Nucleotide polymorphisms in three genes support host and geographic speciation in tree pathogens belonging toGremmeniellaspp.

2002 ◽  
Vol 80 (11) ◽  
pp. 1151-1159 ◽  
Author(s):  
M Dusabenyagasani ◽  
G Laflamme ◽  
R C Hamelin
Keyword(s):  
North America ◽  
Dna Sequences ◽  
North American ◽  
Abies Balsamea ◽  
Host Specialization ◽  
Rrna Genes ◽  
Nucleotide Polymorphisms ◽  
Group I ◽  
Geographic Separation ◽  
Pinus Spp

We detected nucleotide polymorphisms within the genus Gremmeniella in DNA sequences of β-tubulin, glyceraldehyde phosphate dehydrogenase, and mitochondrial small subunit rRNA (mtSSU rRNA) genes. A group-I intron was present in strains originating from fir (Abies spp.) in the mtSSU rRNA locus. This intron in the mtSSU rRNA locus of strains isolated from Abies sachalinensis (Fridr. Schmidt) M.T. Mast in Asia was also found in strains isolated from Abies balsamea (L.) Mill. in North America. Phylogenetic analyses yielded trees that grouped strains by host of origin with strong branch support. Asian strains of Gremmeniella abietina (Lagerberg) Morelet var. abietina isolated from fir (A. sachalinensis) were more closely related to G. abietina var. balsamea from North America, which is found on spruce (Picea spp.) and balsam fir, and European and North American races of G. abietina var. abietina from pines (Pinus spp.) were distantly related. Likewise, North American isolates of Gremmeniella laricina (Ettinger) O. Petrini, L.E. Petrini, G. Laflamme, & G.B. Ouellette, a pathogen of larch, was more closely related to G. laricina from Europe than to G. abietina var. abietina from North America. These data suggest that host specialization might have been the leading evolutionary force shaping Gremmeniella spp., with geographic separation acting as a secondary factor.Key words: Gremmeniella, geographic separation, host specialization, mitochondrial rRNA, nuclear genes.

scholarly journals Inter- and Intra-Continental Genetic Variation in the Generalist Conifer Wood Saprobic Fungus Phlebiopsis gigantea

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 751
Author(s):  
Francesco Dovana ◽  
Paolo Gonthier ◽  
Matteo Garbelotto
Keyword(s):  
North America ◽  
Genetic Differentiation ◽  
Dna Sequences ◽  
North American ◽  
Fungal Species ◽  
Coniferous Forests ◽  
Native Forest ◽  
Western North America ◽  
Phlebiopsis Gigantea ◽  
Conifer Wood

Phlebiopsis gigantea (Fr.) Jülich is a well-known generalist conifer wood saprobe and a biocontrol fungus used in several world countries to prevent stump infection by tree pathogenic Heterobasidion fungal species. Previous studies have reported the presence of regional and continental genetic differentiation in host-specific fungi, but the presence of such differentiation for generalist wood saprobes such as P. gigantea has not been often studied or demonstrated. Additionally, little information exists on the distribution of this fungus in western North America. The main purposes of this study were: (I) to assess the presence of P. gigantea in California, (II) to explore the genetic variability of P. gigantea at the intra and inter-continental levels and (III) to analyze the phylogeographic relationships between American and European populations. Seven loci (nrITS, ML5–ML6, ATP6, RPB1, RPB2, GPD and TEF1-α) from 26 isolates of P. gigantea from coniferous forests in diverse geographic distribution and from different hosts were analyzed in this study together with 45 GenBank sequences. One hundred seventy-four new sequences were generated using either universal or specific primers designed in this study. The mitochondrial ML5–ML6 DNA and ATP6 regions were highly conserved and did not show differences between any of the isolates. Conversely, DNA sequences from the ITS, RPB1, RPB2, GPD and TEF1-α loci were variable among samples. Maximum likelihood analysis of GPD and TEF1-α strongly supported the presences of two different subgroups within the species but without congruence or geographic partition, suggesting the presence of retained ancestral polymorphisms. RPB1 and RPB2 sequences separated European isolates from American ones, while the GPD locus separated western North American samples from eastern North American ones. This study reports the presence of P. gigantea in California for the first time using DNA-based confirmation and identifies two older genetically distinct subspecific groups, as well as three genetically differentiated lineages within the species: one from Europe, one from eastern North America and one from California, with the latter presumably including individuals from the rest of western North America. The genetic differentiation identified here among P. gigantea individuals from coniferous forests from different world regions indicates that European isolates of this fungus should not be used in North America (or vice versa), and, likewise, commercially available eastern North American P. gigantea isolates should not be used in western North America forests. The reported lack of host specificity of P. gigantea was documented by the field survey and further reinforces the need to only use local isolates of this biocontrol fungus, given that genetically distinct exotic genotypes of a broad generalist microbe may easily spread and permanently alter the microbial biodiversity of native forest ecosystems.

scholarly journals First Report of Heterobasidion annosum on the Endemic Abies hickeli of Southern Mexico

