scholarly journals First report of alternate hosts of willow rust disease caused by Melampsora ferrinii in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Zijia Peng ◽  
Chaowei Xiong ◽  
Zeyu Luo ◽  
Xiangyun Hu ◽  
Zhongdong Yu ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Mainland China ◽  
Shaanxi Province ◽  
Alternate Host ◽  
Rust Disease ◽  
Alternate Hosts ◽  
Orange Yellow ◽  
Salix Babylonica ◽  
Type 3

Corydalis acuminata Franch., C. edulis Maxim. and C. racemosa (Thunb.) Pers. of family Papaveraceae are rich in multiple alkaloids and widely used as Chinese medicinal herbs, for treating cough, pruritus, sores tinea and snake venom (Zhang et al. 2008, Iranshahy et al. 2014). In April 2021, orange rust pustules were observed on C. acuminata, C. edulis and C. racemosa in Shaanxi Province (34°4’56’’ N, 108°2’9’’ E, alt. 770 m), China. Samples were collected and voucher specimens were preserved in the Herbarium Mycologicum Academiae Sinicae (nos. HMAS249947–HMAS249949), China. Consequent geospatial investigations revealed that diseased plants can be observed at an altitude of 400–1000 m, and show an incidence from 40% to 80% varied by altitude. Spermogonia epiphyllous, subcuticular, densely grouped, oval or round, 0.14–0.36 × 0.09–0.30 mm, pale orange-yellow, and type 3 of Cummins and Hiratsuka (1963). Aecia mostly hypophyllous, subepidermal without peridia, Caeoma-type, erumpent, densely grouped, oval or round, 0.27–0.85 × 0.15–0.43 mm, and orange-yellow; hyaline peridial cells produced in a periphery of the sorus under the ruptured epidermis of host plants. Aeciospores globoid or broadly ellipsoid, catenulate with intercalary cells, 15.7–20.1 × 10.8–15.7 μm, yellow to pale orange; walls hyaline, verrucose, 1.7–3.1 μm thick. This fungus was morphologically identified as Melampsora (Melampsoraceae). The rDNA-28S and the internal transcribed spacer (ITS) regions were amplified using primers NL1/NL4 and ITS1/ITS4 (Ji et al. 2020; Wang et al. 2020). Bi-directional sequences were assembled and deposited in GenBank (accession nos. MW990091–MW990093 and MW996576–MW996578). Phylogenetic trees were constructed with the ITS+rDNA-28S dataset based on maximum-likelihood (ML), maximum-parsimony (MP) and Bayesian Inference (BI). ML and MP bootstrap values were calculated by bootstrap analyses of 1,000 replicates using MEGA-X (Kumar et al. 2018), while BI posterior probabilities (Bpps) were calculated using MrBayes ver. 3.1.2 (Ji et al. 2020; Wang et al. 2020). Phylogenetic analyses grouped our specimens and Melampsora ferrinii Toome & Aime into one clade, highly supported by bootstrap values of ML, MP, and Bpps of 100%/100%/1. Inoculations were conducted with 1-year-old plants of original host, Salix babylonica L. (Toome & Aime 2015). Aeciospores suspension with a concentration of 106 spores/ml were sprayed on 20 healthy leaves, with another 20 healthy leaves sprayed with sterile water as the control. The inoculated plants were kept in darkness at 20–25 °C for 2 days and then transferred into greenhouse at 23°C with 16 h light per day. After 8–10 days of inoculation, yellow pustules of uredinia appeared on abaxial surfaces of the inoculated leaves, which were identical to Toome & Aime (2015) reported, while the control leaves remained healthy. Inoculations with the same method were conducted by spraying urediniospores, and the same rust symptoms developed after 8 days. Genus Corydalis was verified as the alternate host of M. chelidonii-pierotii Tak. Matsumoto, M. coleosporioides Dietel, M. idesiae Miyabe and M. yezoensis Miyabe & T. Matsumoto (Shinyama & Yamaoka 2012; Okane et al. 2014; Yamaoka & Okane 2019), and C. incisa (Thunb.) Pers. was speculated as the potential alternate host of M. ferrinii (Toome & Aime 2015). Based on morphology, phylogeny and pathogenicity, we firstly report M. ferrinii in mainland China and verify C. acuminata, C. edulis and C. racemosa instead of C. incisa as its alternate hosts.

