scholarly journals An examination of the Iridovirus core genes for reconstructing Ranavirus phylogenies

FACETS ◽  
2020 ◽  
Vol 5 (1) ◽  
pp. 523-533
Author(s):  
D.R. Ballard ◽  
A.J. Davis ◽  
R.B. Fuller ◽  
A.R. Garner ◽  
A.D. Mileham ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Reconstruction ◽  
Emerging Infections ◽  
Capsid Protein Gene ◽  
Reading Frame ◽  
Plot Analysis ◽  
Family Protein ◽  
Major Capsid Protein Gene ◽  
Conserved Core ◽  
Core Genes

Ranaviruses are globally emerging infections of poikilothermic vertebrates and belong to the viral family Iridoviridae. The six species of ranaviruses are responsible for unknown numbers of infections and disease and mortality events around the world in amphibians, fish, and reptiles. Genomic investigations have shown that there are 24 core genes shared by all iridoviruses. In this study, we examine the utility of each of these genes in reconstructing phylogenetic relationships across six species of Ranavirus. We also performed dot-plot analysis for the 17 isolates in the study. For large-scale differentiation, using the major capsid protein gene creates a tree similar to the whole genome tree. Other comparable genes include open reading frame (ORF) 19R (a serine–theonine protein kinase) and ORF 88R (Erv I/Alr Family protein). The poorest candidate for phylogenetic reconstruction, due to high homology, was ORF 1R (a putative replication factor and (or) DNA binding-packing protein). There are a plethora of genes that may be useful to examine phylogenies at smaller scales (e.g., to examine local adaptation); however, they do not necessarily belong to the set of highly conserved core genes.

scholarly journals Phylogeography in an “oyster” shell provides first insights into the genetic structure of an extinct Ostrea edulis population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sarah Hayer ◽  
Dirk Brandis ◽  
Alexander Immel ◽  
Julian Susat ◽  
Montserrat Torres-Oliva ◽  
...  
Keyword(s):  
Large Scale ◽  
Wadden Sea ◽  
Atlantic Coast ◽  
Phylogenetic Reconstruction ◽  
Oyster Shell ◽  
Glacial Refugia ◽  
Late Nineteenth Century ◽  
Ostrea Edulis ◽  
Geographic Ranges ◽  
The North

AbstractThe historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s—including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.

scholarly journals Prevalence and genetic diversity of avian haemosporidian parasites in wild bird species of the order Columbiformes

2021 ◽  
Author(s):  
Yvonne R. Schumm ◽  
Dimitris Bakaloudis ◽  
Christos Barboutis ◽  
Jacopo G. Cecere ◽  
Cyril Eraud ◽  
...  
Keyword(s):  
Host Species ◽  
Large Scale ◽  
Phylogenetic Reconstruction ◽  
Bird Species ◽  
Avian Species ◽  
Blood Parasites ◽  
Migration Strategy ◽  
Haemosporidian Parasites ◽  
Multiplex Pcr Assay ◽  
And Migration

AbstractDiseases can play a role in species decline. Among them, haemosporidian parasites, vector-transmitted protozoan parasites, are known to constitute a risk for different avian species. However, the magnitude of haemosporidian infection in wild columbiform birds, including strongly decreasing European turtle doves, is largely unknown. We examined the prevalence and diversity of haemosporidian parasites Plasmodium, Leucocytozoon and subgenera Haemoproteus and Parahaemoproteus in six species of the order Columbiformes during breeding season and migration by applying nested PCR, one-step multiplex PCR assay and microscopy. We detected infections in 109 of the 259 screened individuals (42%), including 15 distinct haemosporidian mitochondrial cytochrome b lineages, representing five H. (Haemoproteus), two H. (Parahaemoproteus), five Leucocytozoon and three Plasmodium lineages. Five of these lineages have never been described before. We discriminated between single and mixed infections and determined host species-specific prevalence for each parasite genus. Observed differences among sampled host species are discussed with reference to behavioural characteristics, including nesting and migration strategy. Our results support previous suggestions that migratory birds have a higher prevalence and diversity of blood parasites than resident or short-distance migratory species. A phylogenetic reconstruction provided evidence for H. (Haemoproteus) as well as H. (Parahaemoproteus) infections in columbiform birds. Based on microscopic examination, we quantified parasitemia, indicating the probability of negative effects on the host. This study provides a large-scale baseline description of haemosporidian infections of wild birds belonging to the order Columbiformes sampled in the northern hemisphere. The results enable the monitoring of future changes in parasite transmission areas, distribution and diversity associated with global change, posing a potential risk for declining avian species as the European turtle dove.

Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus

2020 ◽  
Vol 84 ◽  
pp. 104379
Author(s):  
Hai-feng Tian ◽  
Qiao-mu Hu ◽  
Han-bing Xiao ◽  
Ling-bing Zeng ◽  
Yan Meng ◽  
...  
Keyword(s):  
Codon Usage ◽  
Capsid Protein ◽  
Codon Usage Bias ◽  
Protein Gene ◽  
Major Capsid Protein ◽  
Capsid Protein Gene ◽  
Major Capsid Protein Gene

Bioinformatics Analysis and Characteristics of Capsular Exopolysaccharide Family Gene and its Encoding Protein in Riemerella Anatipestifer

2013 ◽  
Vol 641-642 ◽  
pp. 630-637
Author(s):  
Hai Bo Yi ◽  
De Kang Zhu ◽  
Xiao Jia Wang ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Capsular Polysaccharide ◽  
Gc Content ◽  
Bioinformatic Analysis ◽  
Biological Information ◽  
Peptide Cleavage ◽  
Reading Frame ◽  
Functional Sites ◽  
Family Protein ◽  
Hydrophilic Region ◽  
Family Gene

To provide some evidence for further research on the biological function of capsular polysaccharide family gene and its endcoding protein of Riemerella anatipestifer.we analyzed the sequence of capsular exopolysaccharide gene and physicochemical properties , structure , function of capsular exopolysaccharide family protein by bioinformatics tools online.We found that capsular exopolysaccharide family gene is an open reading frame with 2373 bp in length and contained a single ORF, which consisted of 732 adenine,443 cytosine,321 guanine,877 thymine and a GC content 32.20%. The NC value of the nucleotides sequence of capsular exopolysaccharide family gene was 44.270. Capsular exopolysaccharide family protein consisted of 790 amino acids and had the following characteristics: numerous highly hydrophilic region, two transmembrane domains, zero signal peptide cleavage site, numerous functional sites. We obtain more biological information about capsular exopolysaccharide family gene and its endcoding protein by bioinformatic analysis, which provide some basic information for further research.

scholarly journals The Full-Length Protein Encoded by Human Cytomegalovirus Gene UL117 Is Required for the Proper Maturation of Viral Replication Compartments

2008 ◽  
Vol 82 (7) ◽  
pp. 3452-3465 ◽  
Author(s):  
Zhikang Qian ◽  
Baoqin Xuan ◽  
Te Tee Hong ◽  
Dong Yu
Keyword(s):  
Human Cytomegalovirus ◽  
Large Scale ◽  
Full Length ◽  
Wild Type ◽  
Virus Growth ◽  
Reading Frame ◽  
Early Proteins ◽  
Immediate Early Proteins ◽  
Novel Transcripts ◽  
Related Proteins

ABSTRACT Previously, two large-scale mutagenic analyses showed that mutations in the human cytomegalovirus (HCMV) gene UL117 resulted in a defect in virus growth in fibroblasts. Early transcriptional analyses have revealed several mRNAs from the UL119-UL115 region; however, specific transcripts encoding UL117-related proteins have not been identified. In this study, we identified two novel transcripts arising from the UL117 gene locus, and we reported that the UL117 open reading frame encoded the full-length protein pUL117 (45 kDa) and the shorter isoform pUL117.5 (35 kDa) as the result of translation initiation at alternative in-frame ATGs. Both proteins were expressed with early kinetics, but pUL117 accumulated at a lower abundance relative to that of pUL117.5. During HCMV infection, both proteins localized predominantly to the nucleus, and the major fraction of pUL117 localized in viral nuclear replication compartments. We constructed mutant HCMV viruses in which the entire UL117 coding sequence was deleted or the expression of pUL117 was specifically abrogated. The growth of mutant viruses was significantly attenuated, indicating that pUL117 was required for efficient virus infection in fibroblasts. Cells infected with the pUL117-deficient mutant virus accumulated representative viral immediate-early proteins and early proteins normally. In the absence of pUL117, the accumulation of replicating viral DNA was reduced by no more than twofold at early times and was indistinguishable from that of the wild type at 72 h postinfection. Strikingly, there was a 12- to 24-h delay in the development of nuclear replication compartments and a marked delay in the expression of late viral proteins. We conclude that pUL117 acts to promote the development of nuclear replication compartments to facilitate viral growth.

Nucleotide sequence and transcriptional mapping of the major capsid protein gene of pseudorabies virus

Virology ◽  
1991 ◽  
Vol 185 (1) ◽  
pp. 56-66 ◽  
Author(s):  
Shunji Yamada ◽  
Tadao Imada ◽  
Wakako Watanabe ◽  
Yoshikazu Honda ◽  
Sadayo Nakajima-Iijima ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Capsid Protein ◽  
Pseudorabies Virus ◽  
Protein Gene ◽  
Major Capsid Protein ◽  
Capsid Protein Gene ◽  
Transcriptional Mapping ◽  
Major Capsid Protein Gene

scholarly journals A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

2020 ◽  
Author(s):  
Granger Sutton ◽  
Gary B. Fogel ◽  
Bradley Abramson ◽  
Lauren Brinkac ◽  
Todd Michael ◽  
...  
Keyword(s):  
Essential Genes ◽  
Considerable Time ◽  
Laboratory Methods ◽  
Pan Genome ◽  
Gene Acquisition ◽  
A Genome ◽  
Low Penetrance Genes ◽  
Almost All ◽  
Conserved Core ◽  
Core Genes

AbstractSynthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. We show that these core regions are very likely to contain all or almost all essential genes. We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.ImportanceThe pan-genome approach presented in this paper can be used to determine core regions of a genome and has many possible applications. Synthetic engineering design can be informed by which genes/regions are more conserved (core) versus less conserved. The level of conservation of adjacent non-core genes tends to define cassettes of genes which may be part of a pathway or system that can inform researchers about possible functional significance. The pattern of gene presence across the different genomes of a species can inform the understanding of evolution and horizontal gene acquisition. The approach saves considerable time and effort relative to laboratory methods used to identify essential genes in species.

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