scholarly journals Recombination and Selection in the Evolution of Picornaviruses and Other Mammalian Positive-Stranded RNA Viruses

2006 ◽  
Vol 80 (22) ◽  
pp. 11124-11140 ◽  
Author(s):  
Peter Simmonds
Keyword(s):  
Large Scale ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Sequence Evolution ◽  
Control Groups ◽  
Evolutionary Mechanisms ◽  
Virus Family ◽  
Selection Processes ◽  
Codon Use ◽  
Structural Region

ABSTRACT Picornaviridae are a large virus family causing widespread, often pathogenic infections in humans and other mammals. Picornaviruses are genetically and antigenically highly diverse, with evidence for complex evolutionary histories in which recombination plays a major part. To investigate the nature of recombination and selection processes underlying the evolution of serotypes within different picornavirus genera, large-scale analysis of recombination frequencies and sites, segregation by serotype within each genus, and sequence selection and composition was performed, and results were compared with those for other nonenveloped positive-stranded viruses (astroviruses and human noroviruses) and with flavivirus and alphavirus control groups. Enteroviruses, aphthoviruses, and teschoviruses showed phylogenetic segregation by serotype only in the structural region; lack of segregation elsewhere was attributable to extensive interserotype recombination. Nonsegregating viruses also showed several characteristic sequence divergence and composition differences between genome regions that were absent from segregating virus control groups, such as much greater amino acid sequence divergence in the structural region, markedly elevated ratios of nonsynonymous-to-synonymous substitutions, and differences in codon usage. These properties were shared with other picornavirus genera, such as the parechoviruses and erboviruses. The nonenveloped astroviruses and noroviruses similarly showed high frequencies of recombination, evidence for positive selection, and differential codon use in the capsid region, implying similar underlying evolutionary mechanisms and pressures driving serotype differentiation. This process was distinct from more-recent sequence evolution generating diversity within picornavirus serotypes, in which neutral or purifying selection was prominent. Overall, this study identifies common themes in the diversification process generating picornavirus serotypes that contribute to understanding of their evolution and pathogenicity.

scholarly journals Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes

2018 ◽  
Vol 115 (11) ◽  
pp. 2794-2799 ◽  
Author(s):  
Dan Sun ◽  
Iksoo Huh ◽  
Wendy M. Zinzow-Kramer ◽  
Donna L. Maney ◽  
Soojin V. Yi
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Large Scale ◽  
Parental Behavior ◽  
Phenotypic Traits ◽  
Sequence Evolution ◽  
Expression Divergence ◽  
Evolutionary Mechanisms ◽  
Behavioral Phenotypes

In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2mversion is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2mchromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2malleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.

scholarly journals Molecular and evolutionary mechanisms of yeast thermotolerance

2020 ◽  
Author(s):  
Melanie B. Abrams ◽  
Claire A. Dubin ◽  
Faisal AlZaben ◽  
Juan Bravo ◽  
Pierre M. Joubert ◽  
...  
Keyword(s):  
Sequence Divergence ◽  
Evolutionary Genetics ◽  
Biomass Accumulation ◽  
Purifying Selection ◽  
Natural World ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Bristlecone Pine ◽  
Pine Trees

ABSTRACTMany familiar traits in the natural world—from lions’ manes to the longevity of bristlecone pine trees—arose in the distant past, and have long since fixed in their respective species. A key challenge in evolutionary genetics is to figure out how and why species-defining traits have come to be. We used the thermotolerance growth advantage of the yeast Saccharomyces cerevisiae over its sister species Saccharomyces paradoxus as a model for addressing these questions. Analyzing loci where the S. cerevisiae allele promotes thermotolerance, we detected marked sequence divergence from S. paradoxus, and conservation within the species, across dozens of S. cerevisiae populations. Such patterns are most consistent with a history in which adaptive alleles arose in the ancestor of modern S. cerevisiae lineages and have been maintained since then by purifying selection. Since sequence-based signatures of selection were particularly strong at the chromosome segregation gene ESP1, we used this locus as a case study for focused mechanistic follow-up. These revealed that, in culture at high temperature, the S. paradoxus ESP1 allele conferred a striking defect in biomass accumulation and cell division relative to the S. cerevisiae allele. Only genetic divergence in the ESP1 coding region mattered phenotypically, with no functional impact detectable from the promoter. This study of an ancient adaptation, originating via selection at many unlinked loci, sets the precedent for complex evolutionary genetics across deep species divergences throughout Eukarya.

scholarly journals Intraspecific Variation in Symbiont Genomes: Bottlenecks and the Aphid-Buchnera Association

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 477-489 ◽  
Author(s):  
Daniel J Funk ◽  
Jennifer J Wernegreen ◽  
Nancy A Moran
Keyword(s):  
Large Scale ◽  
Natural Populations ◽  
Purifying Selection ◽  
Enteric Bacteria ◽  
The United States ◽  
Sequence Evolution ◽  
Deleterious Alleles ◽  
Bacterial Endosymbionts ◽  
Mitochondrial Sequences ◽  
Local Sampling

Abstract Buchnera are maternally transmitted bacterial endosymbionts that synthesize amino acids that are limiting in the diet of their aphid hosts. Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living bacteria, especially for nonsynonymous substitutions. Two mechanisms may explain this acceleration: relaxed purifying selection and increased fixation of slightly deleterious alleles under drift. Here, we test the divergent predictions of these hypotheses for intraspecific polymorphism using Buchnera associated with natural populations of the ragweed aphid, Uroleucon ambrosiae. Contrary to expectations under relaxed selection, U. ambrosiae from across the United States yielded strikingly low sequence diversity at three Buchnera loci (dnaN, trpBC, trpEG), revealing polymorphism three orders of magnitude lower than in enteric bacteria. An excess of nonsynonymous polymorphism and of rare alleles was also observed. Local sampling of additional dnaN sequences revealed similar patterns of polymorphism and no evidence of food plant-associated genetic structure. Aphid mitochondrial sequences further suggested that host bottlenecks and large-scale dispersal may contribute to genetic homogenization of aphids and symbionts. Together, our results support reduced Ne as a primary cause of accelerated sequence evolution in Buchnera. However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced Ne at aphid and endosymbiont loci.