Plant Disease ◽  
2000 ◽  
Vol 84 (9) ◽  
pp. 1047-1047 ◽  
Author(s):  
M. Garbelotto ◽  
I. Chapela
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Heterobasidion Annosum ◽  
Internal Transcribed Spacer Region ◽  
Southern Mexico ◽  
Geographic Ranges ◽  
The North ◽  
Mexican State ◽  
Standing Trees ◽  
Pinus Spp

The basidiomycete Heterobasidion annosum (Fr.:Fr.) Bref. is a pathogen of conifers in the Northern Hemisphere. This fungus has been previously reported from Pinus spp. (1) and from Abies religiosa (H.B.K.) Schl. et Cham. (2) in Central Mexico. In 1998, H. annosum was collected for the first time from stumps of Abies hickeli Flous et Gaussen in the Southern Mexican State of Oaxaca, at an altitude of 2,900 m (Lat 17° 28′ N, Long 96° 31′ W). Although standing trees at the sampled site were asymptomatic, the sapwood and heartwood of several fir stumps were extensively decayed. The white laminated rot was similar to that caused by H. annosum on other Abies spp. Decay pockets extended to the upper surface of the stumps, indicating the fungus had infected and colonized the tree butts prior to tree felling. H. annosum basidiocarps were found both outside the roots in the duff layer and inside the decay pockets. The anamorph of H. annosum (Spiniger meineckellum (A. Olson) Stalpers) was isolated from the context of three basidiocarps. Based on comparative analysis of DNA sequences of the nuclear ribosomal internal transcribed spacer region, all three isolates belonged to the North American S intersterility group (ISG). This report expands the host and the geographic ranges of the North American S ISG, and represents the world's southernmost finding of an Abies species infected by this pathogen. References: (1) R. Martinez Barrera and R. Sanchez Ramirez. Ciencia Forestal 5(26):3, 1980. (2) M. Ruiz-Rodriguez and L. M. Pinzon-Picaseno. Bol. Soc. Bot. Mexico 54:225, 1994.

Determination of the origin of the cold-adapted populations of barnyard grass (Echinochloa crus-galli) in eastern North America: a total-evidence approach using RAPD DNA and DNA sequences

2000 ◽  
Vol 78 (12) ◽  
pp. 1505-1513 ◽  
Author(s):  
Sophie Roy ◽  
Jean-Pierre Simon ◽  
François-Joseph Lapointe
Keyword(s):  
North America ◽  
Dna Sequences ◽  
North American ◽  
Western Europe ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Techniques ◽  
Total Evidence ◽  
Eastern Canada ◽  
Barnyard Grass ◽  
Cold Adapted

This survey attempts to establish the origin of cold-adapted populations of barnyard grass (Echinochloa crus-galli (L.) Beauv.) in North America using molecular techniques, including random amplified polymorphic DNA (RAPD) and two types of sequences: chloroplast intron (trnL (UAA)) and rDNA nuclear spacer (ITS 1). There exists many possible scenarios to explain the origin of E. crus-galli in eastern Canada (Quebec), but we dwelled on two particular hypotheses, which are not mutually exclusive. The first hypothesis stipulates that the populations originated only from Europe, whereas the second implies that native subtropical and warm-temperate populations migrated from the south towards northern regions. To assess the likelihood of these hypotheses, the genetic distance matrices obtained from RAPD markers, nuclear, and chloroplastic sequences were combined and tested against the competing models. A principal coordinate analysis was used to discriminate among populations sampled from three different regions (i.e., Quebec, American east coast, and western Europe) and an analysis of molecular variance (AMOVA) detected a significant genetic structure among these populations (FST = 0.110, p < 0.05). Pairwise comparisons further indicated that European populations were significantly different from all other populations, whereas North American populations were not different from one another. The combined sequences revealed eight different haplotypes. Six populations were characterized by unique haplotypes, while one haplotype was shared by 3 of the 12 North American populations. The last and most common haplotype was observed in 9 of the 18 populations from all three regions. The tests computed thus supported the second hypothesis suggesting that the cold-adapted populations of eastern Canada are probably derived from other North American populations rather than European populations.Key words: AMOVA, RAPD, rDNA, cpDNA, genetic variation, population structure.

scholarly journals First Report of Amylostereum areolatum, the Fungal Symbiont of Sirex noctilio, on Pinus spp. in Canada

Plant Disease ◽  
2008 ◽  
Vol 92 (7) ◽  
pp. 1138-1138 ◽  
Author(s):  
M.-J. Bergeron ◽  
R. C. Hamelin ◽  
I. Leal ◽  
C. Davis ◽  
P. de Groot
Keyword(s):  
Dna Sequences ◽  
North American ◽  
White Rot ◽  
White Rot Fungus ◽  
Malt Extract ◽  
Fungal Symbiont ◽  
Sirex Noctilio ◽  
First Report ◽  
Host Trees ◽  
Pinus Spp

