scholarly journals Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome

2013 ◽  
Vol 94 (9) ◽  
pp. 2082-2093 ◽  
Author(s):  
A. Jeanine Abrams ◽  
David C. Cannatella ◽  
David M. Hillis ◽  
Sara L. Sawyer
Keyword(s):  
Positive Selection ◽  
Synonymous Substitution ◽  
Detection Methods ◽  
Host Switching ◽  
Synonymous Substitution Rate ◽  
Host Shifts ◽  
Selective Pressures ◽  
The Family ◽  
Viral Genes ◽  
Core Genes

Ranaviruses have been implicated in recent declines in global amphibian populations. Compared with the family Iridoviridae, to which the genus Ranavirus belongs, ranaviruses have a wide host range in that species/strains are known to infect fish, amphibians and reptiles, presumably due to recent host-switching events. We used eight sequenced ranavirus genomes and two selection-detection methods (site based and branch based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which were newly acquired genes unique to ranavirus genomes. Using the branch-based method, we identified eight additional candidate genes that exhibited signatures of dN /dS (non-synonymous/synonymous substitution rate) >1 in the clade where intense host switching had occurred. We found that these branch-specific patterns of elevated dN /dS were enriched in a small group of viral genes that have been acquired most recently in the ranavirus genome, compared with core genes that are shared among all members of the family Iridoviridae. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching.

scholarly journals Hadrurid Scorpion Toxins: Evolutionary Conservation and Selective Pressures

Toxins ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 637 ◽  
Author(s):  
Carlos E. Santibáñez-López ◽  
Matthew R. Graham ◽  
Prashant P. Sharma ◽  
Ernesto Ortiz ◽  
Lourival D. Possani
Keyword(s):  
Positive Selection ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Housekeeping Genes ◽  
Evolutionary Conservation ◽  
Gene Duplications ◽  
Scorpion Toxins ◽  
Selective Pressures ◽  
Phylogenetic Inertia ◽  
The Family

Scorpion toxins are thought to have originated from ancestral housekeeping genes that underwent diversification and neofunctionalization, as a result of positive selection. Our understanding of the evolutionary origin of these peptides is hindered by the patchiness of existing taxonomic sampling. While recent studies have shown phylogenetic inertia in some scorpion toxins at higher systematic levels, evolutionary dynamics of toxins among closely related taxa remain unexplored. In this study, we used new and previously published transcriptomic resources to assess evolutionary relationships of closely related scorpions from the family Hadruridae and their toxins. In addition, we surveyed the incidence of scorpine-like peptides (SLP, a type of potassium channel toxin), which were previously known from 21 scorpion species. We demonstrate that scorpine-like peptides exhibit gene duplications. Our molecular analyses demonstrate that only eight sites of two SLP copies found in scorpions are evolving under positive selection, with more sites evolving under negative selection, in contrast to previous findings. These results show evolutionary conservation in toxin diversity at shallow taxonomic scale.

scholarly journals The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR- coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte)

2018 ◽  
Author(s):  
Hong-Rui Zhang ◽  
Qiao-Ping Xiang ◽  
Xian-Chun Zhang
Keyword(s):  
Homologous Recombination ◽  
Vascular Plant ◽  
Synonymous Substitution ◽  
Inverted Repeats ◽  
Synonymous Substitution Rate ◽  
Direct Repeats ◽  
Evolutionary Trajectory ◽  
Link Type ◽  
The Family ◽  
Gc Contents

AbstractBoth direct repeats (DR) and inverted repeats (IR) are documented in the published plastomes of four Selaginella species indicating the unusual and diverse plastome structure in the family Selaginellaceae. In this study, we newly sequenced complete plastomes of seven species from five main lineages of Selaginellaceae and also re-sequenced three species (S. tamariscina, S. uncinata and S. moellendorffii) to explore the evolutionary trajectory of Selaginellaceae plastomes. Our results showed that the plastomes of Selaginellaceae vary remarkably in size, gene contents, gene order and GC contents. Notably, both DR and IR structure existed in the plastomes of Selaginellaceae with DR structure being an early diverged character. The occurrence of DR structure was right after the Permian-Triassic (P-T) extinction (ca. 246 Ma) and remained in most subgenera of Selaginellaceae, whereas IR structure only reoccurred in the most derived subg. Heterostachys (ca. 23 Ma). The presence of a pair of large repeats psbK-trnQ, together with DR/IR region in S. bisulcata, S. pennata, S. uncinata, and S. hainanensis, could frequently mediate diverse homologous recombination and create approximately equal stoichiometric isomers (IR/DR-coexisting) and subgenomes. High proportion of repeats is presumably responsible for the dynamic IR/DR-coexisting plastomes, which possess a lower synonymous substitution rate (dS) compared with DR-possessing plastomes. We propose that the occurrence of DR structure, together with few repeats, is possibly selected to adapt to the environmental upheaval during the P-T crisis and the IR/DR-coexisting plastomes also reached an equilibrium in plastome organization through highly efficient homologous recombination to maintain stability.Data depositionAll the plastomes were deposited in GenBank under accession numbers MG272483-MG272484, MH598531-MH598537 and MK156800.

