DNA sequence-based identification of Fusarium: A work in progress

Plant Disease ◽  
2021 ◽  
Author(s):  
Kerry O'Donnell ◽  
Briana Whitaker ◽  
Imane Laraba ◽  
Robert Proctor ◽  
Daren Brown ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Fusarium Species ◽  
Distinct Species ◽  
Toxin Production ◽  
Disease Diagnosis ◽  
Species Level ◽  
Molecular Systematic ◽  
The Public ◽  
Daunting Task ◽  
Level Identification

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise over 400 phylogenetically distinct species (i.e., phylospecies), with over 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the non-redundant NCBI nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1 and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

scholarly journals The challenge of integrative taxonomy of rare, deep-water gastropods: the genus Exilia (Neogastropoda: Turbinelloidea: Ptychatractidae)

2020 ◽  
Vol 86 (2) ◽  
pp. 120-138
Author(s):  
Yuri I Kantor ◽  
Nicolas Puillandre ◽  
Philippe Bouchet
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
First Record ◽  
Integrative Taxonomy ◽  
Molecular Systematic ◽  
Dna Sequence Data ◽  
In The Wild ◽  
Anatomical Characters

Abstract According to a recent taxonomic revision by Kantor et al. (2001), the neogastropod genus Exilia Conrad, 1860, comprises ten mostly rare species that live at depths between 200 and 2000 m. Adult Exilia measure between 30 and 90 mm in shell length, and the genus is mostly represented in museum collections by empty shells. The abundance of this genus is low in the wild, but recent expeditions organized by the Muséum national d’Histoire naturelle have yielded several dozen specimens. These new collections include samples preserved for molecular studies. Here, we present the results of the first molecular systematic study of Exilia. Our aim was to investigate the species limits proposed by Kantor et al. (2001) on the basis of shell and anatomical characters. Analysis of DNA sequence data for the cytochrome c oxidase I gene suggests that Exilia hilgendorfi, previously considered to be a single, polymorphic and broadly distributed species, is a complex of at least six species (four of which we sequenced). Two of these species, Exilia cognata n. sp. and E. fedosovi n. sp., are described as new to science. Exilia gracilior, E. claydoni and E. prellei are resurrected from the synonymy of Exilia hilgendorfi; of these three, only the last was sequenced. Exilia vagrans is a well-defined taxon, but our molecular systematic data shows that it consists of two distinct species, which occur sympatrically off Taiwan and are strikingly similar in shell and radular morphology; due to the absence of DNA sequence data from the type locality of E. vagrans (Vanuatu), it is unclear to which of these two species the name would apply. Exilia karukera n. sp., which is conchologically very similar to E. vagrans, was discovered off Guadeloupe, represents the first record of the genus from the Atlantic. For E. elegans, which was previously known only from a single shell, we provide new data including new distributional records (South Africa and the Mozambique Channel), details of the radula and DNA sequence data.

scholarly journals First Report of a Gall Midge Species (Diptera: Cecidomyiidae) Associated With Pistachios

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Farshid O Sirjani ◽  
Edwin E Lewis
Keyword(s):  
Gall Midge ◽  
Species Level ◽  
Plant Tissues ◽  
First Report ◽  
Branch Dieback ◽  
First Time ◽  
Level Identification

Abstract A new dipterous pest is reported, for the first time, on commercial pistachios from Sirjan, Kerman province, Iran. The genus of the insect was determined to be Resseliella Seitner (Diptera: Cecidomyiidae). Adults are light brown to brown in color and 0.8–1.5 mm in length with females, generally, slightly larger than males. Females have an elongated ovipositor, which is characteristic of the genus. Larvae are orange in color, 2–3 mm in length in the later instars, feed under bark without inducing galls, and cause branch dieback on trees of various ages. Brown to black discolorations are observed on plant tissues under bark where the larvae feed. Infestations observed on current and the previous—year’s growths, ranged from 0.5 to 1.2 cm in diameter, and all located in outer branches. Dry leaves and fruit clusters on infested branches remain attached, which may be used to recognize infestation by the gall midge. Dark-colored, sunken spots with splits on the bark located at the base of the wilted sections of the shoots also are symptoms of Resseliella sp. larval activity. Species-level identification of the gall midge is currently underway.

scholarly journals Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Matthew C. Canver ◽  
Tsigereda Tekle ◽  
Samantha T. Compton ◽  
Katrina Callan ◽  
Eileen M. Burd ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Species Level ◽  
Accurate Identification ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Staphylococcus Intermedius ◽  
Animal Pathogens ◽  
Tof Ms

