scholarly journals Monilinia Species Associated with Brown Rot of Cultivated Apple and Pear Fruit in China

Plant Disease ◽  
2016 ◽  
Vol 100 (11) ◽  
pp. 2240-2250 ◽  
Author(s):  
Xiao-Qiong Zhu ◽  
Cheng-Wang Niu ◽  
Xiao-Yu Chen ◽  
Li-Yun Guo
Keyword(s):  
Morphological Characteristics ◽  
Brown Rot ◽  
Conventional Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Method ◽  
Monilinia Fructicola ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The North ◽  
Monilia Polystroma ◽  
Species Specific

Monilinia isolates were collected from major apple and pear production regions in China from 2004 to 2011 and identified based on their morphological characteristics and three highly conserved loci. The 247 isolates belonged to three species: Monilinia fructicola, Monilia yunnanensis, and Monilia polystroma. M. yunnanensis was the most prevalent (77%), followed by M. polystroma (20%) and Monilinia fructicola (3%). Monilia yunnanensis is primarily distributed in the south, north, and west of China; M. polystroma is limited to the north and east; and Monilinia fructicola was detected only from a few samples from the north and east. Phylogenetic analysis based on internal transcribed spacer, β-tubulin, and laccase (lcc2) genes suggested that Monilia yunnanensis, M. polystroma, and Monilinia fructigena are closely related, and Monilia yunnanensis is more distantly related. We also found that these three species do not show consistent differences in morphological characteristics, including colony morphology, colony expansion rate, conidial characteristics, and the amount of stroma produced in culture. Thus, these three species are more like phylogenetic species in the process of speciation. In addition, a set of species-specific primers based on single-nucleotide polymorphisms and deletions in the lcc2 gene region were designed and a conventional polymerase chain reaction method successfully developed for differentiating Monilinia fructicola, Monilia yunnanensis, M. polystroma, and Monilinia laxa from the other species.

scholarly journals Population Structure of Brown Rot Fungi on Stone Fruits in China

Plant Disease ◽  
2011 ◽  
Vol 95 (10) ◽  
pp. 1284-1291 ◽  
Author(s):  
Xiao-qiong Zhu ◽  
Xiao-yu Chen ◽  
Li-yun Guo
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Brown Rot ◽  
Monilinia Fructicola ◽  
Stone Fruits ◽  
Phylogenetic Groups ◽  
Brown Rot Fungi ◽  
The Difference ◽  
Monilia Polystroma

In total, 455 Monilinia isolates from stone fruits collected from several provinces (cities) in China from 2003 to 2009 were identified to species based on morphological characteristics, molecular identification, and the sequence of the internal transcribed spacer (ITS) regions 1 and 2 and the 5.8S gene of the ribosomal RNA. Overall, four species were detected (Monilinia fructicola, M. fructigena, M. laxa, and Monilia polystroma). M. fructicola was the most prevalent (93.0%) followed by M. fructigena (4.8%), M. laxa (2.0%), and Monilia polystroma (0.2%). M. fructicola and M. fructigena were found on peach, plum, and apricot; M. laxa was found only on apricot, cherry (in an organic orchard), and wild peach; and Monilia polystroma was found only on plum in Heilongjiang. The pathogenicity of Monilinia fructicola, M. laxa, and M. fructigena did not significantly differ on wounded nectarine and apricot, indicating that the differences in frequency of occurrence were not linked to virulence. Phylogenetic analysis based on ITS sequences showed that the isolates of M. laxa and M. fructigena from China differed from isolates of these species from other countries, and that the difference led to the separation of the isolates from China and those from other countries into different phylogenetic groups. Further study is needed to determine whether they are cryptic species.

scholarly journals Import of Palmer amaranth (Amaranthus palmeri S. Wats.) seed with sweet potato (Ipomea batatas (L.) Lam) slips

2021 ◽  
Author(s):  
Eric Robert Page ◽  
Robert E. Nurse ◽  
Sydney Meloche ◽  
Kerry Bosveld ◽  
Christopher Grainger ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Arable Land ◽  
The United States ◽  
Palmer Amaranth ◽  
Amaranthus Palmeri ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ipomea Batatas ◽  
Amaranth Seed ◽  
Species Specific

Palmer amaranth is one of the most economically important and widespread weeds of arable land in the United States. Although no populations are currently known to exist in Canada, its distribution has expanded northward such that it is present in many of the States bordering Canada and multiple pathways exist for its introduction. In this short communication we report on the transport of viable Palmer amaranth seed on imported sweet potato slips. A reproductive pair of Palmer amaranth seedlings were identified from soil accompanying imported sweet potato slips in 2018. Identification was confirmed using species specific single nucleotide polymorphisms.