scholarly journals First Report of Black Swallow-Wort as an Alternate Host of the Two-Needle Pine Stem Rust Pathogen, Cronartium flaccidum, in France

Plant Disease ◽  
2012 ◽  
Vol 96 (4) ◽  
pp. 585-585
Author(s):  
M.-C. Bon ◽  
F. Guermache
Keyword(s):  
Stem Rust ◽  
Pinus Halepensis ◽  
Yellow Rust ◽  
Early Summer ◽  
Alternate Host ◽  
Rust Disease ◽  
First Report ◽  
Black And White ◽  
Light Yellow ◽  
Orange Yellow

Stem rust disease, caused by Cronartium flaccidum (Alb. & Schwein.) G. Winter, is among the most destructive diseases of the two-needle hard pine in the Northern Hemisphere, including Scots pine but also several Mediterranean pines in southern Europe (2,3). This heteroecious rust has numerous alternate herbaceous hosts spanning different plant families, thereby contributing to epidemic outbreaks when environmental conditions for infection are optimal (2,3). The main alternate host in Europe is the white swallow-wort, Vincetoxicum hirundinaria Medik, a herbaceous perennial in the milkweed family (Asclepiadaceae). At the southwestern edge of its distribution, V. hirundinaria co-occurs with the black swallow-wort, V. nigrum (L.) Moench and cases of misidentification between the two species are not uncommon. Little to no disease occurs to V. nigrum likely because phenanthroindolizidine alkaloid antimicrobial compounds are produced in the weed. In 1918, occurrence of C. flaccidum was reported in Spain and Portugal on black and white swallow-worts albeit as C. asclepadium (1). In the early summer of 2011, at Saint Clément de Rivière in southern France, we detected orange-yellow rust pustules on the lower leaf surfaces of several black swallow-worts growing near Aleppo pines (Pinus halepensis). These orange-yellow pustules were erumpent uredinia in groups (range = 137 to 400 μm in diameter) with peridia that broke with the production of uredinospores. The latter were moderately echinulate, light yellow, broadly ellipsoid (length = 23 ± 4 μm and range = 11 to 33 μm; width = 15 ± 2 μm and range = 9 to 20 μm) with walls of 1 to 2 μm thick (mean 1.3 ± 0.2 μm). Hair-like columnar telia (length = 1123 ± 131 μm and range = 976 to 1280 μm; width = 136 ± 28 μm and range = 104 to 176 μm) were mostly formed from uredinia. Telia were hypophyllous and reddish orange. Teliospores were orange-yellow and ellipsoidal to cylindrical (length 26.3 ± 6.2 μm and range 13.5 to 46 μm; width = 10.5 ± 1.8 μm and range = 6.9 to 14.9 μm). Morphological features of these fruiting structures were consistent with those of C. flaccidum (Alb. & Schwein.) G. Winter on white swallow-worts (2). Additional confirmation was provided by sequencing the two internal transcribed spacer regions (ITS1 and ITS2) and the 5.8S gene (4). The sequence was 843 bp long (GenBank Accession No. JN802139), 99.7% similar to C. flaccidum found on Melampyrum in Finland (Accession No. JF13709), and 99.4% similar to C. flaccidum found on pines in Italy (Accession No. X83900). Voucher material has been deposited at the Herbarium of Montpellier's University under the collection Accession No. MPUØ188846. To our knowledge, this is the first report of the occurrence of uredinia and telia of C. flaccidum on black swallow-worts clearly identified in France. The occurrence of the rust on this understory vine is of critical importance for the economic sustainability of pine forests in France, especially when they are heavily constrained by drought and fire. References: (1) R. Gonzalez Fragoso. Trab. Mus. Nac. Ci. Nat., Ser. Bot. 15:1, 1918. (2) J. Kaitera and H. Nuorteva. For. Pathol. 33:205, 2003. (3) A. Ragazzi. Phytopathol. Medit. 28:5, 1989. (4) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. Academic Press, Inc., San Diego, CA, 1990.

