scholarly journals Phylogenomic characterization of ranaviruses isolated from cultured fish and amphibians in Thailand

FACETS ◽  
2020 ◽  
Vol 5 (1) ◽  
pp. 963-979
Author(s):  
Preeyanan Sriwanayos ◽  
Kuttichantran Subramaniam ◽  
Natalie K. Stilwell ◽  
Kamonchai Imnoi ◽  
Vsevolod L. Popov ◽  
...  
Keyword(s):  
Poecilia Reticulata ◽  
Emerging Pathogens ◽  
Protein Coding ◽  
Frog Virus ◽  
Cytopathic Effects ◽  
Goldfish Carassius Auratus ◽  
Hoplobatrachus Tigerinus ◽  
Transmission Electron ◽  
Cultured Fish ◽  
Phylogenomic Analyses

Ranaviruses are emerging pathogens associated with worldwide epizootics in farmed and wild ectothermic vertebrates. In this study, we determined the full genomes of eight ranaviruses isolated from marbled sleeper goby ( Oxyeleotris marmorata), goldfish ( Carassius auratus), guppy ( Poecilia reticulata), tiger frog ( Hoplobatrachus tigerinus), Asian grass frog ( Fejervarya limnocharis), and East Asian bullfrog ( H. rugulosus) cultured or imported into Thailand. These ranaviral isolates induced the same cytopathic effects (i.e., progression of coalescing round plaques) in epithelioma papulosum cyprini (EPC) cell cultures. Transmission electron microscopy of infected EPC cells revealed cytoplasmic viral particles with ultrastructural features typical for ranaviruses. Pairwise genetic comparisons of the complete major capsid protein coding sequences from the Thai ranaviruses displayed the highest identity (99.8%–100%) to a ranavirus (tiger frog virus; TFV) isolated from diseased tiger frogs cultured in China, a slightly lower identity (99.3%–99.4%) to a ranavirus (Wamena virus; WV) isolated from diseased green tree pythons ( Morelia viridis) illegally exported from Papua New Guinea, and a lower identity to 35 other ranaviruses (93.7%–98.6%). Phylogenomic analyses supported the eight Thai ranaviruses, Chinese TFV, and WV as a subclade within a larger frog virus 3 clade. Our findings confirm the spread of TFV among cultured fish and amphibians in Asia and likely in reptiles in Oceania. Biosecurity measures are needed to ensure TFV does not continue to spread throughout Southeast Asia and to other parts of the world via international trade.

Comparative Genomics Analysis between frog Virus 3-like Ranavirus from the First Canadian Reptile Mortality Event and Similar Viruses from Amphibians

2021 ◽  
Author(s):  
Oliver Lung ◽  
Ayooluwa J. Bolaji ◽  
Michelle Nebroski ◽  
Mat Fisher ◽  
Cody Buchanan ◽  
...  
Keyword(s):  
Animal Health ◽  
Genome Structure ◽  
Leopard Frog ◽  
The Novel ◽  
Emerging Pathogens ◽  
Frog Virus 3 ◽  
Frog Virus ◽  
Usage Patterns ◽  
The Usa ◽  
World Organization

Abstract Ranaviruses are emerging pathogens that threaten the biodiversity of wild and captive cold-blooded vertebrates. Reports of ranavirus-induced mortality events are increasing and ranavirus disease is reportable to the World Organization for Animal Health. Previous studies have suggested interclass transmission of ranaviruses and Frog virus 3 (FV3)-like viruses are of particular interest. This study presents the whole-genome assembly of a 106 kb FV3-like genome obtained from the liver tissue of a reptile (wild Chelydra serpentina, common snapping turtle) that died of ranavirus disease in Canada. The FV3-like ON turtle/2018 strain shares the highest genome-wide nucleotide identity (99.71%) with the wild-type FV3 virus detected in the USA from a Northern leopard frog and an FV3-like strain identified from a wood frog in 2017 in Alberta, Canada. The novel genome contains all 26 Iridoviridae core genes, 11 FV3-like genes, and 9 unique truncations, three of which are core Iridoviridae ORFs. Additionally, the two most closely related FV3-like strains from amphibians, were compared to a non-FV3-like amphibian infecting and a fish infecting ranavirus species that showed similar codon usage patterns. G/C-ending codons were the preferred codons for all five strains. Investigation of putative recombination events identified four potential recombination events in the FV3-like ON turtle/2018 genome consistent with this FV3-like reptile infecting strain originating from an amphibian infecting FV3-like ranavirus. Altogether, this study provides insights into the genome structure and the differences in the novel FV3-like genome compared to other ranavirus genomes.