scholarly journals Single Nucleotide Polymorphisms in the Bovine TLR2 Extracellular Domain Contribute to Breed and Species-Specific Innate Immune Functionality

2021 ◽  
Vol 12 ◽  
Author(s):  
Marie-Christine Bartens ◽  
Amanda J. Gibson ◽  
Graham J. Etherington ◽  
Federica Di Palma ◽  
Angela Holder ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bos Indicus ◽  
Full Length ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Brown Swiss ◽  
Cattle Breeds ◽  
Species Specific ◽  
Mycobacterial Antigens

Recent evidence suggests that several cattle breeds may be more resistant to infection with the zoonotic pathogen Mycobacterium bovis. Our data presented here suggests that the response to mycobacterial antigens varies in macrophages generated from Brown Swiss (BS) and Holstein Friesian (HF) cattle, two breeds belonging to the Bos taurus family. Whole genome sequencing of the Brown Swiss genome identified several potential candidate genes, in particular Toll-like Receptor-2 (TLR2), a pattern recognition receptor (PRR) that has previously been described to be involved in mycobacterial recognition. Further investigation revealed single nucleotide polymorphisms (SNP) in TLR2 that were identified between DNA isolated from cells of BS and HF cows. Interestingly, one specific SNP, H326Q, showed a different genotype frequency in two cattle subspecies, Bos (B.) taurus and Bos indicus. Cloning of the TLR2 gene and subsequent gene-reporter and chemokine assays revealed that this SNP, present in BS and Bos indicus breeds, resulted in a significantly higher response to mycobacterial antigens as well as tri-acylated lipopeptide ligands in general. Comparing wild-type and H326Q containing TLR2 responses, wild-type bovine TLR2 response showed clear, diminished mycobacterial antigen responses compared to human TLR2, however bovine TLR2 responses containing H326Q were found to be partially recovered compared to human TLR2. The creation of human:bovine TLR2 chimeras increased the response to mycobacterial antigens compared to the full-length bovine TLR2, but significantly reduced the response compared to the full-length human TLR2. Thus, our data, not only present evidence that TLR2 is a major PRR in the mammalian species-specific response to mycobacterial antigens, but furthermore, that there are clear differences between the response seen in different cattle breeds, which may contribute to their enhanced or reduced susceptibility to mycobacterial infection.

Neisseria meningitidis and Neisseria gonorrhoeae are differently adapted in the regulation of denitrification: single nucleotide polymorphisms that enable species-specific tuning of the aerobic–anaerobic switch

2012 ◽  
Vol 445 (1) ◽  
pp. 69-79 ◽  
Author(s):  
James Edwards ◽  
Diana Quinn ◽  
Karyn-Anne Rowbottom ◽  
Jean L. Whittingham ◽  
Melanie J. Thomson ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Oxygen Sensor ◽  
Nucleotide Polymorphisms ◽  
Intact Cells ◽  
Single Nucleotide ◽  
Neisseria Species ◽  
Site Analysis ◽  
Polymerase Binding ◽  
Species Specific

The closely related pathogenic Neisseria species N. meningitidis and N. gonorrhoeae are able to respire in the absence of oxygen, using nitrite as an alternative electron acceptor. aniA (copper-containing nitrite reductase) is tightly regulated by four transcriptional regulators: FNR (fumarate and nitrate reductase), NarP, FUR (Ferric uptake regulator) and NsrR. The four regulators control expression of aniA in N. meningitidis by binding to specific and distinct regions of the promoter. We show in the present study that FUR and NarP are both required for the induction of expression of aniA in N. meningitidis, and that they bind adjacent to one another in a non-co-operative manner. Activation via FUR/NarP is dependent on their topological arrangement relative to the RNA polymerase-binding site. Analysis of the sequence of the aniA promoters from multiple N. meningitidis and N. gonorrhoeae strains indicates that there are species-specific single nucleotide polymorphisms, in regions predicted to be important for regulator binding. These sequence differences alter both the in vitro DNA binding and the promoter activation in intact cells by key activators FNR (oxygen sensor) and NarP (which is activated by nitrite in N. meningitidis). The weak relative binding of FNR to the N. gonorrhoeae aniA promoter (compared to N. meningitidis) is compensated for by a higher affinity of the gonococcal aniA promoter for NarP. Despite containing nearly identical genes for catalysing and regulating denitrification, variations in the promoter for the aniA gene appear to have been selected to enable the two pathogens to tune differentially their responses to environmental variables during the aerobic–anaerobic switch.

