scholarly journals Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species

2013 ◽  
Vol 103 (1) ◽  
pp. 43-54 ◽  
Author(s):  
Wen Chen ◽  
Zeinab Robleh Djama ◽  
Michael D. Coffey ◽  
Frank N. Martin ◽  
Guillaume J. Bilodeau ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Phytophthora Species ◽  
Phytophthora Ramorum ◽  
Oligonucleotide Array ◽  
Data Set ◽  
Phytophthora Spp ◽  
Field Samples

Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5′ end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae)

2006 ◽  
Vol 36 (2) ◽  
pp. 337-350 ◽  
Author(s):  
Shelley L Ball ◽  
Karen F Armstrong
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Insect Pest ◽  
Reference Sequence ◽  
Identification System ◽  
Pest Species ◽  
Dna Barcodes ◽  
Data Set

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

Molecular and Ultrastructural Analysis of a Porocephalus sp. (Arthropoda: Pentastomida) Removed from a Rattlesnake

2021 ◽  
Vol Vol 66 (1) (January (1)) ◽  
pp. 1-5
Author(s):  
Jerome Goddard ◽  
Gerald Baker ◽  
Petra Jericke ◽  
Lawrence Birchman ◽  
Ethan Woodward ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Adult Female ◽  
Sequence Data ◽  
Molecular Data ◽  
Ultrastructural Analysis ◽  
Oxidase Subunit ◽  
Data Support ◽  
Partial 18S

Ultrastructural and molecular data are provided from a single adult female pentastomid opportunistically collected from a road-killed rattlesnake in Russell, KS. Ultrastructural data consisted of light and SEM microscopy of the pentastomid and its eggs, while molecular data consisted of partial 18S and 28S ribosomal sequences and a partial cytochrome c oxidase subunit 1 sequence from the same specimen used for SEM. Ultrastructural and molecular data support generic identification of the pentastomid as Porocephalus sp. These molecular data were also used with previously published pentastomid sequence data for a concatenated phylogenetic analysis, which support the current, morphology-based taxonomic placement of the genus.

scholarly journals coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation

Genome ◽  
2020 ◽  
Vol 63 (6) ◽  
pp. 291-305 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Sarah J. Adamowicz
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Data Generation ◽  
Error Identification ◽  
Reading Frame ◽  
Biological Contaminants ◽  
And Function

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.

Adaptation of a Phytophthora ramorum Real-Time Polymerase Chain Reaction Assay Based on a Mitochondrial Gene Region for Use on the Cepheid SmartCycler

2010 ◽  
Vol 11 (1) ◽  
pp. 28
Author(s):  
K. E. Sechler ◽  
M. M. Carras ◽  
N. Shishkoff ◽  
P. W. Tooley
Keyword(s):  
Real Time ◽  
Mitochondrial Gene ◽  
Cross Reactivity ◽  
Phytophthora Species ◽  
Phytophthora Ramorum ◽  
Rt Pcr ◽  
Field Samples ◽  
Symptomatic Tissue ◽  
Polymerase Chain ◽  
High Degree

Detection of Phytophthora ramorum in US commercial nurseries has led to a number of quarantine regulations. Methods such as real-time PCR (RT-PCR) provide rapid and reliable detection that can supplement attempts to culture P. ramorum from symptomatic tissue. We adapted and optimized a previously described mitochondrial gene-based RT-PCR assay for use with a Cepheid SmartCycler v.1 and ready-to-use lyophilized PCR beads. The detection limit was 10 fg of P. ramorum genomic DNA. No cross-reactivity was observed on the SmartCycler for seven additional Phytophthora species tested, which included species known to cross-react in other assays as well as recently described species Phytophthora foliorum and P. kernoviae. The SmartCycler assay described here was used to detect P. ramorum in a set of 2008 California field samples with a high degree of accuracy. Accepted for publication 13 October 2009. Published 13 February 2010.

scholarly journals Infective Potential of Sporangia and Zoospores of Phytophthora ramorum

Plant Disease ◽  
2009 ◽  
Vol 93 (1) ◽  
pp. 30-35 ◽  
Author(s):  
T. L. Widmer
Keyword(s):  
Leaf Area ◽  
Phytophthora Species ◽  
Phytophthora Ramorum ◽  
Inoculum Potential ◽  
Phytophthora Spp ◽  
Zoospore Formation ◽  
Inoculum Type ◽  
Infective Potential ◽  
Disk Area ◽  
Leaf Disks

Phytophthora species produce sporangia that either germinate directly or release zoospores, depending upon environmental conditions. Previous Phytophthora spp. inoculation trials have used both sporangia and zoospores as the inoculum type. However, it is unknown what impact propagule type has on disease. Rhododendron leaf disks were inoculated with P. ramorum zoospores (75, 500, or 2,400 per disk), sporangia (75 per disk), or sporangia plus trifluoperazine hydrochloride (TFP) (75 per disk), a chemical that inhibits zoospore formation. Combining results from two different isolates, the highest concentration of zoospores (2,400 per disk) induced a significantly higher percentage of necrotic leaf disk area (96.6%) than sporangia (87.6%) and 500 zoospores per disk (88.7%). The sporangia plus TFP treatment had the lowest necrosis at 47.5%. Rooted rhododendron cuttings had a higher percentage of necrotic leaves per plant when inoculated with zoospores (3,000 or 50,000 per ml) or cysts (50,000 per ml) than with sporangia (3,000 per ml) with or without TFP. The percentage of necrotic leaf area was significantly higher when cysts or zoospores were inoculated at 50,000 per ml than sporangia without TFP and zoospores at 3,000 per ml. All treatments were significantly higher in the percentage of necrotic leaf area than the leaves treated with sporangia plus TFP. This demonstrates that the full inoculum potential may not be achieved when sporangia are used as the inoculum propagule.

scholarly journals coil: an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation

2019 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Sarah J. Adamowicz
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Data Generation ◽  
Error Identification ◽  
Reading Frame ◽  
Biological Contaminants ◽  
And Function

AbstractBiological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The five-prime region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil (https://CRAN.R-project.org/package=coil), an R package for the pre-processing and error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10,000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.