Amylostereum areolatum (Fr.) Boidin (Russulales: Stereaceae) is a white rot fungus that has a symbiotic relationship with several woodwasps including Sirex noctilio Fabricius (Hymenoptera: Siricidae). The vectored fungus together with a phytotoxic mucus, both injected during oviposition by the female S. noctilio, rapidly weaken the host tree, rendering it susceptible to larval development (3). Host trees of A. areolatum include species of Pinus (mainly), Abies, Larix, and Picea and Cryptomeria japonica and Pseudotsuga menziesii (Fungal Databases [online]; USDA). The siricid woodwasp is native to Eurasia and North Africa and has been introduced into New Zealand, Australia, South America, and South Africa (1). In July of 2005, the first established North American population of S. noctilio was reported in Oswego, NY. Prompted by this initial discovery, a trap survey of Ontario counties located along the Canada-U.S. border, close to Upstate New York, was conducted in September and October of 2005. S. noctilio females were captured in four locations in southern Ontario. Two additional locations for S. noctilio were also reported in a survey conducted independently (2). In September and October of 2006, logs of Scots pines showing current Sirex oviposition sites were harvested from the Ontario area bordered by Lakes Huron, Erie, and Ontario to determine the presence of the species-specific fungal symbiont of S. noctilio, A. areolatum. Fungal isolates were obtained by surface sterilizing wood chips showing decay columns followed by incubation at 20°C on 2% malt extract agar. Cultures with morphological characteristics typical of A. areolatum–presence of clamp connections and arthrospores–were used for DNA analysis to confirm species identification. DNA sequences of the internal transcribed spacer (ITS) of the ribosomal RNA gene were queried against the NCBI GenBank database. There was a 99 to 100% match between the ITS sequences from the Ontario isolates and sequences from European and Asian A. areolatum isolates (GenBank Accession Nos. EU249343 and EU249344 versus AF454428, AF506405, AY781245, and AF218389). Matches with A. chailletii (Pers.) Boidin, a native related species, were around 97%. These results confirmed the presence of A. areolatum in the infested material. Cultures were deposited in the National Mycological Herbarium of Canada (DAOM 239280–DAOM 239295). To our knowledge, this represents the first report of A. areolatum in Canada. In its natural range, the insect-fungal complex exists in equilibrium with its host trees and parasites, thus, few negative impacts are observed. However, in the Southern Hemisphere where it has been introduced, it has become a major pest, attacking many important commercial North American species planted as exotics (1). Conifer forests in Canada are threatened by the spread of the S. noctilio/A. areolatum complex, particularly plantations and stands of Pinus banksiana, P. contorta, P. ponderosa, P. resinosa, P. strobus, and P. sylvestris. A survey of Eastern Canada to detect the presence of S. noctilio is on going, and genetics work is being conducted to determine the origin of the introduction of A. areolatum. References: (1) W. M. Ciesla. J. For. 101:18, 2003. (2) P. de Groot et al. Gt. Lakes Entomol. 39:49, 2006. (3) B. Slippers et al. S. Afr. J. Sci. 99:70, 2003.

scholarly journals Progress in Diagnosing Primary Ciliary Dyskinesia: The North American Perspective

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1278
Author(s):  
Michael Glenn O’Connor ◽  
Amjad Horani ◽  
Adam J. Shapiro
Keyword(s):  
Genetic Testing ◽  
North America ◽  
North American ◽  
Primary Ciliary Dyskinesia ◽  
Clinical Phenotype ◽  
The United States ◽  
Diagnostic Process ◽  
The North ◽  
Diagnostic Guideline ◽  
Ciliary Dyskinesia

Primary Ciliary Dyskinesia (PCD) is a rare, under-recognized disease that affects respiratory ciliary function, resulting in chronic oto-sino-pulmonary disease. The PCD clinical phenotype overlaps with other common respiratory conditions and no single diagnostic test detects all forms of PCD. In 2018, PCD experts collaborated with the American Thoracic Society (ATS) to create a clinical diagnostic guideline for patients across North America, specifically considering the local resources and limitations for PCD diagnosis in the United States and Canada. Nasal nitric oxide (nNO) testing is recommended for first-line testing in patients ≥5 years old with a compatible clinical phenotype; however, all low nNO values require confirmation with genetic testing or ciliary electron micrograph (EM) analysis. Furthermore, these guidelines recognize that not all North American patients have access to nNO testing and isolated genetic testing is appropriate in cases with strong clinical PCD phenotypes. For unresolved diagnostic cases, referral to a PCD Foundation accredited center is recommended. The purpose of this narrative review is to provide insight on the North American PCD diagnostic process, to enhance the understanding of and adherence to current guidelines, and to promote collaboration with diagnostic pathways used outside of North America.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 901-910 ◽  
Author(s):  
Joel P. Olfelt ◽  
William A. Freyman
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Phylogenetic Analyses ◽  
Black Hills ◽  
Trnl Intron ◽  
The North ◽  
Alpine Habitats ◽  
Rare And Endangered ◽  
Chloroplast Dna Sequences ◽  
Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

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