ABSTRACT The Staphylococcus intermedius group (SIG) is a collection of coagulase-positive staphylococci consisting of four distinct species, namely, Staphylococcus cornubiensis, Staphylococcus delphini, Staphylococcus intermedius, and Staphylococcus pseudintermedius. SIG members are animal pathogens and rare causes of human infection. Accurate identification of S. pseudintermedius has important implications for interpretation of antimicrobial susceptibility testing data and may be important for other members of the group. Therefore, we sought to evaluate the performance of five commercially available identification platforms with 21 S. delphini isolates obtained from a variety of animal and geographic sources. Here, we show that automated biochemical platforms were unable to identify S. delphini to the species level, a function of its omission from their databases, but could identify isolates to the SIG level with various degrees of success. However, all automated systems misidentified at least one isolate as Staphylococcus aureus. One matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system was able to identify S. delphini to the species level, suggesting that MALDI-TOF MS is the best option for distinguishing members of the SIG. With the exception of S. pseudintermedius, it is unclear if other SIG members should be routinely identified to the species level; however, as our understanding of their role in animal and human diseases increases, it may be necessary and important to do so.

scholarly journals Programming Native CRISPR Arrays for the Generation of Targeted Immunity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Alexander P. Hynes ◽  
Simon J. Labrie ◽  
Sylvain Moineau
Keyword(s):  
Immune System ◽  
Nucleic Acid ◽  
Genome Editing ◽  
Dna Sequence ◽  
Adaptive Immune System ◽  
Natural Process ◽  
The Public ◽  
Adaptive Immune ◽  
Public Consciousness ◽  
Industrial Settings

ABSTRACT The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes), results in specific cleavage of invading nucleic acid sequences recognized by the cell’s “memory” of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural “memorization” process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence. IMPORTANCE CRISPR-Cas systems have entered the public consciousness as genome editing tools due to their readily programmable nature. In industrial settings, natural CRISPR-Cas immunity is already exploited to generate strains resistant to potentially disruptive viruses. However, the natural process by which bacteria acquire new target specificities (adaptation) is difficult to study and manipulate. The target against which immunity is conferred is selected stochastically. By biasing the immunization process, we offer a means to generate customized immunity, as well as provide a new tool to study adaptation.

Morphological and molecular evidence places Maronina into synonymy with Protoparmelia (Ascomycota: Lecanorales)

2011 ◽  
Vol 43 (6) ◽  
pp. 561-567 ◽  
Author(s):  
K. PAPONG ◽  
G. KANTVILAS ◽  
H. T. LUMBSCH
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Distinct Species ◽  
Genetic Distances ◽  
Molecular Evidence ◽  
New Combinations ◽  
Secondary Chemistry ◽  
Phenotypic Characters ◽  
Dna Sequence Data ◽  
Phylogenetic Placement

AbstractThe phylogenetic placement of the genus Maronina was studied, based chiefly on phenotypic characters such as thallus colour and anatomy, secondary chemistry, the anatomy of the excipulum and the ascus-type. DNA sequence data of mitochondrial and nuclear ribosomal loci from some of the species support the hypothesis that Maronina is nested within Protoparmelia. Hence, Maronina is reduced to synonymy with Protoparmelia. Comparison of genetic distances suggests that the two varieties within M. orientalis should be regarded as distinct species. Consequently, the new combinations Protoparmelia australiensis (Hafellner & R. W. Rogers) Kantvilas et al., P. corallifera (Kantvilas & Papong) Kantvilas et al., P. hesperia (Kantvilas & Elix) Kantvilas et al., P. multifera (Nyl.) Kantvilas et al., and P. orientalis (Kantvilas & Papong) Kantvilas et al. are proposed.

scholarly journals A Novel Disease of Big-Leaf Mahogany Caused by Two Fusarium Species in Mexico

Plant Disease ◽  
2018 ◽  
Vol 102 (10) ◽  
pp. 1965-1972 ◽  
Author(s):  
R. Santillán-Mendoza ◽  
S. P. Fernández-Pavía ◽  
K. O’Donnell ◽  
R. C. Ploetz ◽  
R. Ortega-Arreola ◽  
...  
Keyword(s):  
Species Complex ◽  
Fusarium Species ◽  
Urban Landscapes ◽  
Western Region ◽  
New Disease ◽  
Molecular Systematic ◽  
Lateral Buds ◽  
Mango Malformation ◽  
First Time ◽  
Important Disease

Big-leaf mahogany (Swietenia macrophylla) is valued for its high-quality wood and use in urban landscapes in Mexico. During surveys of mango-producing areas in the central western region of Mexico, symptoms of malformation, the most important disease of mango in the area, were observed on big-leaf mahogany trees. The objectives of this research were to describe this new disease and determine its cause. Symptoms on big-leaf mahogany at four sites in Michoacán, Mexico resembled those of the vegetative phase of mango malformation, including compact, bunched growth of apical and lateral buds, with greatly shortened internodes and small leaves that curved back toward the supporting stem. Of 163 isolates that were recovered from symptomatic tissues, most were identified as Fusarium pseudocircinatum (n = 121) and F. mexicanum (n = 39) using molecular systematic data; two isolates represented unnamed phylospecies within the F. incarnatum-equiseti species complex (FIESC 20-d and FIESC 37-a) and another was in the F. solani species complex (FSSC 25-m). However, only F. mexicanum and F. pseudocircinatum induced malformation symptoms on 14-day-old seedlings of big-leaf mahogany. The results indicate that F. mexicanum and F. pseudocircinatum, previously reported in Mexico as causal agents of mango malformation disease, also affect big-leaf mahogany. This is the first report of this new disease and the first time that F. mexicanum was shown to affect a host other than mango.