A new species of planthopper in the genus Agoo (Hemiptera: Fulgoroidea: Derbidae) from coquito palms (Astrocaryum alatum) in Costa Rica

Zootaxa ◽  
2020 ◽  
Vol 4779 (3) ◽  
pp. 409-418 ◽  
Author(s):  
BRIAN W. BAHDER ◽  
MARCO A. ZUMBADO ECHAVARRIA ◽  
EDWIN A. BARRANTES BARRANTES ◽  
GERNOT KUNZ ◽  
ERICKA E. HELMICK ◽  
...  
Keyword(s):  
New Species ◽  
Costa Rica ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
The Novel ◽  
La Selva ◽  
Biological Station ◽  
Oxidase Subunit ◽  
A New Species

An ongoing survey to document planthopper diversity on palms (Arecaceae) is being conducted in Costa Rica. During these efforts a new species of derbid planthopper belonging to the genus Agoo was found on Astrocaryum alatum Loomis in the Heredia province at La Selva Biological Station and is described here as Agoo luzdenia Bahder & Bartlett sp. n., bringing the genus to four described taxa—A. dahliana, A. luzdenia Bahder & Bartlett sp. n., A rubrimarginata, and A. xavieri. Sequence data for the cytochrome c oxidase subunit I (COI) and 18S genes was generated for the novel taxon and strongly supports its placement in the genus Agoo. 

scholarly journals Molecular and morphological characterisation of new species in the trapdoor spider genus Aname (Araneae: Mygalomorphae: Nemesiidae) from the Pilbara bioregion of Western Australia

Zootaxa ◽  
2012 ◽  
Vol 3383 (1) ◽  
pp. 15 ◽  
Author(s):  
FRANCES S. B. HARVEY ◽  
VOLKER W. FRAMENAU ◽  
JANINE M. WOJCIESZEK ◽  
MICHAEL G. RIX ◽  
MARK S. HARVEY
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Western Australia ◽  
Adult Male ◽  
Sequence Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Morphological Characterisation ◽  
Mitochondrial Sequence

A study of selected species in the nemesiid spider genus Aname L. Koch, 1873 from the Pilbara bioregion of Western Australia was undertaken using molecular and morphological techniques. Bayesian and parsimony analyses of mitochondrial sequence data from the Cytochrome c Oxidase subunit I (COI) gene found evidence for four species, confirming our initial morphological examination of adult male specimens. These four species are here described as A. mellosa n. sp., A. aragog n. sp., A. ellenae n. sp. and A. marae n. sp. Only the female of A. mellosa n. sp. is described.

scholarly journals Evaluation of Molecular Markers for Phytophthora ramorum Detection and Identification: Testing for Specificity Using a Standardized Library of Isolates

2009 ◽  
Vol 99 (4) ◽  
pp. 390-403 ◽  
Author(s):  
F. N. Martin ◽  
M. D. Coffey ◽  
K. Zeller ◽  
R. C. Hamelin ◽  
P. Tooley ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Real Time ◽  
Pathogen Detection ◽  
Species Group ◽  
False Positives ◽  
Phytophthora Ramorum ◽  
Sscp Analysis ◽  
Oxidase Gene ◽  
Phytophthora Spp ◽  
Field Samples

Given the importance of Phytophthora ramorum from a regulatory standpoint, it is imperative that molecular markers for pathogen detection are fully tested to evaluate their specificity in detection of the pathogen. In an effort to evaluate 11 reported diagnostic techniques, we assembled a standardized DNA library using accessions from the World Phytophthora Genetic Resource Collection for 315 isolates representing 60 described Phytophthora spp. as well as 11 taxonomically unclassified isolates. These were sent blind to collaborators in seven laboratories to evaluate published diagnostic procedures using conventional (based on internal transcribed spacer [ITS] and cytochrome oxidase gene [cox]1 and 2 spacer regions) and real-time polymerase chain reaction (based on ITS and cox1 and 2 spacer regions as well as β-tubulin and elicitin genes). Single-strand conformation polymorphism (SSCP) analysis using an automated sequencer for data collection was also evaluated for identification of all species tested. In general, the procedures worked well, with varying levels of specificity observed among the different techniques. With few exceptions, all assays correctly identified all isolates of P. ramorum and low levels of false positives were observed for the mitochondrial cox spacer markers and most of the real-time assays based on nuclear markers (diagnostic specificity between 96.9 and 100%). The highest level of false positives was obtained with the conventional nested ITS procedure; however, this technique is not stand-alone and is used in conjunction with two other assays for diagnostic purposes. The results indicated that using multiple assays improved the accuracy of the results compared with looking at a single assay alone, in particular when the markers represented different genetic loci. The SSCP procedure accurately identified P. ramorum and was helpful in classification of a number of isolates to a species level. With one exception, all procedures accurately identified P. ramorum in blind evaluations of 60 field samples that included examples of plant infection by 11 other Phytophthora spp. The SSCP analysis identified eight of these species, with three identified to a species group.

Sign in / Sign up

Export Citation Format

Share Document