Evolutionary Theory

We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers’ yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.

scholarly journals Molecular organization of the uvomorulin-catenin complex.

1992 ◽  
Vol 116 (4) ◽  
pp. 989-996 ◽  
Author(s):  
M Ozawa ◽  
R Kemler
Keyword(s):  
Gene Family ◽  
Cell Adhesion Molecule ◽  
Molecular Organization ◽  
Beta Catenin ◽  
Crucial Importance ◽  
Precursor Molecule ◽  
Dependent Cell ◽  
Single Complex ◽  
Alpha Beta ◽  
Biochemical Analyses

The Ca(2+)-dependent cell adhesion molecule uvomorulin is a member of the cadherin gene family. Its cytoplasmic region complexes with structurally defined proteins termed alpha-, beta-, and gamma-catenins. Here we show that A-CAM (N-cadherin), another member of this gene family, also associates with catenins suggesting that this complex formation may be a general property of the cadherins. For uvomorulin it has been found that this association with catenins is of crucial importance for the adhesive function, but little is known about the molecular organization of the uvomorulin-catenin complex. Using a combination of biochemical analyses we show that a single complex is composed of one molecule of uvomorulin, one or two molecules of beta-catenin, and one molecule of alpha-catenin. Furthermore, beta-catenin seems to interact more directly with uvomorulin. In pulse-chase experiments beta-catenin is already associated with the 135-kD uvomorulin precursor molecule but the assembly of the newly synthesized alpha-catenin into the complex is only detected around the time of endoproteolytic processing.

scholarly journals Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids

2005 ◽  
Vol 35 (2) ◽  
pp. 399-409 ◽  
Author(s):  
Ying Li ◽  
Chun Ye ◽  
Peng Shi ◽  
Xiao-Ju Zou ◽  
Rui Xiao ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Gene Family ◽  
New World ◽  
Death Process ◽  
New World Monkeys ◽  
Old World Monkeys ◽  
Gene Duplications ◽  
Birth And Death Process ◽  
Old World ◽  
Evolutionary Pattern

The growth hormone (GH) gene family represents an erratic and complex evolutionary pattern, involving many evolutionary events, such as multiple gene duplications, positive selection, the birth-and-death process and gene conversions. In the present study, we cloned and sequenced GH-like genes from three species of New World monkeys (NWM). Phylogenetic analysis strongly suggest monophyly for NWM GH-like genes with respect to those of Old World monkeys (OWM) and hominoids, indicating that independent gene duplications have occurred in NWM GH-like genes. There are three main clusters of genes in putatively functional NWM GH-like genes, according to our gene tree. Comparison of the ratios of nonsynonymous and synonymous substitutions revealed that these three clusters of genes evolved under different kinds of selective pressures. Detailed analysis of the evolution of pseudogenes showed that the evolutionary pattern of this gene family in platyrrhines is in agreement with the so-called birth-and-death process.

scholarly journals Comparable Rates of Gene Loss and Functional Divergence After Genome Duplications Early in Vertebrate Evolution

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1259-1266 ◽  
Author(s):  
Joseph H Nadeau ◽  
David Sankoff
Keyword(s):  
Gene Family ◽  
Protein Function ◽  
Gene Loss ◽  
Functional Divergence ◽  
Gene Families ◽  
High Rate ◽  
Vertebrate Evolution ◽  
Duplicated Genes ◽  
Apparent Contradiction ◽  
Genome Duplications

Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2n, where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3,..., 2n, reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways.

scholarly journals A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

2019 ◽  
Author(s):  
Drew A. Larson ◽  
Joseph F. Walker ◽  
Oscar M. Vargas ◽  
Stephen A. Smith
Keyword(s):  
Gene Tree ◽  
Gene Duplications ◽  
Species Relationships ◽  
Rapid Radiation ◽  
Genome Duplications ◽  
Tree Inference ◽  
History Of ◽  
Rapid Diversification ◽  
Clustering Approach ◽  
Edge Based

ABSTRACTPremise of studyLarge genomic datasets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.MethodsWe used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods and is summarized in a consensus framework.Key ResultsOur consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole genome duplication before the radiation of all or most ericalean families and demonstrate that tree topology and heterogeneous evolutionary rates impact the inferred placement of genome duplications.ConclusionsOur approach provides a novel hypothesis regarding the history of Ericales and confidently resolves most nodes. We demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

scholarly journals Analytical performance of eleven SARS-CoV-2 antigen-detecting rapid tests for Delta variant

2021 ◽  
Author(s):  
Meriem Bekliz ◽  
Kenneth Adea ◽  
Manel Essaidi-Laziosi ◽  
Camille Escadafal ◽  
Jilian Sacks ◽  
...  
Keyword(s):  
Diagnostic Tests ◽  
Diagnostic Performance ◽  
Rapid Diagnostic Tests ◽  
Analytical Performance ◽  
Rapid Tests ◽  
Alpha Beta ◽  
Few Data

Global concerns arose as the emerged and rapidly spreading SARS-CoV-2 Delta variant. To date, few data on routine diagnostic performance for Delta are available. Here, we investigate the analytical performance of eleven commercially available antigen-detecting rapid diagnostic tests (Ag-RDTs) for Delta VOC in comparison with current and earlier VOCs (Alpha, Beta and Gamma) and early pandemic variant using cultured SARS-CoV-2. Comparable sensitivity was observed for Delta for the majority of Ag-RDTs.

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