scholarly journals Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Andrej Benjak ◽  
Charlotte Avanzi ◽  
Yvonne Benito ◽  
Franck Breysse ◽  
Christophe Chartier ◽  
...  
Keyword(s):  
Causative Agent ◽  
Clinical Manifestations ◽  
Distinct Species ◽  
Close Relative ◽  
Protein Coding ◽  
Content Type ◽  
Mycobacterial Genome ◽  
Mycobacterium Lepromatosis ◽  
Dairy Animals ◽  
Phylogenomic Analyses

ABSTRACT Nodular thelitis is a chronic enzootic infection affecting dairy cows and goats. The causative agent was recently shown to be related to the leprosy-causing bacilli Mycobacterium leprae and Mycobacterium lepromatosis. In this study, the genome of this pathogen was sequenced and analyzed. Phylogenomic analyses confirmed that the pathogen present in nodular thelitis and tuberculoid scrotitis is a distinct species related to the leprosy bacilli and Mycobacterium haemophilum. Because the pathogen was originally isolated from a bovine udder, it was named “Mycobacterium uberis.” The genome of “M. uberis” is only 3.12 Mb in length, which represents the smallest mycobacterial genome identified so far but which is close to that of leprosy bacilli in size. The genome contains 1,759 protein-coding genes and 1,081 pseudogenes, indicative of extensive reductive evolution and likely the reason that M. uberis cannot be grown axenically. The pseudogenization and genome reduction in M. uberis seem to have been to some extent independent from the results determined for the genomes of the leprosy bacilli. IMPORTANCE M. uberis is an emerging skin pathogen in dairy animals. Its genome underwent massive reduction and gene decay, leading to a minimal set of genes required for an obligatory intracellular lifestyle, which highly resembles the evolution of the leprosy agents M. leprae and M. lepromatosis. The genomic similarity between M. uberis and the leprosy bacilli can help in identifying key virulence factors of these closely related species or in identifying genes responsible for the distinct differences between thelitis or scrotitis and leprosy with respect to clinical manifestations. Specific DNA markers can now be developed for quick detection of this pathogen.

scholarly journals Isolation of Tetrahymena pyriformis From Several Infected Pet Fish Species And a Regime For Its Treatment

2005 ◽  
Vol 29 (1) ◽  
pp. 190-195
Author(s):  
Omar Bassim Ahmed Al- Tayyar
Keyword(s):  
Methylene Blue ◽  
Water Temperature ◽  
Carassius Auratus ◽  
Poecilia Reticulata ◽  
Tetrahymena Pyriformis ◽  
Infected Fish ◽  
Mucus Hypersecretion ◽  
Goldfish Carassius Auratus ◽  
Poecilia Sphenops ◽  
Pterophyllum Scalare

Tetrahymena pyriformis has been firstly isolated from brood Goldfish(Carassius auratus) Common, Fantail, Ryukin, Veiltail and Moor, Black molly(Poecilia sphenops), Gourami (Trichogaster trichopterus), red Swordtail(Xiphophorus helleri), Guppy (Poecilia reticulata), deep Angelfish(Pterophyllum scalare) and brood Algae eater (Hypostomus plecostomus) inIraq. The infected fish suffered from mucus hypersecretion large hyperemicareas on the skin, and slight shedding of the scales. The incidence percentage ofinfection was 100 %. Rising water temperature was up to 29 – 30cْ for one timeand methylene blue was at a concentration of 5 ppm for 24 hours. Sodiumchloride at a concentration of 2 % for one minute and two minutes has noobvious effect on Tetrahymena pyriformis. Treatment with NaCl at theconcentration of 1% for 20 minutes for three consecutive days achieved the bestresults.

