scholarly journals A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira"

2021 ◽  
Author(s):  
Marcus M de M. Teixeira ◽  
Jason E. Stajich ◽  
Jason W Sahl ◽  
George R Thompson ◽  
Heather L Mead ◽  
...  
Keyword(s):  
Single Molecule ◽  
Population Genomics ◽  
Copy Number Variants ◽  
Laboratory Strain ◽  
Gene Gain ◽  
Coccidioides Immitis ◽  
Coccidioides Posadasii ◽  
Valley Fever ◽  
Chromosomal Structure ◽  
Functional Studies

Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and C. posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation was made available. In the current study, the genome of the Silveira strain was sequenced using Single Molecule Real Time Sequencing (SMRT) PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (transversion, translocation, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.

scholarly journals Real-time PCR assay for detection and differentiation of Coccidioides immitis and Coccidioides posadasii from culture and clinical specimens

2021 ◽  
Author(s):  
Sudha Chaturvedi ◽  
Tanya R Victor ◽  
Anuradha Marathe ◽  
Ketevan Sidamonidze ◽  
Kelly L Crucillo ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Limit Of Detection ◽  
Cross Reactivity ◽  
Coccidioides Immitis ◽  
Coccidioides Posadasii ◽  
Pcr Assay ◽  
Valley Fever ◽  
Clinical Specimens ◽  
Wide Range

Coccidioidomycosis (Valley Fever) is a pulmonary and systemic fungal disease with increasing incidence and expanding endemic areas. The differentiation of etiologic agents Coccidioides immitis and C. posadasii remains problematic in the clinical laboratories as conventional PCR and satellite typing schemes are not facile. Therefore, we developed Cy5- and FAM-labeled TaqMan-probes for duplex real-time PCR assay for rapid differentiation of C. immitis and C. posadasii from culture and clinical specimens. The RRA2 gene encoding proline-rich antigen 2, specific for Coccidioides genus, was the source for the first set of primers and probe. Coccidioides immitis contig 2.2 (GenBank: AAEC02000002.1) was used to design the second set of primers and probe. The second primers/probe did not amplify the corresponding C. posadasii DNA, because of an 86-bp deletion in the contig. The assay was highly sensitive with limit of detection of 0.1 pg gDNA/PCR reaction, which was equivalent to approximately ten genome copies of C. immitis or C. posadasii. The assay was highly specific with no cross-reactivity to the wide range of fungal and bacterial pathogens. Retrospective analysis of fungal isolates and primary specimens submitted from 1995 to 2020 confirmed 129 isolates and three primary specimens as C. posadasii and 23 isolates as C. immitis from human coccidioidomycosis cases, while all eight primary samples from two animals were confirmed as C. posadasii. A preliminary analysis of cerebrospinal fluid (CSF) and pleural fluid samples showed positive correlation between serology tests and real-time PCR for two of the 15 samples. The Coccidioides spp. duplex real-time PCR will allow rapid differentiation of C. immitis and C. posadasii from clinical specimens and further augment the surveillance of coccidioidomycosis.

scholarly journals Local population structure and patterns of Western Hemisphere dispersal forCoccidioides spp., the fungal cause of Valley Fever

2015 ◽  
Author(s):  
David M. Engelthaler ◽  
Chandler C. Roe ◽  
Crystal M. Hepp ◽  
Marcus Teixeira ◽  
Elizabeth M. Driebe ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Local Population ◽  
The United States ◽  
Western Hemisphere ◽  
Phylogeographic Structure ◽  
High Morbidity ◽  
Coccidioides Immitis ◽  
Valley Fever ◽  
Desert Southwest

AbstractCoccidioidomycosis (or Valley Fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species,Coccidioides immitisandC. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding as new endemic clusters have been identified in the state of Washington, well outside of the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we perform multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure inC. posadasiiand demonstrate presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America and Central America. Although a smaller number ofC. immitisstrains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja Mexico. Bayesian analyses indicated thatC. posadasiiis the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin forC. posadasiiand describe a pathway for dispersal and distribution out of this region.