scholarly journals Novel Genetic Polymorphisms That Further Delineate the Phylogeny of the Mycobacterium tuberculosis Complex

2006 ◽  
Vol 188 (12) ◽  
pp. 4271-4287 ◽  
Author(s):  
Richard C. Huard ◽  
Michel Fabre ◽  
Petra de Haas ◽  
Luiz Claudio Oliveira Lazzarini ◽  
Dick van Soolingen ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Deletions ◽  
History Of ◽  
Species Specific ◽  
Mycobacterium Africanum ◽  
Mycobacterium Microti ◽  
First Time ◽  
Fine Tune

ABSTRACT In a previous report, we described a PCR protocol for the differentiation of the various species of the Mycobacterium tuberculosis complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol. 41:1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (n = 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various Mycobacterium tuberculosis strains, new species-specific SNPs were identified for “Mycobacterium canettii,” Mycobacterium microti, and Mycobacterium pinnipedii, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two Mycobacterium africanum subtype I variants. Surprisingly, coincident polymorphisms linked one M. africanum subtype I genotype with the dassie bacillus and M. microti with M. pinnipedii, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.

scholarly journals Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

2015 ◽  
Vol 72 (6) ◽  
pp. 1790-1801 ◽  
Author(s):  
Dorte Bekkevold ◽  
Sarah J. Helyar ◽  
Morten T. Limborg ◽  
Einar E. Nielsen ◽  
Jakob Hemmer-Hansen ◽  
...  
Keyword(s):  
Clupea Harengus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The North ◽  
Sustainable Products ◽  
The North Sea ◽  
Commercially Important ◽  
Mixed Origin ◽  
The Baltic ◽  
Management Issues

Abstract Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating management issues. We report novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea, and find support that western Baltic feeding aggregations mainly constitute herring from the western Baltic with contributions from the Eastern Baltic. Our study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution.

scholarly journals The Role of Nonshivering Thermogenesis Genes on Leptin Levels Regulation in Residents of the Coldest Region of Siberia

2021 ◽  
Vol 22 (9) ◽  
pp. 4657
Author(s):  
Alena A. Nikanorova ◽  
Nikolay A. Barashkov ◽  
Vera G. Pshennikova ◽  
Sergey S. Nakhodkin ◽  
Nyurgun N. Gotovtsev ◽  
...  
Keyword(s):  
Climate Adaptation ◽  
Cold Climate ◽  
The Arctic ◽  
Human Adaptation ◽  
Nucleotide Polymorphisms ◽  
Nonshivering Thermogenesis ◽  
Single Nucleotide ◽  
The North ◽  
Selection For

Leptin plays an important role in thermoregulation and is possibly associated with the microevolutionary processes of human adaptation to a cold climate. In this study, based on the Yakut population (n = 281 individuals) living in the coldest region of Siberia (t°minimum −71.2 °C), we analyze the serum leptin levels and data of 14 single nucleotide polymorphisms (SNPs) of 10 genes (UCP1, UCP2, UCP3, FNDC5, PPARGC1A, CIDEA, PTGS2, TRPV1, LEPR, BDNF) that are possibly involved in nonshivering thermogenesis processes. Our results demonstrate that from 14 studied SNPs of 10 genes, 2 SNPs (the TT rs3811787 genotype of the UCP1 gene and the GG rs6265 genotype of the BDNF gene) were associated with the elevated leptin levels in Yakut females (p < 0.05). Furthermore, of these two SNPs, the rs3811787 of the UCP1 gene demonstrated more indications of natural selection for cold climate adaptation. The prevalence gradient of the T-allele (rs3811787) of UCP1 increased from the south to the north across Eurasia, along the shore of the Arctic Ocean. Thereby, our study suggests the potential involvement of the UCP1 gene in the leptin-mediated thermoregulation mechanism, while the distribution of its allelic variants is probably related to human adaptation to a cold climate.

