Molecular evolution of candidate sour taste receptor gene PKD1L3 in mammals

Genome ◽  
2011 ◽  
Vol 54 (11) ◽  
pp. 890-897 ◽  
Author(s):  
Dazhi Chen ◽  
Ping Li ◽  
Wenhu Guo ◽  
Fang Ye ◽  
Jian Wu ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Receptor Gene ◽  
Mammalian Species ◽  
Taste Receptor ◽  
Purifying Selection ◽  
Evolutionary Patterns ◽  
Sour Taste ◽  
Selection Force ◽  
Stimulus Recognition

The PKD1L3 gene encodes an ion channel protein that can interact with the PKD2L1 protein to form a candidate sour taste receptor. In the present study, we have analyzed the evolutionary patterns of PKD1L3 genes from 10 mammalian species. The results showed that PKD1L3 genes have evolved under a dominant purifying selection force. However, for some branches and sites, PKD1L3 genes were detected to have been operated by positive selection. Moreover, some of these positive evolutionary sites are likely to participate in acid stimulus recognition. In rodents, PKD1L3 genes evolved more rapidly than other mammalian lineages. Combined with other functional research reports, our results suggest that rodents may not be the most appropriate model for functional research on the PKD1L3 gene.

scholarly journals Natural Selection and Molecular Evolution in PTC, a Bitter-Taste Receptor Gene

2004 ◽  
Vol 74 (4) ◽  
pp. 637-646 ◽  
Author(s):  
Stephen Wooding ◽  
Un-kyung Kim ◽  
Michael J. Bamshad ◽  
Jennifer Larsen ◽  
Lynn B. Jorde ◽  
...  
Keyword(s):  
Natural Selection ◽  
Molecular Evolution ◽  
Bitter Taste ◽  
Receptor Gene ◽  
Taste Receptor ◽  
Bitter Taste Receptor ◽  
Bitter Taste Receptor Gene

scholarly journals The Role of Co-Deleted Genes in Neurofibromatosis Type 1 Microdeletions: An Evolutive Approach

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 839
Author(s):  
Larissa Brussa Reis ◽  
Andreia Carina Turchetto-Zolet ◽  
Maievi Fonini ◽  
Patricia Ashton-Prolla ◽  
Clévia Rosset
Keyword(s):  
Positive Selection ◽  
Neurofibromatosis Type 1 ◽  
Mammalian Species ◽  
Ring Finger ◽  
Purifying Selection ◽  
Neurofibromatosis Type ◽  
Evolutionary Constraint ◽  
Loss Of Function ◽  
Cancer Predisposition Syndrome

Neurofibromatosis type 1 (NF1) is a cancer predisposition syndrome that results from dominant loss-of-function mutations mainly in the NF1 gene. Large rearrangements are present in 5–10% of affected patients, generally encompass NF1 neighboring genes, and are correlated with a more severe NF1 phenotype. Evident genotype–phenotype correlations and the importance of the co-deleted genes are difficult to establish. In our study we employed an evolutionary approach to provide further insights into the understanding of the fundamental function of genes that are co-deleted in subjects with NF1 microdeletions. Our goal was to access the ortholog and paralog relationship of these genes in primates and verify if purifying or positive selection are acting on these genes. Fourteen genes were analyzed in twelve mammalian species. Of these, four and ten genes showed positive selection and purifying selection, respectively. The protein, RNF135, showed three sites under positive selection at the RING finger domain, which may have been selected to increase efficiency in ubiquitination routes in primates. The phylogenetic analysis suggests distinct evolutionary constraint between the analyzed genes. With these analyses, we hope to help clarify the correlation of the co-deletion of these genes and the more severe phenotype of NF1.

scholarly journals Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates

2019 ◽  
Vol 12 (1) ◽  
pp. 3615-3634 ◽  
Author(s):  
Guangshuai Liu ◽  
Huanxin Zhang ◽  
Chao Zhao ◽  
Honghai Zhang
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Receptor Gene ◽  
Purifying Selection ◽  
Protein Architecture ◽  
Wide Range ◽  
History Of ◽  
Membrane Bound

Abstract Adaptation to a wide range of pathogenic environments is a major aspect of the ecological adaptations of vertebrates during evolution. Toll-like receptors (TLRs) are ancient membrane-bound sensors in animals and are best known for their roles in detecting and defense against invading pathogenic microorganisms. To understand the evolutionary history of the vertebrate TLR gene family, we first traced the origin of single-cysteine cluster TLRs that share the same protein architecture with vertebrate TLRs in early-branching animals and then analyzed all members of the TLR family in over 200 species covering all major vertebrate clades. Our results indicate that although the emergence of single-cysteine cluster TLRs predates the separation of bilaterians and cnidarians, most vertebrate TLR members originated shortly after vertebrate emergence. Phylogenetic analyses divided 1,726 vertebrate TLRs into 8 subfamilies, and TLR3 may represent the most ancient subfamily that emerged before the branching of deuterostomes. Our analysis reveals that purifying selection predominated in the evolution of all vertebrate TLRs, with mean dN/dS (ω) values ranging from 0.082 for TLR21 in birds to 0.434 for TLR11 in mammals. However, we did observe patterns of positive selection acting on specific codons (527 of 60,294 codons across all vertebrate TLRs, 8.7‰), which are significantly concentrated in ligand-binding extracellular domains and suggest host–pathogen coevolutionary interactions. Additionally, we found stronger positive selection acting on nonviral compared with viral TLRs, indicating the more essential nonredundant function of viral TLRs in host immunity. Taken together, our findings provide comprehensive insight into the complex evolutionary processes of the vertebrate TLR gene family, involving gene duplication, pseudogenization, purification, and positive selection.

