scholarly journals Evolution of Homospermidine Synthase in the Convolvulaceae: A Story of Gene Duplication, Gene Loss, and Periods of Various Selection Pressures

2013 ◽  
Vol 25 (4) ◽  
pp. 1213-1227 ◽  
Author(s):  
Elisabeth Kaltenegger ◽  
Eckart Eich ◽  
Dietrich Ober
Keyword(s):  
Gene Duplication ◽  
Gene Loss ◽  
Selection Pressures ◽  
Homospermidine Synthase

scholarly journals Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

2016 ◽  
Author(s):  
Juan C Opazo ◽  
Kattina Zavala ◽  
Paola Krall ◽  
Rodrigo A Arias
Keyword(s):  
Gene Duplication ◽  
Common Ancestor ◽  
Gene Loss ◽  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Single Gene ◽  
Biological Significance ◽  
Gene Copy ◽  
Last Common Ancestor ◽  
Extant Species

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.

Evolution of Base Excision Repair in Entamoeba histolytica is shaped by gene loss, gene duplication, and lateral gene transfer

DNA Repair ◽  
2019 ◽  
Vol 76 ◽  
pp. 76-88 ◽  
Author(s):  
Carlos H. Trasviña-Arenas ◽  
Sheila S. David ◽  
Luis Delaye ◽  
Elisa Azuara-Liceaga ◽  
Luis G. Brieba
Keyword(s):  
Gene Transfer ◽  
Gene Duplication ◽  
Entamoeba Histolytica ◽  
Lateral Gene Transfer ◽  
Base Excision Repair ◽  
Gene Loss ◽  
Excision Repair ◽  
Base Excision

scholarly journals The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41175 ◽  
Author(s):  
Matthew A. Carrigan ◽  
Oleg Uryasev ◽  
Ross P. Davis ◽  
LanMin Zhai ◽  
Thomas D. Hurley ◽  
...  
Keyword(s):  
Natural History ◽  
Gene Duplication ◽  
Gene Conversion ◽  
Gene Loss ◽  
Class I ◽  
Alcohol Dehydrogenases ◽  
History Of

scholarly journals Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2901 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala ◽  
Paola Krall ◽  
Rodrigo A. Arias
Keyword(s):  
Gene Duplication ◽  
Common Ancestor ◽  
Gene Loss ◽  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Single Gene ◽  
Biological Significance ◽  
Gene Copy ◽  
Last Common Ancestor ◽  
Extant Species

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.

scholarly journals Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

2016 ◽  
Author(s):  
Juan C Opazo ◽  
Kattina Zavala ◽  
Paola Krall ◽  
Rodrigo A Arias
Keyword(s):  
Gene Duplication ◽  
Common Ancestor ◽  
Gene Loss ◽  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Single Gene ◽  
Biological Significance ◽  
Gene Copy ◽  
Last Common Ancestor ◽  
Extant Species

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.

scholarly journals The tree of life of polyamine oxidases

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Daniele Salvi ◽  
Paraskevi Tavladoraki
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Duplication ◽  
Subcellular Localization ◽  
Phylogenetic Trees ◽  
Gene Loss ◽  
Catalytic Properties ◽  
Specific Gene ◽  
Cellular Processes ◽  
Domains Of Life ◽  
Polyamine Oxidases

Abstract Polyamine oxidases (PAOs) are characterized by a broad variability in catalytic properties and subcellular localization, and impact key cellular processes in diverse organisms. In the present study, a comprehensive phylogenetic analysis was performed to understand the evolution of PAOs across the three domains of life and particularly within eukaryotes. Phylogenetic trees show that PAO-like sequences of bacteria, archaea, and eukaryotes form three distinct clades, with the exception of a few procaryotes that probably acquired a PAO gene through horizontal transfer from a eukaryotic donor. Results strongly support a common origin for archaeal PAO-like proteins and eukaryotic PAOs, as well as a shared origin between PAOs and monoamine oxidases. Within eukaryotes, four main lineages were identified that likely originated from an ancestral eukaryotic PAO before the split of the main superphyla, followed by specific gene losses in each superphylum. Plant PAOs show the highest diversity within eukaryotes and belong to three distinct clades that underwent to multiple events of gene duplication and gene loss. Peptide deletion along the evolution of plant PAOs of Clade I accounted for further diversification of function and subcellular localization. This study provides a reference for future structure–function studies and emphasizes the importance of extending comparisons among PAO subfamilies across multiple eukaryotic superphyla.

