Diversity and cross-infection potential of Colletotrichum causing fruit rots in mixed-fruit orchards in Kentucky

Plant Disease ◽  
2020 ◽  
Author(s):  
Madison Julia McCulloch ◽  
Shanice Edwards ◽  
Harrison Inocencio ◽  
Franklin Machado ◽  
Etta Nuckles ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Single Gene ◽  
Cross Infection ◽  
Fruit Rot ◽  
Gene Trees ◽  
Accurate Identification ◽  
Factors Affecting ◽  
Colletotrichum Species ◽  
Species Specific ◽  
Fruit Orchards

Fungi in the genus Colletotrichum cause apple, blueberry, and strawberry fruit rots, which can result in significant losses. Accurate identification is important because species differ in aggressiveness, fungicide sensitivity, and other factors affecting management. Multiple Colletotrichum species can cause similar symptoms on the same host, while more than one fruit type can be infected by a single Colletotrichum species. Mixed-fruit orchards may facilitate cross-infection, with significant management implications. Colletotrichum isolates from small fruits in Kentucky orchards were characterized and compared with apple isolates by using a combination of morphotyping, sequencing of voucher loci and whole genomes, and cross-inoculation assays. Seven morphotypes representing two species complexes (C. acutatum and C. gloeosporioides) were identified. Morphotypes corresponded with phylogenetic species C. fioriniae, C. fructicola, C. nymphaeae, and C. siamense, identified by TUB2 and GAPDH barcodes. Phylogenetic trees built from nine single gene sequences matched barcoding results with one exception, later determined to belong to an undescribed species. Comparison of single gene trees with representative whole genome sequences revealed that CHS and ApMat were the most informative for diagnosis of fruit rot species and individual morphotypes within the C. acutatum or C. gloeosporioides complexes, respectively. All blueberry isolates belonged to C. fioriniae, and most strawberry isolates were C. nymphaeae, with a few C. siamense and C. fioriniae also recovered. All three species cause fruit rot on apples in Kentucky. Cross-inoculation assays on detached apple, blueberry, and strawberry fruits showed that all species were pathogenic on all three hosts, but with species-specific differences in aggressiveness.

scholarly journals A New Accurate Genotyping HRM Method for Alternaria Species Related to Fruit Rot Diseases of Apple and Pomegranate

2016 ◽  
Vol 4 (3) ◽  
pp. 159-165 ◽  
Author(s):  
Antonios Zambounis ◽  
Aliki Xanthopoulou ◽  
George Karaoglanidis ◽  
Athanasios Tsaftaris ◽  
Panagiotis Madesis
Keyword(s):  
Morphological Characteristics ◽  
Curve Analysis ◽  
Fruit Rot ◽  
Nucleotide Polymorphisms ◽  
Postharvest Diseases ◽  
Accurate Identification ◽  
Complex Species ◽  
Alternaria Species ◽  
Species Specific ◽  
Pomegranate Fruit

Alternaria core rot and Alternaria black heart rot of apple and pomegranate fruit, respectively, are major pre- and postharvest diseases worldwide. However, it is very difficult to differentiate the rot related Alternaria species in the Alternaria complex as they are not always correlate to species-groups based upon morphological characteristics and due to the limited genetic variation these species exhibit among each other. Therefore, it is crucial to exploit novel assays towards the accurate identification and differentiation of these Alternaria species. We have developed, a real-time PCR assay [using species specific primers targeting the endopolygalacturonase (EndoPG) gene] combined with a high-resolution melting (HRM) curve analysis for discrimination of the 14 single nucleotide polymorphisms (SNPs)-based Alternaria haplotypes, which were assigned based on the aligned sequence profiles of 138 Alternaria spp. strains previously isolated from apple and pomegranate rotted fruit. This analysis specifically generated 14 unique HRM curve haplotype profiles among the Alternaria complex species tested. The results showed that HRM curve analysis allows the rapid and adequate identification and genotyping of the three Alternaria species (A. alternata, A. tenuissima and A. arborescens) responsible mostly for the apple and pomegranate fruit rot diseases.