scholarly journals Coccidioides immitisCervical Lymphadenitis Complicated by Esophageal Fistula

2016 ◽  
Vol 2016 ◽  
pp. 1-4
Author(s):  
Michael Loudin ◽  
Daniel R. Clayburgh ◽  
Morgan Hakki
Keyword(s):  
Lymphatic Spread ◽  
Fistula Formation ◽  
Esophageal Fistula ◽  
Coccidioides Immitis ◽  
Coccidioides Posadasii ◽  
Dimorphic Fungi ◽  
Valley Fever ◽  
Exposure History ◽  
Extrapulmonary Manifestation ◽  
Mediastinal Extension

Coccidioidomycosis (valley fever) is caused by the dimorphic fungiCoccidioides immitisorCoccidioides posadasii. Most infections are asymptomatic or result in self-limited pneumonia; extrapulmonary dissemination via either hematogenous or lymphatic spread is rare. Here, we present a case of cervicalC. immitislymphadenitis that resulted in fistula formation to the esophagus via mediastinal extension. This case highlights a very unusual extrapulmonary manifestation of coccidioidomycosis, the difficulty in diagnosing coccidioidal infection when it is not suspected, and the importance of obtaining a thorough exposure history to assist with diagnosis.

scholarly journals Real-time PCR assay for detection and differentiation of Coccidioides immitis and Coccidioides posadasii from culture and clinical specimens

2021 ◽  
Vol 15 (9) ◽  
pp. e0009765
Author(s):  
Sudha Chaturvedi ◽  
Tanya R. Victor ◽  
Anuradha Marathe ◽  
Ketevan Sidamonidze ◽  
Kelly L. Crucillo ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Limit Of Detection ◽  
Cross Reactivity ◽  
Coccidioides Immitis ◽  
Coccidioides Posadasii ◽  
Pcr Assay ◽  
Valley Fever ◽  
Clinical Specimens ◽  
Wide Range

Coccidioidomycosis (Valley Fever) is a pulmonary and systemic fungal disease with increasing incidence and expanding endemic areas. The differentiation of etiologic agents Coccidioides immitis and C. posadasii remains problematic in the clinical laboratories as conventional PCR and satellite typing schemes are not facile. Therefore, we developed Cy5- and FAM-labeled TaqMan-probes for duplex real-time PCR assay for rapid differentiation of C. immitis and C. posadasii from culture and clinical specimens. The RRA2 gene encoding proline-rich antigen 2, specific for Coccidioides genus, was the source for the first set of primers and probe. Coccidioides immitis contig 2.2 (GenBank: AAEC02000002.1) was used to design the second set of primers and probe. The second primers/probe did not amplify the corresponding C. posadasii DNA, because of an 86-bp deletion in the contig. The assay was highly sensitive with limit of detection of 0.1 pg gDNA/PCR reaction, which was equivalent to approximately ten genome copies of C. immitis or C. posadasii. The assay was highly specific with no cross-reactivity to the wide range of fungal and bacterial pathogens. Retrospective analysis of fungal isolates and primary specimens submitted from 1995 to 2020 confirmed 168 isolates and four primary specimens as C. posadasii and 30 isolates as C. immitis from human coccidioidomycosis cases, while all eight primary samples from two animals (rhesus monkey and rhinoceros) were confirmed as C. posadasii. A preliminary analysis of cerebrospinal fluid (CSF) and pleural fluid samples showed positive correlation between serology tests and real-time PCR for two of the 15 samples. The Coccidioides spp. duplex real-time PCR will allow rapid differentiation of C. immitis and C. posadasii from clinical specimens and further augment the treatment and surveillance of coccidioidomycosis.