scholarly journals Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Teame Gereziher MEHARI ◽  
Yanchao XU ◽  
Richard Odongo MAGWANGA ◽  
Muhammad Jawad UMER ◽  
Joy Nyangasi KIRUNGU ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gossypium Hirsutum ◽  
Abiotic Stresses ◽  
Substitution Rate ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)

2021 ◽  
Author(s):  
John Shaheen ◽  
Austin B Mudd ◽  
Thomas G H Diekwisch ◽  
John Abramyan
Keyword(s):  
Tooth Loss ◽  
Tooth Enamel ◽  
Synonymous Substitution ◽  
Bufo Bufo ◽  
Molecular Dating ◽  
Bufo Gargarizans ◽  
The Family ◽  
Synonymous Substitution Rates ◽  
Mandibular Teeth ◽  
Early Tooth Loss

Abstract Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary timeline of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In the present study we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86–93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison to functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 MYA in the lineage leading to modern true toads, a timeline that coincides with the rise of the family Bufonidae.

scholarly journals Viruses and Virus Diseases of Rubus

Plant Disease ◽  
2013 ◽  
Vol 97 (2) ◽  
pp. 168-182 ◽  
Author(s):  
Robert R. Martin ◽  
Stuart MacFarlane ◽  
Sead Sabanadzovic ◽  
Diego Quito ◽  
Bindu Poudel ◽  
...  
Keyword(s):  
Far East ◽  
Fruit Production ◽  
Detection Methods ◽  
Center Of Origin ◽  
The Family ◽  
Production Stages ◽  
Rubus Species ◽  
Polymerase Chain ◽  
Made In

Blackberry and raspberry are members of the family Rosaceae. They are classified in the genus Rubus, which comprises hundreds of species and has a center of origin in the Far East. Rubus is divided into 15 subgenera with blackberries classified in the Rubus (formerly Eubatus) and raspberries in the Idaeobatus subgenera. Rubus species are propagated vegetatively and are subject to infection by viruses during development, propagation, and fruit production stages. Reports of initial detection and symptoms of more than 30 viruses, virus-like diseases, and phytoplasmas affecting Rubus spp. were reviewed more than 20 years ago. Since the last review on Rubus viruses, significant progress has been made in the molecular characterization of many of the viruses that infect Rubus spp. Currently, reverse transcription–polymerase chain reaction detection methods are available for most of the viruses known to infect Rubus. The goals of this article are to update the knowledge on previously characterized viruses of Rubus, highlight recently described viruses, review the virus-induced symptoms, describe the advances made in their detection, and discuss our knowledge about several virus complexes that cause serious diseases in Rubus. Virus complexes have been identified recently as the major cause of diseases in blackberries and raspberries.

scholarly journals Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.

2020 ◽  
Vol 8 (5) ◽  
pp. 634 ◽  
Author(s):  
Zhenxing Xu ◽  
Yoko Masuda ◽  
Chie Hayakawa ◽  
Natsumi Ushijima ◽  
Keisuke Kawano ◽  
...  
Keyword(s):  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Genomic Comparison ◽  
Novel Genus ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Type Strains ◽  
Core Genes

Bacteria of the family Geobacteraceae are particularly common and deeply involved in many biogeochemical processes in terrestrial and freshwater environments. As part of a study to understand biogeochemical cycling in freshwater sediments, three iron-reducing isolates, designated as Red96T, Red100T, and Red88T, were isolated from the soils of two paddy fields and pond sediment located in Japan. The cells were Gram-negative, strictly anaerobic, rod-shaped, motile, and red-pigmented on agar plates. Growth of these three strains was coupled to the reduction of Fe(III)-NTA, Fe(III) citrate, and ferrihydrite with malate, methanol, pyruvate, and various organic acids and sugars serving as alternate electron donors. Phylogenetic analysis based on the housekeeping genes (16S rRNA gene, gyrB, rpoB, nifD, fusA, and recA) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family Geobacteraceae. Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly differentiated the strains Red96T, Red100T, and Red88T from other species in the family Geobacteraceae, with values below the thresholds for species delineation. Along with the genomic comparison, the chemotaxonomic features further helped distinguish the three isolates from each other. In addition, the lower values of average amino acid identity and percentage of conserved protein, as well as biochemical differences with their relatives, indicated that the three strains represented a novel genus in the family Geobacteraceae. Hence, we concluded that strains Red96T, Red100T, and Red88T represented three novel species of a novel genus in the family Geobacteraceae, for which the names Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. are proposed, with type strains Red96T (= NBRC 114286T = MCCC 1K04376T), Red100T (= NBRC 114287T = MCCC 1K04377T), and Red88T (= MCCC 1K03694T = JCM 33033T), respectively.