Use of telomere fingerprinting to identify clonal lineages of Colletotrichum fioriniae in Kentucky mixed-fruit orchards

Plant Disease ◽  
2021 ◽  
Author(s):  
Madison Julia McCulloch ◽  
Nicole A Ward Gauthier ◽  
Lisa Vaillancourt
Keyword(s):  
Direct Evidence ◽  
Test Group ◽  
Cross Infection ◽  
Fruit Rot ◽  
Individual Species ◽  
Pathogen Population ◽  
Fruit Species ◽  
Close Proximity ◽  
Multiple Species ◽  
Fruit Orchards

Multiple species in the fungal genus Colletotrichum cause anthracnose fruit rot diseases that are responsible for major yield losses of as much as 100%. Individual species of Colletotrichum typically have broad host ranges and can infect multiple fruit species. Colletotrichum fioriniae causes anthracnose fruit rots of apples, blueberries and strawberries in Kentucky orchards where these fruits grow in close proximity. This raises the possibility of cross-infection, which may have significant management implications. The potential occurrence of cross-infection was investigated by using telomere fingerprinting to identify C. fioriniae clones in several mixed-fruit orchards. Telomere fingerprints were highly polymorphic among a test group of C. fioriniae strains and effectively defined clonal lineages. Fingerprints were compared among apple, blueberry and strawberry isolates of C. fioriniae from three different orchards and similarity matrices were calculated to build phylograms for each orchard group. Multiple clonal lineages of C. fioriniae were identified within each orchard on the same fruit host. Related lineages were found among isolates from different hosts, but the results did not provide direct evidence for cross-infection of different fruit species by the same clones. Recovery of the same clonal lineages within orchards across multiple years suggested that local dispersal was important in pathogen population structure and that C. fioriniae strains persisted within orchards over time. Isolates from blueberry were less diverse than isolates from apple, perhaps related to more intensive anthracnose management protocols on apple versus blueberry. Telomere fingerprinting is a valuable tool for understanding population dynamics of Colletotrichum fruit rot fungi.

scholarly journals An investigation of irreproducibility in maximum likelihood phylogenetic inference

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xing-Xing Shen ◽  
Yuanning Li ◽  
Chris Todd Hittinger ◽  
Xue-xin Chen ◽  
Antonis Rokas
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Single Gene ◽  
Phylogenetic Inference ◽  
Gene Trees ◽  
Seed Number ◽  
Substitution Model ◽  
Individual Gene ◽  
Considerable Fraction ◽  
Log Files

AbstractPhylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible when executing two replicates (Run1 and Run2) for each of 19,414 gene alignments in 15 animal, plant, and fungal phylogenomic datasets. Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 and Run2 sets of individual gene trees are topologically irreproducible for 9/15 phylogenomic datasets, whereas concatenation-based phylogenies inferred twice from the same supermatrix are reproducible. Our simulations further show that irreproducible phylogenies are more likely to be incorrect than reproducible phylogenies. These results suggest that a considerable fraction of single-gene ML trees may be irreproducible. Increasing reproducibility in ML inference will benefit from providing analyses’ log files, which contain typically reported parameters (e.g., program, substitution model, number of tree searches) but also typically unreported ones (e.g., random starting seed number, number of threads, processor type).

ISSR-Derived Species-Specific SCAR Marker for Rapid and Accurate Authentication of Ocimum tenuiflorum L.

Planta Medica ◽  
2017 ◽  
Vol 84 (02) ◽  
pp. 117-122 ◽  
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Priyanka Mishra ◽  
Kuppusamy Baskaran ◽  
Ashutosh Shukla ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
High Volume ◽  
Inter Simple Sequence Repeat ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Accurate Identification ◽  
Sequence Characterized Amplified Region ◽  
Medicinal Value ◽  
Ocimum Tenuiflorum ◽  
Species Specific

Abstract Ocimum tenuiflorum has been widely used in traditional medicine and has high medicinal value. High volume trade of this potential medicinal plant species led to unscrupulous adulteration of both crude drugs as well as formulations. Morphology-based authentication is difficult in cases of incomplete or damaged samples and in dried herbal materials. In such cases, PCR-based molecular methods may aid in accurate identification. The present study aimed at developing species-specific DNA marker(s) for the authentication of O. tenuiflorum. A species-specific amplicon (279 bp) generated through an inter-simple sequence repeat marker (UBC 835) in all individuals of O. tenuiflorum was cloned, sequenced, and a primer pair was developed (designated as CIM-OT-835F/CIM-OT-835R). The newly developed sequence characterized amplified region marker was validated through PCR amplification in all available seven species of Ocimum, and its specificity for O. tenuiflorum was confirmed with the consistent generation of an amplicon of 177 bp. The developed marker can be used for accurate and rapid identification of the species for certification purposes and will be useful in quality control of medicinal preparations containing this important medicinal species.

