Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis

Purpose. We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. Methods. Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. Results. Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. Conclusion. Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.

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Adaptive evolution ofMoniliophthoraPR-1 proteins towards its pathogenic lifestyle

10.1101/2021.03.07.434232 ◽

2021 ◽

Author(s):

Adrielle A. Vasconcelos ◽

Juliana José ◽

Paulo M. Tokimatu Filho ◽

Antonio P. Camargo ◽

Paulo J. P. L. Teixeira ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Positive Selection ◽

Adaptive Evolution ◽

Theobroma Cacao ◽

Main Function ◽

Moniliophthora Perniciosa ◽

Induced Expression ◽

Pathogenesis Related ◽

Parasitic Lifestyle ◽

Moniliophthora Roreri

AbstractMoniliophthora perniciosaandMoniliophthora roreriare hemibiotrophic fungi that harbor a large number of Pathogenesis-Related 1 genes, many of which are induced in the biotrophic interaction withTheobroma cacao.Here, we provide evidence that the evolution of PR-1 inMoniliophthorawas adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Phylogenetic analysis revealed conserved PR-1 genes, shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity inMoniliophthora, as well as in recent specialization cases within both species. PR-1 families inMoniliophthorawith higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host-pathogen arm race. Furthermore, we show that the highly diversifiedMpPR-1genes are not induced by two phytoalexins, suggesting detoxification might not be their main function as proposed before.

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A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

Systematic Biology ◽

10.1093/sysbio/syz075 ◽

2019 ◽

Vol 69 (4) ◽

pp. 722-738 ◽

Cited By ~ 2

Author(s):

Christopher T Jones ◽

Noor Youssef ◽

Edward Susko ◽

Joseph P Bielawski

Keyword(s):

Positive Selection ◽

Adaptive Evolution ◽

Evolutionary History ◽

Life History Trait ◽

Molecular Adaptation ◽

Simulation Studies ◽

Site Model ◽

Branch Site ◽

A Site ◽

Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

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Complete genome analysis identifies recombinant events and positive selection sites of hepatitis C virus from mainland China during 2010–2019

Virus Research ◽

10.1016/j.virusres.2021.198354 ◽

2021 ◽

Vol 296 ◽

pp. 198354

Author(s):

Mengdi Qi ◽

Mengmei Yang ◽

Liangzi Xu ◽

Chunli Ma ◽

Pu Huang ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Positive Selection ◽

Genome Analysis ◽

Complete Genome ◽

Mainland China ◽

Complete Genome Analysis

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Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone

Biology ◽

10.3390/biology10010028 ◽

2021 ◽

Vol 10 (1) ◽

pp. 28

Author(s):

Umaru Bangura ◽

Jacob Buanie ◽

Joyce Lamin ◽

Christopher Davis ◽

Gédéon Ngiala Bongo ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Sierra Leone ◽

Small Mammal ◽

Hemorrhagic Fever ◽

Lassa Fever ◽

Lassa Virus ◽

Sierra Leonean ◽

Bayesian Phylogenetic Analysis ◽

Prevalent Species ◽

Lineage Iv

Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.

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Case of Human Infestation with Dermanyssus gallinae (Poultry Red Mite) from Swallows (Hirundinidae)

Pathogens ◽

10.3390/pathogens10030299 ◽

2021 ◽

Vol 10 (3) ◽

pp. 299

Author(s):

Georgios Sioutas ◽

Styliani Minoudi ◽

Katerina Tiligada ◽

Caterina Chliva ◽

Alexandros Triantafyllidis ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Clinical Symptoms ◽

Skin Lesions ◽

Coi Gene ◽

Dermanyssus Gallinae ◽

Poultry Red Mite ◽

Human Form ◽

Bayesian Phylogenetic Analysis

Dermanyssus gallinae (the poultry red mite, PRM) is an important ectoparasite in the laying hen industry. PRM can also infest humans, causing gamasoidosis, which is manifested as skin lesions characterized by rash and itching. Recently, there has been an increase in the reported number of human infestation cases with D. gallinae, mostly associated with the proliferation of pigeons in cities where they build their nests. The human form of the disease has not been linked to swallows (Hirundinidae) before. In this report, we describe an incident of human gamasoidosis linked to a nest of swallows built on the window ledge of an apartment in the island of Kefalonia, Greece. Mites were identified as D. gallinae using morphological keys and amplifying the Cytochrome C oxidase subunit I (COI) gene by PCR. Bayesian phylogenetic analysis and median-joining network supported the identification of three PRM haplogroups and the haplotype isolated from swallows was identical to three PRM sequences isolated from hens in Portugal. The patient was treated with topical corticosteroids, while the house was sprayed with deltamethrin. After one week, the mites disappeared and clinical symptoms subsided. The current study is the first report of human gamasoidosis from PRM found in swallows’ nest.

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A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽

10.1093/genetics/165.2.613 ◽

2003 ◽

Vol 165 (2) ◽

pp. 613-621 ◽

Cited By ~ 2

Author(s):

Douglas R Dorer ◽

Jamie A Rudnick ◽

Etsuko N Moriyama ◽

Alan C Christensen

Keyword(s):

Phylogenetic Analysis ◽

Drosophila Melanogaster ◽

Anopheles Gambiae ◽

Evolutionary History ◽

Codon Bias ◽

Good Target ◽

The Family ◽

Genes Encoding ◽

And Function ◽

Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

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Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium

Research in Microbiology ◽

10.1016/j.resmic.2004.01.002 ◽

2004 ◽

Vol 155 (4) ◽

pp. 290-296 ◽

Cited By ~ 11

Author(s):

Didier Hatsch ◽

Vincent Phalip ◽

Jean-Marc Jeltsch

Keyword(s):

Phylogenetic Analysis ◽

Topoisomerase Ii ◽

Genes Encoding

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The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

BMC Ecology and Evolution ◽

10.1186/s12862-021-01803-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Fan Li ◽

Yunyun Lv ◽

Zhengyong Wen ◽

Chao Bian ◽

Xinhui Zhang ◽

...

Keyword(s):

Positive Selection ◽

Adaptive Evolution ◽

Physiological Activity ◽

Complete Mitochondrial Genome ◽

Dynamic Environment ◽

Data Set ◽

History Of ◽

Complete Mitogenome ◽

Selection Signal ◽

Positive Selection Signal

Abstract Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

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