scholarly journals Long-Term Persistence of Infection in Chimpanzees Inoculated with an Infectious Hepatitis C Virus Clone Is Associated with a Decrease in the Viral Amino Acid Substitution Rate and Low Levels of Heterogeneity

2004 ◽  
Vol 78 (18) ◽  
pp. 9782-9789 ◽  
Author(s):  
Javier Fernandez ◽  
Deborah Taylor ◽  
Duncan R. Morhardt ◽  
Kathleen Mihalik ◽  
Montserrat Puig ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Substitution Rate ◽  
Selective Pressure ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Nonsynonymous Substitution Rate ◽  
Over Time

ABSTRACT Two chimpanzees, 1535 and 1536, became persistently infected following inoculation with RNA transcripts from cDNA clones of hepatitis C virus (HCV). Analysis of the HCV genomes from both animals showed an accumulation of amino acid substitutions over time. The appearance of substitutions in the envelope genes was associated with increased antienvelope antibody titers. However, extensive mutations were not incorporated into hypervariable region 1 (HVR1). A comparison of the nonsynonymous substitution rate/synonymous substitution rate was made at various time points to analyze selective pressure. The highest level of selective pressure occurred during the acute phase and decreased as the infection continued. The nonsynonymous substitution rate was initially higher than the synonymous substitution rate but decreased over time from 3.3 × 10−3 (chimpanzee 1535) and 3.2 × 10−3 (chimpanzee 1536) substitutions/site/year at week 26 to 1.4 × 10−3 (chimpanzee 1535) and 1.7 × 10−3 (chimpanzee 1536) at week 216, while the synonymous substitution rate remained steady at ∼1 × 10−3 substitutions/site/year. Analysis of PCR products using single-stranded conformational polymorphism indicated a low level of heterogeneity in the viral genome. The results of these studies confirm that the persistence of infection is not solely due to changes in HVR1 or heterogeneity and that the majority of variants observed in natural infections could not arise simply through mutation during the time period most humans and chimpanzees are observed. These data also indicate that immune pressure and selection continue throughout the chronic phase.

Phylogenetic relationships of the family Campulidae (Trematoda) based on 18S rRNA sequences

Parasitology ◽  
1998 ◽  
Vol 117 (4) ◽  
pp. 383-391 ◽  
Author(s):  
M. FERNANDEZ ◽  
D. T. J. LITTLEWOOD ◽  
A. LATORRE ◽  
J. A. RAGA ◽  
D. ROLLINSON
Keyword(s):  
18S Rrna ◽  
Fasciola Hepatica ◽  
18S Rrna Gene ◽  
Host Switching ◽  
Rrna Gene ◽  
Intermediate Hosts ◽  
Marine Gastropods ◽  
Echinostoma Caproni ◽  
The Family ◽  
Rrna Sequences

Traditionally, the family Campulidae has been associated either with the family Fasciolidae, parasites of ruminants, or the Acanthocolpidae, parasites of fishes, based on morphological similarities. Since morphology does not seem to resolve clearly the problem of the relationships of campulids, we have used the sequences of the 18S rRNA gene of the campulids Zalophotrema hepaticum, Campula oblonga and Nasitrema globicephalae, the fasciolid Fasciola hepatica, the acanthocolpid Stephanostomum baccatum and the outgroup Schistosoma mansoni to infer a phylogeny. Maximum parsimony and neighbour-joining methods were applied. Both methods indicated that campulids are closer to acanthocolpids than fasciolids. In order to confirm this relationship, we generated a second phylogeny using all the partial sequences of the 18S published for trematodes: Lobatostoma manteri, Echinostoma caproni, Calicophoron calicophorum, Tetracerasta blepta, Gyliauchen sp. and Opistorchis viverrini, plus those mentioned above, and Dicrocoelium dendriticum. The aspidogastrean L. manteri was used as the outgroup. Results were identical to the first analysis. According to this and the most recent Digenean phylogeny, which considers campulids and acanthocolpids as sister groups, we suggest that a common origin for these 2 groups would imply a host-switching process. The life-cycle of acanthocolpids includes marine gastropods as first intermediate hosts, and fishes as second intermediate and definitive hosts. In this context, the hypothesis would be that trematodes whose cycle ended in fishes were able to switch to mammalian hosts.

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