Relationship between total plasma homocysteine and the risk of aneurysms – a meta-analysis

VASA ◽  
2020 ◽  
pp. 1-6
Author(s):  
Hanji Zhang ◽  
Dexin Yin ◽  
Yue Zhao ◽  
Yezhou Li ◽  
Dejiang Yao ◽  
...  
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
Single Species ◽  
Total Plasma ◽  
Control Groups ◽  
Randomized Controlled ◽  
Randomized Controlled Studies ◽  
The Difference ◽  
The Relationship ◽  
Healthy Participants

Summary: Our meta-analysis focused on the relationship between homocysteine (Hcy) level and the incidence of aneurysms and looked at the relationship between smoking, hypertension and aneurysms. A systematic literature search of Pubmed, Web of Science, and Embase databases (up to March 31, 2020) resulted in the identification of 19 studies, including 2,629 aneurysm patients and 6,497 healthy participants. Combined analysis of the included studies showed that number of smoking, hypertension and hyperhomocysteinemia (HHcy) in aneurysm patients was higher than that in the control groups, and the total plasma Hcy level in aneurysm patients was also higher. These findings suggest that smoking, hypertension and HHcy may be risk factors for the development and progression of aneurysms. Although the heterogeneity of meta-analysis was significant, it was found that the heterogeneity might come from the difference between race and disease species through subgroup analysis. Large-scale randomized controlled studies of single species and single disease species are needed in the future to supplement the accuracy of the results.

scholarly journals Sustainable Spatial Energy Planning of Large-Scale Wind and PV Farms in Israel: A Collaborative and Participatory Planning Approach

Energies ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 551
Author(s):  
Sofia Spyridonidou ◽  
Georgia Sismani ◽  
Eva Loukogeorgaki ◽  
Dimitra G. Vagiona ◽  
Hagit Ulanovsky ◽  
...  
Keyword(s):  
Large Scale ◽  
Wind Farms ◽  
Field Investigation ◽  
Participatory Planning ◽  
Energy Planning ◽  
Environmentally Sustainable ◽  
Selection Processes ◽  
Planning Framework ◽  
Planning Approach ◽  
Near Future

In this work, an innovative sustainable spatial energy planning framework is developed on national scale for identifying and prioritizing appropriate, technically and economically feasible, environmentally sustainable as well as socially acceptable sites for the siting of large-scale onshore Wind Farms (WFs) and Photovoltaic Farms (PVFs) in Israel. The proposed holistic framework consists of distinctive steps allocated in two successive modules (the Planning and the Field Investigation module), and it covers all relevant dimensions of a sustainable siting analysis (economic, social, and environmental). It advances a collaborative and participatory planning approach by combining spatial planning tools (Geographic Information Systems (GIS)) and multi-criteria decision-making methods (e.g., Analytical Hierarchy Process (AHP)) with versatile participatory planning techniques in order to consider the opinion of three different participatory groups (public, experts, and renewable energy planners) within the site-selection processes. Moreover, it facilitates verification of GIS results by conducting appropriate field observations. Sites of high suitability, accepted by all participatory groups and field verified, form the final outcome of the proposed framework. The results illustrate the existence of high suitable sites for large-scale WFs’ and PVFs’ siting and, thus, the potential deployment of such projects towards the fulfillment of the Israeli energy targets in the near future.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 912
Author(s):  
Andreas Martin Lisewski
Keyword(s):  
Large Scale ◽  
The Other ◽  
Yeast Cells ◽  
Virus Family ◽  
Spike Gene ◽  
Viral Replicase ◽  
Genomic Editing ◽  
Chromosomal Sequences ◽  
Bat Coronavirus ◽  
Origin Hypothesis

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered.    Results: Here we show that the genomes from SARS-CoV-2 and from SARS-CoV-1 are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1.   Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13, BANAL-20-52 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.

scholarly journals The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xu Wang ◽  
Lihua Jia ◽  
Mingdao Wang ◽  
Hao Yang ◽  
Mingyue Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Core Protein ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Purifying Selection ◽  
Intron Loss ◽  
Gene Rearrangements ◽  
Total Size ◽  
Medicinal Fungus ◽  
Taiwanofungus Camphoratus

Abstract Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

scholarly journals Gene Families, Epistasis and the Amino Acid Preferences of Protein Homologs

2019 ◽  
Vol 15 ◽  
pp. 117693431987048
Author(s):  
Evandro Ferrada
Keyword(s):  
Amino Acid ◽  
Genetic Background ◽  
Sequence Divergence ◽  
Gene Families ◽  
Structure And Function ◽  
Sequence Evolution ◽  
Systematic Analysis ◽  
Fitness Effects ◽  
Computational Work ◽  
And Function

In order to preserve structure and function, proteins tend to preferentially conserve amino acids at particular sites along the sequence. Because mutations can affect structure and function, the question arises whether the preference of a protein site for a particular amino acid varies between protein homologs, and to what extent that variation depends on sequence divergence. Answering these questions can help in the development of models of sequence evolution, as well as provide insights on the dependence of the fitness effects of mutations on the genetic background of sequences, a phenomenon known as epistasis. Here, I comment on recent computational work providing a systematic analysis of the extent to which the amino acid preferences of proteins depend on the background mutations of protein homologs.

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