scholarly journals Factors Affecting Zoo Visitors’ Conservation Beliefs and Knowledge of Large Carnivores in 2009 and a Dozen Years Later

2022 ◽  
Vol 14 (2) ◽  
pp. 890
Author(s):  
Vesna Oražem ◽  
Aleksandra Majić Skrbinšek ◽  
Andrej Šorgo ◽  
Iztok Tomažič
Keyword(s):  
Brown Bear ◽  
Eurasian Lynx ◽  
Factors Affecting ◽  
Large Carnivore ◽  
Gender Influence ◽  
Carnivore Species ◽  
Conservation Actions ◽  
Species Specific ◽  
Gender Factor ◽  
Learning Institutions

Teaching in a formal learning environment mainly focuses on gaining knowledge, and scarcely on the development of pro-environmental attitudes. Knowledge can also be gained in informal learning institutions, such as zoos, and their potential use in general public education should not be neglected. This paper explores factors influencing the conservation beliefs of zoo visitors about brown bears, grey wolves, and Eurasian lynx. The study undertaken in Zoo Ljubljana (Slovenia) consisted of surveys performed in 2009 (n = 613) and in 2021 (n = 257). The levels of knowledge and education influenced both supporting and opposing beliefs about the three large carnivore species. The gender factor was less uniform: both supporting and opposing beliefs about lynx were demonstrated, but only opposing beliefs about brown bear and wolf. The study indicates that knowledge has the most significant influence on conservation beliefs, thus highlighting the importance of educational and communication activities in management and conservation actions regarding large carnivore species. The varied gender influence suggests that species-specific educational activities should be encouraged.

scholarly journals FACTORS AFFECTING INTERNATIONAL VISITORS’ PREFERENCE FOR LOCAL FRUITS IN THE MEKONG DELTA, VIETNAM

2020 ◽  
pp. 70-74
Author(s):  
Nguyen Quoc Nghi ◽  
Bui Thi Yen Ni
Keyword(s):  
Linear Regression ◽  
Sampling Method ◽  
Perceived Value ◽  
Mekong Delta ◽  
Factors Affecting ◽  
Product Features ◽  
Quota Sampling ◽  
Fruit Orchards ◽  
International Visitors ◽  
Culinary Culture

The objective of this study is to identify the factors affecting the taste of specialty fruits in the Mekong Delta of international visitors. The quota sampling method was used to interview 180 international visitors who have visited fruit orchards and enjoyed specialty fruits in the Mekong Delta. Applying the linear regression with the study has identified 4 factors affecting the preference for fruit specialties in the Mekong Delta of international tourists, namely "Culinary culture", "Information and experience", "Product features”, and “Perceived value". In particular, the factor "Information and experience" most strongly influences international visitors’ preference for fruit specialties in the Mekong Delta. KEYWORDS: Preference, specialties, fruit, Mekong Del

scholarly journals Developing, Modifying, and Validating a TaqMan Real-Time PCR Technique for Accurate Identification of Leishmania Parasites Causing Most Leishmaniasis in Iran

2021 ◽  
Vol 11 ◽  
Author(s):  
Reza Fotouhi-Ardakani ◽  
Seyedeh Maryam Ghafari ◽  
Paul Donald Ready ◽  
Parviz Parvizi
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Leishmania Major ◽  
Taqman Probe ◽  
Amino Acid Permease ◽  
Specific Primers ◽  
Accurate Identification ◽  
Parasitic Load ◽  
Species Specific