scholarly journals Transposable Elements and the Evolution of Insects

2021 ◽  
Vol 66 (1) ◽  
pp. 355-372
Author(s):  
Clément Gilbert ◽  
Jean Peccoud ◽  
Richard Cordaux
Keyword(s):  
Transposable Elements ◽  
Related Species ◽  
Horizontal Transfer ◽  
Population Genomics ◽  
Antiviral Immunity ◽  
Closely Related Species ◽  
Phylogenetic Relatedness ◽  
Functional Studies ◽  
Insect Symbionts

Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.

scholarly journals Modern Techniques in Colorado Potato Beetle (Leptinotarsa decemlineata Say) Control and Resistance Management: History Review and Future Perspectives

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 581 ◽  
Author(s):  
Martina Kadoić Balaško ◽  
Katarina M. Mikac ◽  
Renata Bažok ◽  
Darija Lemic
Keyword(s):  
Colorado Potato Beetle ◽  
Leptinotarsa Decemlineata ◽  
New Technologies ◽  
Population Genomics ◽  
Resistance Management ◽  
Successful Implementation ◽  
Nucleotide Polymorphisms ◽  
Functional Studies ◽  
Potato Beetle ◽  
Leptinotarsa Decemlineata Say

Colorado potato beetle, CPB (Leptinotarsa decemlineata Say), is one of the most important pests of the potato globally. Larvae and adults can cause complete defoliation of potato plant leaves and can lead to a large yield loss. The insect has been successfully suppressed by insecticides; however, over time, has developed resistance to insecticides from various chemical groups, and its once successful control has diminished. The number of available active chemical control substances is decreasing with the process of testing, and registering new products on the market are time-consuming and expensive, with the possibility of resistance ever present. All of these concerns have led to the search for new methods to control CPB and efficient tools to assist with the detection of resistant variants and monitoring of resistant populations. Current strategies that may aid in slowing resistance include gene silencing by RNA interference (RNAi). RNAi, besides providing an efficient tool for gene functional studies, represents a safe, efficient, and eco-friendly strategy for CPB control. Genetically modified (GM) crops that produce the toxins of Bacillus thuringiensis (Bt) have many advantages over agro-technical, mechanical, biological, and chemical measures. However, pest resistance that may occur and public acceptance of GM modified food crops are the main problems associated with Bt crops. Recent developments in the speed, cost, and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs) and field of population genomics. There is a need for effective resistance monitoring programs that are capable of the early detection of resistance and successful implementation of integrated resistance management (IRM). The main focus of this review is on new technologies for CPB control (RNAi) and tools (SNPs) for detection of resistant CPB populations.

scholarly journals Genomic and Population Analyses of the Mating Type Loci in Coccidioides Species Reveal Evidence for Sexual Reproduction and Gene Acquisition

2007 ◽  
Vol 6 (7) ◽  
pp. 1189-1199 ◽  
Author(s):  
M. Alejandra Mandel ◽  
Bridget M. Barker ◽  
Scott Kroken ◽  
Steven D. Rounsley ◽  
Marc J. Orbach
Keyword(s):  
Sexual Reproduction ◽  
Mating Type ◽  
Mating Types ◽  
Coccidioides Immitis ◽  
Genome Sequences ◽  
Valley Fever ◽  
Population Analyses ◽  
Gene Acquisition ◽  
Close Proximity