scholarly journals Molecular evolution of GDP-L-galactose phosphorylase, a key regulatory gene in plant ascorbate biosynthesis

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Junjie Tao ◽  
Zhuan Hao ◽  
Chunhui Huang
Keyword(s):  
Molecular Evolution ◽  
Abiotic Stress Tolerance ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Rapid Expansion ◽  
Whole Genome ◽  
Evolutionary Patterns ◽  
Whole Genome Duplications ◽  
Genome Duplications

Abstract Ascorbic acid (AsA) is a widespread antioxidant in living organisms, and plays essential roles in the growth and development of animals and plants as well as in the response to abiotic stress tolerance. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood; however, the molecular evolutionary patterns of the gene remain unclear. In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, and the phylogenetic relationships, gene duplication and molecular evolution analyses of the genes were systematically investigated. Results showed that GGP genes are present throughout the plant kingdom and five shared whole-genome duplications and several lineage-specific whole-genome duplications were found, which led to the rapid expansion of GGPs in seed plants, especially in angiosperms. The structure of GGP genes was more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins had a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that GGP genes were predominated by purifying selection, indicating that the gene is functionally conserved due to its vital importance in AsA biosynthesis. Most of the branches under positive selection identified by the branch-site model were mainly in the chlorophytes lineage, indicating episodic diversifying selection may contribute to the evolution of GGPs, especially in the chlorophyte lineage. The conserved function of GGP and its rapid expansion in angiosperms maybe one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

scholarly journals Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green algaOstreobium quekettii

2016 ◽  
Author(s):  
Vanessa R. Marcelino ◽  
Ma Chiela M. Cremen ◽  
Christopher J. Jackson ◽  
Anthony W.D. Larkum ◽  
Heroen Verbruggen
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Chloroplast Genome ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Light Sensitivity ◽  
Light Limitation ◽  
Comparative Genomic ◽  
Low Light ◽  
Chloroplast Genomes

Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species genome. Here we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. Given the exceptional ability of our model organism to photosynthesize under extreme low light conditions, we expected to observe positive selection in genes related to the photosynthetic machinery. However, we observed stronger purifying selection in these genes, which might either reflect a lack of power to detect episodic positive selection followed by purifying selection and/or a strengthening of purifying selection due to the loss of a gene related to light sensitivity. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

scholarly journals Molecular evolution of GDP-L-galactose phosphorylase (GGP), a key regulatory gene in plant ascorbate biosynthesis

2019 ◽  
Author(s):  
Junjie Tao ◽  
Zhuan Hao ◽  
Chunhui Huang
Keyword(s):  
Molecular Evolution ◽  
Plant Species ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Rapid Expansion ◽  
Evolutionary Patterns ◽  
Site Model ◽  
Early Stages ◽  
Evolutionary Innovation

Abstract Background Ascorbic acid (AsA) is a multi-functional molecule and plays essential roles in maintaining the normal life activities of living organisms. Although widely present in plants, the concentration of AsA varies greatly in different plant species. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood in previous works. However, the molecular evolutionary patterns of the gene remain unclear.Results In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, including angiosperms, gymnosperms, lycophytes, bryophytes and chlorophytes, and their phylogenetic relationships, gene duplication and molecular evolution analyses were investigated. Phylogenetic analysis showed that GGP exists widely in various plants, and five major duplication events and several taxon-specific duplications were found, which led to the rapid expansion of GGP genes in seed plants, especially in angiosperms. The structure of GGP genes were more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins have a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that plant GGP genes was predominated by strong purifying selection, indicating the functional importance and conservativeness of plant GGP genes during evolution. Most of the branches under positive selection identified by branch-site model were mainly in the chlorophytes lineage, indicating the evolutionary innovation of GGP genes also mainly occurred in the early stages of plant evolution and episodic diversifying selection contributed to the evolution of plant GGP genes.Conclusions The molecular evolutionary patterns of GGP were first systematically explored in this study. The conservative function of GGP and its rapid expansion in angiosperms may be one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

scholarly journals Molecular evolution of DNMT1 in vertebrates: duplications in marsupials followed by positive selection

2018 ◽  
Author(s):  
David Alvarez-Ponce ◽  
María Torres-Sánchez ◽  
Felix Feyertag ◽  
Asmita Kulkarni ◽  
Taylen Nappi
Keyword(s):  
Dna Methylation ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Single Copy ◽  
Tammar Wallaby ◽  
Dna Methyltransferases ◽  
Tasmanian Devil ◽  
Genes Encoding

AbstractDNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes five Dnmts: Dnmt1, Dnmt2, Dnmt3a, Dnmt3b and Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of DNMT1, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which exhibits two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the divergence of marsupials (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

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