Many laboratory methods are used to diagnose leishmaniasis because it is characterized by varied symptoms and caused by different Leishmania species. A quantitative real-time PCR method based on a TaqMan probe was developed and modified for accurate identification of human cutaneous leishmaniasis (caused by Leishmania major or Leishmania tropica) from endemic areas of Iran. Two gene regions of amino acid permease 3 (AAP3) and cytochrome oxidase II (COII) were considered. Six new sets of species-specific primers and probes were designed. A total of 123 samples were examined and employed to evaluate and validate real-time PCR. According to parasitic load of the genesig®Leishmania Advanced Standard Kit, a serial dilution of purified plasmid (2–2×107 copies/reaction) was prepared under the same conditions for both genes. Specific primers and probes were able to detect three and six parasite copies in AAP3 and COII genes, respectively, and were able to detect three copies of parasites for L. major and L. tropica. The sensitivities of the reference kit and our method were 98.7 and 98.1%, respectively, and specificity was 100% for detecting parasite genomes in all assays. Designed primers and probes performed well in terms of efficiency and regression coefficient. For AAP3 and COII genes, respectively, the linear log range was 7 and the correlation coefficient (R2) was 0.749 and 0.996 for the reference kit using the standard generated curve and 0.98 and 0.96 with serial dilutions of parasite DNA. This research detected L. major and L. tropica definitely and opens the horizon for the other scientists in the multiplex reactions in designing and optimization of the conditions in silico and in vivo.

scholarly journals Is cytochrome c oxidase subunit I (COI) the right DNA barcoding marker for the Chaetopteryx villosa group?

2021 ◽  
Vol 4 ◽  
Author(s):  
Dalila Destanović ◽  
Lejla Ušanović ◽  
Lejla Lasić ◽  
Jasna Hanjalić ◽  
Belma Kalamujić Stroil
Keyword(s):  
Phylogenetic Trees ◽  
Pairwise Distance ◽  
Zoological Museum ◽  
Species Determination ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Software Analysis ◽  
Group Data ◽  
Species Specific ◽  
The Right

Chaetopteryx villosa (Fabricius, 1798) is a caddisfly species distributed throughout Europe, except in the Balkan and Apennine Peninsula. However, phylogenetically close species belonging to the C. villosa group are widespread throughout entire Europe. Species of this group (C. villosa, C. gessneri, C. fusca, C. sahlbergi, C. atlantica, C. bosniaca, C. vulture, and C. trinacriae) have distinct distributions with some overlaps. Adult forms of these species are morphologically similar, whereas larval morphology is only known for some species. There are also indications of species hybridization (e.g., C. villosa x fusca). Presumably, the molecular approach for the species determination of this group would be highly beneficial. In the BOLD database, there are 154 specimens with COI-5P barcodes of C. villosa species. Out of the remaining species, C. sahlbergi has 27 specimens with a barcode, C. fusca 20, C. gessneri 5, C. bosniaca 5, and C. atlantica 1, whereas sequences from the species C. vulture and C. trinacriae are missing. Therefore, we tested the power of discrimination of the COI-5P marker in the C. villosa group, as the most common barcoding markers for species identification in animals. Only sequences from public records originating from experienced research groups or taxonomists and containing a specimen photograph were taken as input. A total of 75 sequences from the BOLD database were obtained. Out of these sequences, 11 belonged to C. fusca, 5 to C. gessneri, 52 to C. villosa, 5 to C. bosniaca, and 2 to C. sahlbergi. For the generation of overview trees, COI-5P barcodes of Rhyacophila fasciata and Rh. nubila were used as outgroups. All sequences were trimmed at 5’ and 3’ ends, resulting in a final alignment length of 516 base pairs. Multiple sequence alignments and editing were done in the MEGA-X software. Analysis of nucleotide polymorphism was done in DNASP6 software. MEGA-X was used to calculate the pairwise distance and overall mean p-distance, and to construct the overview trees. Analysis of DNA polymorphism revealed 14 haplotypes of C. villosa, 3 haplotypes of C. fusca, 2 haplotypes of C. gessneri, and one for species C. bosniaca and C. sahlbergi. There were no significant interspecific and intraspecific differences among haplotypes based on pairwise distances. The p-distance between one of the haplotypes of C. fusca and C. villosa was 0.000, whereas the p-distance among haplotypes of C. villosa varied from 0.001 to about 0.055. The mean overall p-distance among haplotypes of all species equaled 0.03. No species-specific clusters were observed when phylogenetic trees were constructed except for C. gessneri, regardless of the method used (i.e., NJ, UPGMA, ML, ME, or MP). To minimize the possibility of species misidentification, we used only records submitted by NTNU-Norwegian University of Science and Technology (Norway), SNSB-Zoologische Staatssammlung Muenchen (Germany), Zoologisches Forschungsmuseum Alexander Koenig (Germany), University of Oulu, Zoological Museum (Finland), prof Hans Malicky and prof Mladen Kučinić. No records identified as hybrids were included in the analyses. With the exception of C. gessneri, COI-5P marker failed to separate the species of the C. villosa group. However, it is highly unlikely that poor species determination was the basis for such a result. To enable the comprehensive and unbiased evaluation of the relationships within this group, data coverage in BOLD database for most of the studied species should be enhanced, encompassing different geographical distribution of samples. Further studies are needed to detect the array of molecular markers suitable for the species delineation in a complex group such as C. villosa.

