scholarly journals The Evolutionary Rate Variation Among Genes of MVA and MEP Pathways in Plant Terpenoid Biosynthesis

2020 ◽  
Author(s):  
Ji-peng Mao ◽  
Lin-wang Huang ◽  
Jing Hao ◽  
Tian-yi Liu ◽  
Shao-wei Huang
Keyword(s):  
Positive Selection ◽  
Evolutionary Rate ◽  
Selective Constraint ◽  
Mep Pathway ◽  
Sequence Length ◽  
Rate Variation ◽  
Variation Pattern ◽  
Mva Pathway ◽  
Significant Difference ◽  
Terpenoid Pathway

Abstract Background: Terpenoids are one of the most important compounds in plants, play an significant biological defense and developmental roles in numerous plant species, and widely used for industrial chemicals. Many previous studies have completed the identification of terpenoid biosynthetic pathway and related genes. However, few studies have focused on the molecular evolution analysis of terpenoid pathway genes in plants. In this study, we researched the evolutionary rate variation pattern of 16 terpenoid pathway genes in 12 species with a broad taxonomic span. Results: We retrieved 14 genes in MVA and MEP pathways and 2 extra genes from 12 species, respectively. The evolutionary parameters dN values and dN/ dS ratios are varied significantly among genes, and the dN/ dS ratios of most genes are varied substantially among lineages. The MVA and MEP pathways genes have different evolutionary rate variation pattern, although no significant difference in dN/ dS ratios between two pathways genes. For MVA pathway, the downstream genes exhibits the greater dN/ dS ratio than upstream genes. For MEP pathway, the three midstream genes evolves more rapidly than other genes, and most of MEP pathway genes were detected the signature of positive selection under random sites models. Moreover, the dN/ dS ratios of MVA and MEP pathways genes are negatively correlated with pathway position and PPI, and coding sequence length, respectively. Conclusions: Taken together, the results indicated that the evolutionary rate variation of MVA pathway genes is mainly attributed to differential selective constraint rather than the positive selection. However, the differential selective constraint relaxation and positive selection collectively shaped the evolutionary rate heterogeneity of MEP pathway genes.

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.

Chromosomal location and evolutionary rate variation in enterobacterial genes

Science ◽  
1989 ◽  
Vol 246 (4931) ◽  
pp. 808-810 ◽  
Author(s):  
P. Sharp ◽  
D. Shields ◽  
K. Wolfe ◽  
W. Li
Keyword(s):  
Evolutionary Rate ◽  
Chromosomal Location ◽  
Rate Variation

scholarly journals In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes

2018 ◽  
Vol 10 (9) ◽  
pp. 2218-2239 ◽  
Author(s):  
Fidel Botero-Castro ◽  
Marie-Ka Tilak ◽  
Fabienne Justy ◽  
François Catzeflis ◽  
Frédéric Delsuc ◽  
...  
Keyword(s):  
Positive Selection ◽  
Evolutionary Rate ◽  
Compositional Bias ◽  
Mitochondrial Genomes ◽  
Vampire Bats ◽  
Cold Blood ◽  
In Cold Blood

scholarly journals Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Paul J. F. Rider ◽  
Lyndon M. Coghill ◽  
Misagh Naderi ◽  
Jeremy M. Brown ◽  
Michal Brylinski ◽  
...  
Keyword(s):  
Herpes Simplex ◽  
Evolutionary Rate ◽  
Quantitative Measure ◽  
Rate Variation ◽  
Human Pathogens ◽  
Herpes Simplex Viruses ◽  
Varicella Zoster ◽  
Conserved Sequence ◽  
Glycoprotein K ◽  
Herpes Simplex Virus Glycoprotein

Abstract Alphaherpesviruses are a subfamily of herpesviruses that include the significant human pathogens herpes simplex viruses (HSV) and varicella zoster virus (VZV). Glycoprotein K (gK), conserved in all alphaherpesviruses, is a multi-membrane spanning virion glycoprotein essential for virus entry into neuronal axons, virion assembly, and pathogenesis. Despite these critical functions, little is known about which gK domains and residues are most important for maintaining these functions across all alphaherpesviruses. Herein, we employed phylogenetic and structural analyses including the use of a novel model for evolutionary rate variation across residues to predict conserved gK functional domains. We found marked heterogeneity in the evolutionary rate at the level of both individual residues and domains, presumably as a result of varying selective constraints. To clarify the potential role of conserved sequence features, we predicted the structures of several gK orthologs. Congruent with our phylogenetic analysis, slowly evolving residues were identified at potentially structurally significant positions across domains. We found that using a quantitative measure of amino acid rate variation combined with molecular modeling we were able to identify amino acids predicted to be critical for gK protein structure/function. This analysis yields targets for the design of anti-herpesvirus therapeutic strategies across all alphaherpesvirus species that would be absent from more traditional analyses of conservation.

scholarly journals Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

2013 ◽  
Vol 368 (1614) ◽  
pp. 20120334 ◽  
Author(s):  
Austin G. Meyer ◽  
Eric T. Dawson ◽  
Claus O. Wilke
Keyword(s):  
Protein Structure ◽  
Sialic Acid ◽  
Avian Influenza ◽  
Evolutionary Rate ◽  
Solvent Accessibility ◽  
Rate Variation ◽  
Structural Constraints ◽  
Binding Region ◽  
Site Specific ◽  
Sialic Acid Binding

We investigate the causes of site-specific evolutionary-rate variation in influenza haemagglutinin (HA) between human and avian influenza, for subtypes H1, H3, and H5. By calculating the evolutionary-rate ratio, ω = d N /d S as a function of a residue's solvent accessibility in the three-dimensional protein structure, we show that solvent accessibility has a significant but relatively modest effect on site-specific rate variation. By comparing rates within HA subtypes among host species, we derive an upper limit to the amount of variation that can be explained by structural constraints of any kind. Protein structure explains only 20–40% of the variation in ω . Finally, by comparing ω at sites near the sialic-acid-binding region to ω at other sites, we show that ω near the sialic-acid-binding region is significantly elevated in both human and avian influenza, with the exception of avian H5. We conclude that protein structure, HA subtype, and host biology all impose distinct selection pressures on sites in influenza HA.

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