Production of uredinia and telia by stalactiform blister rust in British Columbia

1993 ◽  
Vol 71 (3) ◽  
pp. 519-521 ◽  
Author(s):  
B. J. van der Kamp
Keyword(s):  
British Columbia ◽  
Life Cycle ◽  
Key Words ◽  
Alternate Host ◽  
Alternate Hosts ◽  
Blister Rust ◽  
Dry Areas ◽  
Do So

Records of uredinia and telia production on the alternate hosts of Cronartium coleosporioides in British Columbia and inoculation of Castilleja miniata with aeciospores collected from various locations showed that rust isolates from dry areas of the interior of British Columbia do not produce uredinia and may have lost the ability to do so. Collections from somewhat wetter areas produced uredinia or mixtures of uredinia and telia immediately following aeciospore inoculations, and field collections from such areas in June commonly had mixtures of uredinia and telia. Loss of the uredinial stage may be a response to climates that are often unsuitable for the spread or survival of the rust on the alternate host. Key words: stalactiform rust, uredinia, telia, rust life cycle.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Genome-scale reconstructions to assess metabolic phylogeny and organism clustering

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240953
Author(s):  
Christian Schulz ◽  
Eivind Almaas
Keyword(s):  
Phylogenetic Trees ◽  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Significant Heterogeneity ◽  
Metabolic Reaction ◽  
High Quality ◽  
Conserved Genes ◽  
Genome Scale

Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.

scholarly journals Phylogenetic analysis of canine parvoviruses from Turkey

2020 ◽  
Vol 76 (01) ◽  
pp. 6334-2020
Author(s):  
ZEYNEP AKKUTAY-YOLDAR ◽  
TAYLAN KOÇ B.
Keyword(s):  
High Mortality ◽  
Phylogenetic Trees ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Canine Parvovirus ◽  
Mortality And Morbidity ◽  
Identity Match ◽  
Genomic Characterization

Canine parvovirus (CPV) type 2 is the causative agent of acute hemorrhagic enteritis and high mortality in the affected dogs. Numerous studies have been done to understand the origin of the virus and to exhibit new variants and circulating strains. This report describes the detection and genomic characterization of CPV strains from indoor and outdoor dogs in Ankara, Turkey. Samples were sent to our laboratory due to clinical symptoms in puppies. We tested blood and swab samples to determine the presence of canine parvovirus (CPV) in three puppies and two adult dogs by reverse transcription-polymerase chain reaction (RT-PCR) using VP2 (capsid protein) region primers of canine parvoviruses. Following that, to provide molecular characterization data Maximum Likelihood (ML) method was used for phylogenetic analyses. Constructed phylogenetic trees from the aligned nucleotide sequences revealed that our CPV strains demonstrated high genetic similarities, with 100% identity match on nucleotide alignments with each other and classified in CPV-2b genotypes.They have placed on a monophyletic clade as a sister branch with CPV VAC S quantum with 98.9% nucleotide homology. Our findings suggest that CPV-2b is actual and frequently seen variant in Turkey and shows high similarities with other CPV variants and a bit less with FPVs in Turkey and around the world. CPV causes high mortality and morbidity in dogs and to develop effective vaccines for protection of dogs in Turkey where there are few numbers of studies that have been done, field strains should be isolated and characterised.

scholarly journals Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

2021 ◽  
Author(s):  
Blessing Amaka Ezeonuegbu ◽  
Dauda Abdullahi Machido ◽  
Clement Z. Whong ◽  
Wisdom S. Japhet ◽  
Clement Ameh Yaro ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Industrial Effluent ◽  
Pcr Amplification ◽  
Morphological Characterization ◽  
Likelihood Method ◽  
Internal Transcribed Spacer Region ◽  
Fungal Isolates ◽  
Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

Lifeforms as criterion for species delimitation: Are Aristida adscensionis and A. coerulescens (Aristidoideae, Poaceae) two species?

Phytotaxa ◽  
2019 ◽  
Vol 393 (1) ◽  
pp. 67 ◽  
Author(s):  
MIKE THIV ◽  
J. ALFREDO REYES-BETANCORT ◽  
ORI FRAGMAN-SAPIR
Keyword(s):  
Morphometric Analysis ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Life Forms ◽  
Clear Separation ◽  
Taxonomic Treatment ◽  
Molecular Phylogenetic ◽  
The Mediterranean

The distinction of the perennial Aristida coerulescens from the annual A. adscensionis and its taxonomic treatment has been subject of long discussions. We here include accessions from the Mediterranean and Macaronesia for molecular phylogenetic analyses and conducted a morphometric analysis. A lineage of A. adscensionis, A. coerulescens and A. effusa is well supported in phylogenetic trees. Moreover, a group of Mediterranean, Macaronesia and Arabian A. coerulescens and A. adscensionis is revealed where both taxa are intermingled. A morphological analysis of traditionally used spikelet characters did not indicate a clear separation of both taxa. We therefore conclude that A. coerulescens should best be treated as synonym of A. adscensionis. The differential character of annual and perennial life forms seems to be plastic in this taxon indicating rapid shifts between these two strategies. 