ABSTRACT Coccidioides species, the fungi responsible for the valley fever disease, are known to reproduce asexually through the production of arthroconidia that are the infectious propagules. The possible role of sexual reproduction in the survival and dispersal of these pathogens is unexplored. To determine the potential for mating of Coccidioides, we analyzed genome sequences and identified mating type loci characteristic of heterothallic ascomycetes. Coccidioides strains contain either a MAT1-1 or a MAT1-2 idiomorph, which is 8.1 or 9 kb in length, respectively, the longest reported for any ascomycete species. These idiomorphs contain four or five genes, respectively, more than are present in the MAT loci of most ascomycetes. Along with their cDNA structures, we determined that all genes in the MAT loci are transcribed. Two genes frequently found in common sequences flanking MAT idiomorphs, APN2 and COX13, are within the MAT loci in Coccidioides, but the MAT1-1 and MAT1-2 copies have diverged dramatically from each other. Data indicate that the acquisition of these genes in the MAT loci occurred prior to the separation of Coccidioides from Uncinocarpus reesii. An analysis of 436 Coccidioides isolates from patients and the environment indicates that in both Coccidioides immitis and C. posadasii, there is a 1:1 distribution of MAT loci, as would be expected for sexually reproducing species. In addition, an analysis of isolates obtained from 11 soil samples demonstrated that at three sampling sites, strains of both mating types were present, indicating that compatible strains were in close proximity in the environment.

scholarly journals Reevaluation of the Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1 with Single-Molecule Real-Time Sequencing Data

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
René Uebe ◽  
Dirk Schüler ◽  
Christian Jogler ◽  
Sandra Wiegand
Keyword(s):  
Single Molecule ◽  
Complete Genome Sequence ◽  
Type Strain ◽  
Point Mutations ◽  
Laboratory Strain ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Content Type ◽  
Magnetospirillum Gryphiswaldense ◽  
Genomic Plasticity

ABSTRACT Magnetospirillum gryphiswaldense is a key organism for understanding magnetosome formation and magnetotaxis. As earlier studies suggested a high genomic plasticity, we (re)sequenced the type strain MSR-1 and the laboratory strain R3/S1. Both sequences differ by only 11 point mutations, but organization of the magnetosome island deviates from that of previous genome sequences.

scholarly journals A Recombinant β-1,3-Glucanosyltransferase Homolog of Coccidioides posadasii Protects Mice against Coccidioidomycosis

2003 ◽  
Vol 71 (6) ◽  
pp. 3010-3019 ◽  
Author(s):  
Nelson Delgado ◽  
Jianmin Xue ◽  
Jieh-Juen Yu ◽  
Chiung-Yu Hung ◽  
Garry T. Cole
Keyword(s):  
Protective Efficacy ◽  
Respiratory Pathogen ◽  
Coccidioides Posadasii ◽  
Intranasal Route ◽  
Lethal Challenge ◽  
Valley Fever ◽  
High Sequence Homology ◽  
Parasitic Phase ◽  
Full Length Gene ◽  
Human Vaccine

ABSTRACT Coccidioides posadasii is a fungal respiratory pathogen which is responsible for recurrent epidemics of San Joaquin Valley fever (coccidioidomycosis) in desert regions of the southwestern United States. Numerous studies have revealed that the cell wall of the parasitic phase of the fungus is a reservoir of immunoreactive macromolecules and a potential source of a vaccine against this mycosis. A 495-bp fragment of a C. posadasii gene which encodes a putative wall-associated, glycosylphosphatidylinositol (GPI)-anchored β-1,3-glucanosyltransferase was identified by computational analysis of the partially sequenced genome of this pathogen. The translated, full-length gene (GEL1) showed high sequence homology to a reported β-1,3-glucanosyltransferase of Aspergillus fumigatus (70% identity, 90% similarity) and was selected for further study. The GEL1 mRNA of C. posadasii was detected at the highest level during the endosporulation stage of the parasitic cycle, and the mature protein was immunolocalized to the surface of endospores. BALB/c or C57BL/6 mice were immunized subcutaneously with the bacterium-expressed recombinant protein (rGel1p) to evaluate its protective efficacy against a lethal challenge of C. posadasii by either the intraperitoneal or intranasal route. In both cases, rGel1p-immune mice infected with the pathogen showed a significant reduction in fungal burden and increased survival compared to nonimmune mice. The recombinant β-1,3-glucanosyltransferase is a valuable addition to an arsenal of immunoreactive proteins which could be incorporated into a human vaccine against coccidioidomycosis.

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