scholarly journals Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hyung-Bae Jeon ◽  
Hari Won ◽  
Ho Young Suk
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Duplication ◽  
East Asia ◽  
Allelic Diversity ◽  
Intron Loss ◽  
Selection Pressures ◽  
Historical Processes ◽  
Mhc Class Iib ◽  
Class Iib ◽  
Rhodeus Sinensis

Abstract Background Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings. Results Using cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The β1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths. Conclusions A great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.

scholarly journals ASTRAL-Pro: quartet-based species tree inference despite paralogy

2019 ◽  
Author(s):  
Chao Zhang ◽  
Celine Scornavacca ◽  
Erin K. Molloy ◽  
Siavash Mirarab
Keyword(s):  
Gene Duplication ◽  
Gene Loss ◽  
Incomplete Lineage Sorting ◽  
Single Copy ◽  
Species Tree ◽  
Alternative Methods ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Inference ◽  
Species Tree Inference

AbstractSpecies tree inference via summary methods that combine gene trees has become an increasingly common analysis in recent phylogenomic studies. This broad adoption has been partly due to the greater availability of genome-wide data and ample recognition that gene trees and species trees can differ due to biological processes such as gene duplication and gene loss. This increase has also been encouraged by the recent development of accurate and scalable summary methods, such as ASTRAL. However, most of these methods, including ASTRAL, can only handle single-copy gene trees and do not attempt to model gene duplication and gene loss. In this paper, we introduce a measure of quartet similarity between single-copy and multi-copy trees (accounting for orthology and paralogy relationships) that can be optimized via a scalable dynamic programming similar to the one used by ASTRAL. We then present a new quartet-based species tree inference method: ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs). By studying its performance on an extensive collection of simulated datasets and on a real plant dataset, we show that ASTRAL-Pro is more accurate than alternative methods when gene trees differ from the species tree due to the simultaneous presence of gene duplication, gene loss, incomplete lineage sorting, and estimation errors.

scholarly journals Establishment, maintenance, and biological roles of non-CG methylation in plants

2019 ◽  
Vol 63 (6) ◽  
pp. 743-755 ◽  
Author(s):  
Sunil K. Kenchanmane Raju ◽  
Eleanore Jeanne Ritter ◽  
Chad E. Niederhuth
Keyword(s):  
Dna Methylation ◽  
Gene Duplication ◽  
Transposable Elements ◽  
Gene Loss ◽  
Genome Integrity ◽  
Plant Genomes ◽  
Cpg Sites ◽  
Environmental Responses

Abstract Cytosine DNA methylation is prevalent throughout eukaryotes and prokaryotes. While most commonly thought of as being localized to dinucleotide CpG sites, non-CG sites can also be modified. Such non-CG methylation is widespread in plants, occurring at trinucleotide CHG and CHH (H = A, T, or C) sequence contexts. The prevalence of non-CG methylation in plants is due to the plant-specific CHROMOMETHYLASE (CMT) and RNA-directed DNA Methylation (RdDM) pathways. These pathways have evolved through multiple rounds of gene duplication and gene loss, generating epigenomic variation both within and between species. They regulate both transposable elements and genes, ensure genome integrity, and ultimately influence development and environmental responses. In these capacities, non-CG methylation influence and shape plant genomes.

Sign in / Sign up

Export Citation Format

Share Document