scholarly journals The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 456 ◽  
Author(s):  
Cornelius M. Kyalo ◽  
Zhi-Zhong Li ◽  
Elijah M. Mkala ◽  
Itambo Malombe ◽  
Guang-Wan Hu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Structural Features ◽  
Base Pairs ◽  
Protein Coding ◽  
Variable Regions ◽  
Morphological Heterogeneity ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Phylogenomic Analyses

Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.

scholarly journals Infection With a Novel Rickettsiella Species in Emperor Scorpions (Pandinus imperator)

2020 ◽  
Vol 57 (6) ◽  
pp. 858-870
Author(s):  
Sushan Han ◽  
Aníbal G. Armién ◽  
Janet E. Hill ◽  
Champika Fernando ◽  
Dan S. Bradway ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Rapid Progression ◽  
Protein Coding ◽  
Hematopoietic Organ ◽  
Transmission Electron ◽  
History Of ◽  
Gross Lesions ◽  
Membrane Bound ◽  
Methenamine Silver

Rickettsiella infection was diagnosed in 4 adult emperor scorpions ( Pandinus imperator) from 2 different collections over a 3-year period. One case had a 2-day history of weakness, failure to lift the tail, or respond to stimulation, with rapid progression to death. The other 3 cases were found dead. There were no gross lesions, but histologically the hemolymphatic vasculature and sinuses, presumed hematopoietic organ, heart, midgut and midgut diverticula, nerves, and skeletal muscle were infiltrated with phagocytic and granular hemocytes with necrosis. Phagocytic hemocytes contained abundant intracellular microorganisms that were Fite’s acid-fast-positive, Macchiavello-positive, variably gram-positive or gram-negative, and Grocott’s methenamine silver-negative. By transmission electron microscopy, hemocytes contained numerous phagocytic vacuoles with small dense bacterial forms (mean 0.603 × 0.163 μm) interspersed with large bacterial forms (mean 1.265 × 0.505 μm) and few intermediary forms with electron-dense nucleoids and membrane-bound crystalline arrays (average 4.72 μm). Transmission electron microscopy findings were consistent with bacteria of the family Coxiellaceae. Based on sequencing the 16S ribosomal RNA gene, the identity was confirmed as Rickettsiella, and phylogenetic analysis of protein-coding genes gidA, rspA, and sucB genes suggested the emperor scorpion pathogen as a new species. This study identifies a novel Rickettsiella causing infection in emperor scorpions and characterizes the unique pathological findings of this disease. We suggest this organism be provisionally named Rickettsiella scorpionisepticum.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3941 ◽  
Author(s):  
Alejandra Panzera ◽  
Adam D. Leaché ◽  
Guillermo D’Elía ◽  
Pedro F. Victoriano
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
Molecular Systematic ◽  
Data Set ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

scholarly journals Mitochondrial genome evolution of placozoans: gene rearrangements and repeat expansions

2020 ◽  
Author(s):  
Hideyuki Miyazawa ◽  
Hans-Jürgen Osigus ◽  
Sarah Rolfes ◽  
Kai Kamm ◽  
Bernd Schierwater ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gc Content ◽  
Distribution Patterns ◽  
Sister Group ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Inverted Repeats ◽  
Protein Coding ◽  
Group I ◽  
Phylogenomic Analyses

Abstract Placozoans, non-bilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNA are circular chromosomes of 32-43 kbp in size, which encode 12 protein-coding genes, 24 tRNAs, and 2 rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Since P. mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2463 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V. Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

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