scholarly journals Molecular diversity of Scutellonema bradys populations from Benin, based on ITS1 rDNA and COI mtDNA

2018 ◽  
Vol 43 (4) ◽  
pp. 323-332
Author(s):  
Sètondji Alban Paterne Etchiha Afoha ◽  
Antoine Affokpon ◽  
Lieven Waeyenberge ◽  
Nancy de Sutter ◽  
Clément Agbangla ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Molecular Level ◽  
Cropping System ◽  
Dry Rot ◽  
Production Constraints ◽  
Efficient Management ◽  
Yield And Quality ◽  
Its1 Rdna ◽  
Management Techniques ◽  
Species Specific

Abstract In Benin, yam production continues to face numerous production constraints, including yield and quality reduction by Scutellonema bradys. Implementation of efficient management techniques against this pest requires an improved understanding, including at the molecular level, of the pest. The current study aimed at identifying the Scutellonema spp. associated with yam in Benin and investigating the phylogenetic relationships between populations. Nematodes of the genus Scutellonema were obtained from tubers exhibiting external dry rot symptoms. DNA was extracted from nematodes belonging to 138 populations collected from 49 fields from 29 villages. For 51 of these populations, both the ITS1 and COI regions could be amplified via PCR, sequenced, compared with available sequences in the NCBI database and were identified as S. bradys. Maximum likelihood was used to construct 60% consensus phylogenetic trees based on 51 sequences. This phylogenetic analysis did not reveal any genetic separation between populations by cultivar, village, cropping system nor by agroecological zone. Neither could any subgroups within S. bradys be separated, indicating that no subspecies were present. An earlier published species-specific primer set was verified with the DNA of the 51 sequences and was considered a reliable and rapid method for S. bradys identification.

Contemplating the Five Domains model of animal welfare assessment: UK horse owner perceptions of equine well-being

2021 ◽  
Vol 30 (3) ◽  
pp. 259-268
Author(s):  
KA Fletcher ◽  
LJ Cameron ◽  
M Freeman
Keyword(s):  
Animal Welfare ◽  
Online Survey ◽  
Empirical Studies ◽  
Affective State ◽  
Well Being ◽  
Factors Affecting ◽  
Equine Welfare ◽  
Species Specific ◽  
Sentient Beings ◽  
Horse Owners

Traditionally, assessment of animal welfare generally focused on physiological signs of health with less consideration of psychological well-being. More recently, the Five Domains model highlighted the concept of all aspects of an animal's life influencing their affective state. In equestrianism, however, there is a lack of awareness of the Five Domains model and, specifically, how different factors may affect the mental well-being of horses (Equus caballus). This divide between scientific research and lay horse owners could compromise equine welfare by failing to recognise horses as sentient beings with species-specific needs. The present study therefore aimed to explore how evidence-based information can be effectively communicated to equestrians (n = 259) through an online survey and whether increased knowledge of equine welfare needs has any impact on horse caregivers' assessment of their own horses' quality of life. Results showed that a simple educational infographic based on the Five Domains model had a significant impact on equestrians' assessment of equine welfare, although longitudinal, empirical studies are needed. Scores on a Likert scale for health, behaviour/human interactions and overall welfare were significantly lower following the intervention but scores for emotional well-being were significantly higher. This may suggest that, whilst the infographic increased participant awareness of the importance of emotional state and the factors affecting welfare, there were difficulties or inconsistencies in objectively assessing these emotions. This highlights the need for equine welfare science to be communicated more proactively to horse owners in an accessible, engaging format.

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