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.

scholarly journals Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 347 ◽  
Author(s):  
Mark J. Hanemaaijer ◽  
Parker D. Houston ◽  
Travis C. Collier ◽  
Laura C. Norris ◽  
Abdrahamane Fofana ◽  
...  
Keyword(s):  
Sub Saharan Africa ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Chromosomal Form ◽  
Operational Taxonomic Units ◽  
Mitogenome Sequence ◽  
Mitochondrial Sequences ◽  
Sub Saharan ◽  
Species Specific

Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the following Anopheles species and chromosomal forms: An. arabiensis, An. coluzzii (The Forest and Mopti chromosomal forms) and An. gambiae (The Bamako and Savannah chromosomal forms).  The raw Illumina sequencing reads were mapped to the NC_002084 reference mitogenome sequence. A total of 783 single nucleotide polymorphisms (SNPs) were detected on the mitochondrial genome, of which 460 are singletons (58.7%). None of these SNPs are suitable as molecular markers to distinguish among An. arabiensis, An. coluzzii and An. gambiae or any of the chromosomal forms. The lack of species or chromosomal form specific markers is also reflected in the constructed phylogenetic tree, which shows no clear division among the operational taxonomic units considered here.

scholarly journals First Report of Peach Brown Rot Caused by Monilinia fructicola in Central and Western China

Plant Disease ◽  
2013 ◽  
Vol 97 (9) ◽  
pp. 1255-1255 ◽  
Author(s):  
L. F. Yin ◽  
S. N. Chen ◽  
N. N. Yuan ◽  
L. X. Zhai ◽  
G. Q. Li ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Direct Sequencing ◽  
Eastern China ◽  
Morphological Characteristics ◽  
Brown Rot ◽  
Its Sequences ◽  
Western China ◽  
Its2 Region ◽  
Monilinia Fructicola ◽  
First Report

Brown rot of peach (Prunus persica) in China has been reported to be caused by at least three Monilinia species (1). In the present study, peaches with symptoms resembling brown rot caused by Monilinia species were collected from commercial orchards in the northwestern province of Gansu in August 2010, the southwestern province of Yunnan in July 2011, and in the central province of Hubei in July 2012. Affected fruit showed the typical symptoms of brown rot with zones of sporulation. Fungal isolates were single-spored and cultured on potato dextrose agar (PDA). Colonies showed grayness with concentric rings of sporulation after incubation at 25°C in the dark. Mean mycelial growth of isolates YHC11-1a and YHC11-2a from Yunnan, GTC10-1a and GTC10-2a from Gansu, and HWC12-14a and HWC12-23a from Hubei, was 4.6 ± 0.4 and 7.5 ± 0.7 cm after 3 and 5 days incubation, respectively. Conidia were lemon shaped and formed in branched monilioid chains, and the mean size was 9.3 (6.7 to 11.5) × 12.5 (7.9 to 17.8) μm, which was consistent with the characteristics of Monilinia fructicola (1,2). The species identification was confirmed by sequencing of the ribosomal ITS sequences. The ribosomal ITS1-5.8S-ITS2 region was amplified from each of the six isolates using primers ITS1 and ITS4 (3). Results indicated that the ITS sequences of these isolates were identical and showed the highest similarity (100%) with M. fructicola ITS sequences from isolates collected in China (GenBank Accession Nos. HQ893748, FJ515894, and AM887528), Slovenia (GU967379), Italy (FJ411109), and Spain (EF207423). The pathogen was also confirmed to be M. fructicola based on the detection of an M. fructicola- specific band (534 bp) using a PCR-based molecular tool developed for distinguishing Chinese Monilinia species affecting peach (1). Pathogenicity was tested on surface-sterilized, mature peaches (Shui Mi Tao) with representative isolates. Fruits were holed at three equidistant positions to a depth of 5 mm using a sterile cork borer. Mycelial plugs (5 mm in diameter) from the periphery of a 4-day-old colony of each isolate were placed upside down into each hole, control fruits received water agar. After 3 days of incubation at 22°C in a moist chamber, inoculated fruits developed typical brown rot symptoms while control fruits remained healthy. Pathogens from the inoculated fruit were confirmed to be M. fructicola based on morphological characteristics. To our knowledge, this is the first report of occurrence of M. fructicola in Gansu, Yunnan, and Hubei provinces, thousands of kilometers away from eastern China where occurrence of peach brown rot caused by M. fructicola has been confirmed (2,4). The results indicated the further geographical spread of the M. fructicola in China. References: (1) M. J. Hu et al. Plos One 6(9):e24990, 2011. (2) M. J. Hu et al. Plant Dis. 95:225, 2011. (3) T. J. White et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Academic Press, San Diego, 1990. (4) X. Q. Zhu et al. Plant Pathol. 54:575, 2005.

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