Protist Homologs of the Meiotic Spo11 Gene and Topoisomerase VI reveal an Evolutionary History of Gene Duplication and Lineage-Specific Loss

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

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Gene Duplication Is Infrequent in the Recent Evolutionary History of RNA Viruses

Molecular Biology and Evolution ◽

10.1093/molbev/mst044 ◽

2013 ◽

Vol 30 (6) ◽

pp. 1263-1269 ◽

Cited By ~ 26

Author(s):

Etienne Simon-Loriere ◽

Edward C. Holmes

Keyword(s):

Gene Duplication ◽

Evolutionary History ◽

Rna Viruses ◽

History Of

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A Revised Evolutionary History of the CYP1A Subfamily: Gene Duplication, Gene Conversion, and Positive Selection

Journal of Molecular Evolution ◽

10.1007/s00239-005-0134-z ◽

2006 ◽

Vol 62 (6) ◽

pp. 708-717 ◽

Cited By ~ 77

Author(s):

Heather M. H. Goldstone ◽

John J. Stegeman

Keyword(s):

Gene Duplication ◽

Positive Selection ◽

Gene Conversion ◽

Evolutionary History ◽

History Of

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Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the GenusAcidithiobacillus

Applied and Environmental Microbiology ◽

10.1128/aem.02153-18 ◽

2018 ◽

Vol 85 (2) ◽

Cited By ~ 2

Author(s):

Liangzhi Li ◽

Zhenghua Liu ◽

Delong Meng ◽

Xueduan Liu ◽

Xing Li ◽

...

Keyword(s):

Gene Duplication ◽

Resistance Genes ◽

Evolutionary History ◽

Genomic Analysis ◽

Purifying Selection ◽

Metal Resistance ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Content Type ◽

History Of

ABSTRACTMembers of the genusAcidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genusAcidithiobacillusto answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes inAcidithiobacillusspp. The results showed that the evolutionary history of metal resistance genes inAcidithiobacillusspp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes inAcidithiobacillusspp. were acquired by early HGT events from species that shared habitats withAcidithiobacillusspp., such asAcidihalobacter,Thiobacillus,Acidiferrobacter, andThiomonasspecies. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizingAcidithiobacillus ferridurans,Acidithiobacillus ferrivorans, andAcidithiobacillus ferrooxidansand were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability ofAcidithiobacillusspp. to adapt to harsh environments. Altogether, the results suggested thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes inAcidithiobacillusspp.IMPORTANCEHorizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT inAcidithiobacillusspecies in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved inAcidithiobacillusare still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies ofAcidithiobacillusspp.

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EVOLUTIONARY HISTORY OF THE SOX GENES THROUGHOUT GENE DUPLICATION

REBIOL ◽

10.17268/rebiol.2019.39.02.06 ◽

2019 ◽

Vol 39 (2) ◽

pp. 58-69

Author(s):

Anthony Leon

Keyword(s):

Gene Duplication ◽

Evolutionary History ◽

History Of ◽

Sox Genes

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The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression

Trends in Plant Science ◽

10.1016/j.tplants.2007.06.012 ◽

2007 ◽

Vol 12 (8) ◽

pp. 358-367 ◽

Cited By ~ 74

Author(s):

Douglas E. Soltis ◽

Hong Ma ◽

Michael W. Frohlich ◽

Pamela S. Soltis ◽

Victor A. Albert ◽

...

Keyword(s):

Gene Expression ◽

Gene Duplication ◽

Evolutionary History ◽

History Of

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Complex Evolution of the Mismatch Repair System in Eukaryotes is Illuminated by Novel Archaeal Genomes

Journal of Molecular Evolution ◽

10.1007/s00239-020-09979-5 ◽

2021 ◽

Author(s):

Paulo G. Hofstatter ◽

Daniel J. G. Lahr

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Gene Duplication ◽

Mismatch Repair ◽

Evolutionary History ◽

Repair System ◽

System Evolution ◽

Mismatch Repair System ◽

History Of ◽

Complex Evolutionary History

AbstractRepairing DNA damage is one of the most important functions of the ‘housekeeping’ proteins, as DNA molecules are constantly subject to different kinds of damage. An important mechanism of DNA repair is the mismatch repair system (MMR). In eukaryotes, it is more complex than it is in bacteria or Archaea due to an inflated number of paralogues produced as a result of an extensive process of gene duplication and further specialization upon the evolution of the first eukaryotes, including an important part of the meiotic machinery. Recently, the discovery and sequencing of Asgard Archaea allowed us to revisit the MMR system evolution with the addition of new data from a group that is closely related to the eukaryotic ancestor. This new analysis provided evidence for a complex evolutionary history of eukaryotic MMR: an archaeal origin for the nuclear MMR system in eukaryotes, with subsequent acquisitions of other MMR systems from organelles.

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Evolution of 14-3-3 Proteins in Angiosperm Plants: Recurring Gene Duplication and Loss

Plants ◽

10.3390/plants10122724 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2724

Author(s):

Yulia V. Mikhaylova ◽

Roman K. Puzanskiy ◽

Maria F. Shishova

Keyword(s):

Gene Duplication ◽

Evolutionary History ◽

Basal Angiosperm ◽

Physiological Processes ◽

Gene Duplication And Loss ◽

Duplication Events ◽

History Of ◽

Angiosperm Species ◽

Opposite Manner ◽

Recent Duplication

14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We addressed the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. Orthologs of Arabidopsis isoforms were detected. There were several rounds of duplication events in the evolutionary history of the 14-3-3 protein family in plants. At least four subfamilies (iota, epsilon, kappa, and psi) formed as a result of ancient duplication in a common ancestor of angiosperm plants. Recent duplication events followed by gene loss in plant lineage, among others Brassicaceae, Fabaceae, and Poaceae, further shaped the high diversity of 14-3-3 isoforms in plants. Coexpression data showed that 14-3-3 proteins formed different functional groups in different species. In some species, evolutionarily related groups of 14-3-3 proteins had coexpressed together under certain physiological conditions, whereas in other species, closely related isoforms expressed in the opposite manner. A possible explanation is that gene duplication and loss is accompanied by functional plasticity of 14-3-3 proteins.

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