scholarly journals Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

2019 ◽  
Vol 39 (8) ◽  
Author(s):  
Jian-Qiu Li ◽  
Li Li ◽  
Bao-Quan Fu ◽  
Hong-Bin Yan ◽  
Wan-Zhong Jia
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Evolutionary Relationship ◽  
Sister Group ◽  
Trna Genes ◽  
Mammal Species ◽  
Qinghai Province ◽  
Loop Region ◽  
Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

scholarly journals A51 Genetic variability of small ruminant lentiviruses in sheep and goats from single-species flocks from Poland

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Monika Olech ◽  
Jacek Kuźmak
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Phylogenetic Trees ◽  
Small Ruminant ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Genetic Distances ◽  
Sheep And Goats ◽  
Viral Recombination ◽  
Species Flocks

Abstract Previous phylogenetic analyses of small ruminant lentivirus (SRLV) sequences found in Poland revealed the circulation of subtype A1 in both sheep and goats, subtypes B1 in goats, and subtypes B2, A12, and A13 in sheep only. This study aimed to analyze the genetic nature of SRLV circulating in sheep and goats from single-species flocks. In order to analyze the degree of genetic variability, the fragments of gag and env genes of 24 SRLV strains were amplified by PCR, cloned into plasmid vectors, sequenced, and consensus sequences were aligned to each other and to reference sequences available from GenBank. Phylogenetic analysis was performed using the Geneious tree-builder tool, and phylogenetic trees were constructed using Mr Bayes (using the general time reversible substitution model) within Geneious Pro 5.3. Pairwise genetic distances were calculated in MEGA 6. Phylogenetic analysis revealed that the strains were highly heterogeneous and represented ovine strains belonging to subtypes A12 and B2 and caprine strains grouped in subtypes B1, B2, A1, and A12. In addition, two novel subtypes, A16 and A17, were found in goats. The mean pairwise genetic distances of gag and env sequences of both clusters were above 15 per cent nucleotide divergence when compared to all other subtypes within group A, which is a criterion required to distinguish a new subtype. Additionally, the existence of two separated clusters was confirmed by high bootstrap values. Co-infections with strains belonging to different subtypes within A and B groups were detected in one sheep and four goats originating from four flocks. Since the co-infection with more than one lentivirus genotype offers an opportunity for viral recombination, the possible recombination events were tested based on RDP analysis. For all co-infected animals, no evidence of recombination was found within the gag gene; however, env sequences showed some recombination patterns in three samples. In conclusion, we have demonstrated extended genetic variability of SRLV in sheep and goats from Poland with the existence of co-infection and recombination events.

Morphological and molecular characterisation of Distolabrellus veechi (Rhabditida: Mesorhabditidae) from India

Nematology ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 439-452 ◽  
Author(s):  
Suman ◽  
Aashaq Hussain Bhat ◽  
Aasha ◽  
Ashok Kumar Chaubey ◽  
Joaquín Abolafia
Keyword(s):  
Phylogenetic Trees ◽  
Agricultural Soils ◽  
Phylogenetic Analyses ◽  
Uttar Pradesh ◽  
Sister Group ◽  
Molecular Characterisation ◽  
Soil Baiting ◽  
Its Rrna ◽  
First Time ◽  
Rrna Sequences

Summary A redescription of Distolabrellus veechi (Rhabditida: Mesorhabditidae) from agricultural soils in Uttarakhand and Uttar Pradesh, India, is provided. Specimens were extracted from soil using the Galleria soil baiting technique, with two strains of nematodes named JP1 and JP2 being obtained. Morphological and morphometric studies on the species agree well with previous records. Molecular analyses are provided using 18S, 28S and ITS rRNA sequences, the ITS sequences being obtained for the first time in this species. These analyses show that the material examined agrees well with previously studied populations. Phylogenetic analyses showed Distolabrellus to be the sister group of Crustorhabditis and Teratorhabditis, all having the male spicules fused for more than 50% of their length. Illustrations and phylogenetic trees based on 18S, 28S and ITS rRNA sequences are provided.

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