SISTEM PAKAR MENENTUKAN PENYAKIT GINJAL DENGAN METODE FORWARD CHAINING

2020 ◽  
Vol 11 (1) ◽  
pp. 27-32
Author(s):  
Wahyu Alfandry Pulungan
Keyword(s):  
Expert System ◽  
Kidney Disease ◽  
Disease Diagnosis ◽  
Metabolic System ◽  
Consultation Process ◽  
The Public ◽  
System Disease ◽  
Visual Basic 6.0 ◽  
High Calorie ◽  
Selection Of

Selection of issues regarding the kind of kidney disease as a sample of this study, is the fact that diseases Kidney is an important organ in our body's metabolic system, because the density of activity, we often forget to take care of. Irregular diet, inadequate intake of fiber and mineral water, as well as the consumption of food or drink high calorie instant, unwittingly aggravate the kidneys. Starting from the filtration, reabsorption, to augmentation of nutrients that under to the kidneys via the blood. The purpose of this research is to build an expert system Kidney disease using Visual Basic 6.0 programming language that is capable of providing services to the public and delivery of information related to kidney disease. In this research, data collection is done by using the method of observation, interviews, and literature. From the results of this study indicate that the presence of kidney disease diagnosis expert system in humans can provide significant benefits, among others, the processing of data and consultation process carried out quickly and produce a fairly accurate report, thus making the job more effectively and efficiently. Keywords: Expert System, Disease, Kidney, Human.

scholarly journals Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus

2016 ◽  
Vol 10 (1) ◽  
pp. 202-208 ◽  
Author(s):  
Marisa Almuzara ◽  
Claudia Barberis ◽  
Viviana Rojas Velázquez ◽  
Maria Soledad Ramirez ◽  
Angela Famiglietti ◽  
...  
Keyword(s):  
Extraction Methods ◽  
Species Level ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Genus Level ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Level Identification ◽  
Gram Positive Cocci ◽  
Tof Ms

Objective:To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates.Methods:All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and <1.700 no reliable identification) and lower cut-off scores (≥1.500 for genus level, ≥ 1.700 for species-level and score <1.500 no reliable identification) were considered for identification. A minimum difference of 10% between the top and next closest score was required for a different genus or species.MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result.When both methods gave discordant results, the 16S rDNA orsodAgenes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S orsodA identification were considered incorrect.Results:Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained.Conclusion:The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis asHelcococcus,Abiotrophia,Granulicatella, among others. Nevertheless, expansion of the library, especially including more strains with different spectra on the same species might overcome potential “intraspecies” variability problems. Moreover, a decrease of the identification scores for species and genus-level identification must be considered since it may improve the MALDI-TOF MS accuracy.

scholarly journals Analysis of the genetic polymorphism of Paracoccidioides brasiliensis and Paracoccidioides cerebriformis "Moore" by random amplified polymorphic DNA (RAPD) and 28S ribosomal DNA sequencing: Paracoccidioides cerebriformis revisited

2005 ◽  
Vol 47 (3) ◽  
pp. 119-123 ◽  
Author(s):  
Sarah Desirée Barbosa Cavalcanti ◽  
José Eduardo Levi ◽  
Kátia Cristina Dantas ◽  
José Eduardo Costa Martins
Keyword(s):  
Genetic Polymorphism ◽  
Dna Sequence ◽  
Ribosomal Dna ◽  
Dna Analysis ◽  
Paracoccidioides Brasiliensis ◽  
Random Amplified Polymorphic Dna ◽  
Distinct Species ◽  
De Medicina ◽  
28S Ribosomal Dna ◽  
Mycological Laboratory

Our purpose was to compare the genetic polymorphism of six samples of P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1), with four samples of P. cerebriformis (735, 741, 750, 361) from the Mycological Laboratory of the Instituto de Medicina Tropical de São Paulo, using Random Amplified Polymorphic DNA Analysis (RAPD). RAPD profiles clearly segregated P. brasiliensis and P. cerebriformis isolates. However, the variation on band patterns among P. cerebriformis isolates was high. Sequencing of the 28S rDNA gene showed nucleotide conservancy among P. cerebriformis isolates, providing basis for taxonomical grouping, and disclosing high divergence to P. brasiliensis supporting that they are in fact two distinct species. Moreover, DNA sequence suggests that P. cerebriformis belongs in fact to the Aspergillus genus.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

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