Phylogenetic relationships of Neonectria/Cylindrocarpon on Fagus in North AmericaMention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.

2006 ◽  
Vol 84 (9) ◽  
pp. 1417-1433 ◽  
Author(s):  
Lisa A. Castlebury ◽  
Amy Y. Rossman ◽  
Aimee S. Hyten
Keyword(s):  
North America ◽  
Rna Polymerase Ii ◽  
Elongation Factor ◽  
The United States ◽  
Molecular Data ◽  
Specific Information ◽  
Beech Bark Disease ◽  
Separate Species ◽  
Additional Species ◽  
Trade Names

The relationship of two species of Neonectria associated with beech bark canker in North America was evaluated by comparing isolates of these and additional species of the Neonectria coccinea (Pers.:Fr.) Rossman & Samuels group found on Fagus. Gene regions in the translation elongation factor 1-alpha (EF1-α), RNA polymerase II second largest subunit (RPB2), and β-tubulin were sequenced and analyzed. Results indicate that the fungus associated with beech bark disease previously known as Neonectria coccinea var. faginata Lohman et al. (≡ Nectria coccinea (Pers.:Fr.) Fr. var. faginata Lohman et al.) should be recognized as a separate species, Neonectria faginata , distinct from Neonectria coccinea . Neonectria faginata including its anamorphic state, Cylindrocarpon faginatum C. Booth, is known only on Fagus in North America. A second species associated with beech bark disease in North America is Neonectria ditissima (Tul. & C. Tul.) Samuels & Rossman, which can be distinguished morphologically from Neonectria faginata based on ascospore size, conidial size and shape, and colony pigmentation. Morphological and molecular data indicate that Neonectria ditissima represents an older name for Neonectria galligena Bres. Similarly, the anamorphic state of Neonectria ditissima is the older epithet Cylindrocarpon heteronema with Cylindrocarpon willkommii as a synonym. Neonectria ditissima occurs on a variety of hardwood trees in North America and Europe. Neonectria coccinea occurs only on Fagus in Europe. Neonectria major (Wollenw.) Castl. & Rossman is recognized as a species that occurs only on Alnus in Canada (British Columbia), France, Norway, and the United States (Washington). The following nomenclatural changes are proposed: Neonectria faginata comb. and stat. nov., Neonectria fuckeliana comb. nov., Neonectria hederae comb. nov., Neonectria major comb. and stat. nov., and Neonectria punicea comb. nov.

scholarly journals Sub1 associates with Spt5 and influences RNA polymerase II transcription elongation rate

2012 ◽  
Vol 23 (21) ◽  
pp. 4297-4312 ◽  
Author(s):  
Alicia García ◽  
Alejandro Collin ◽  
Olga Calvo
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Molecular Data ◽  
Elongation Rate ◽  
Dependent Manner ◽  
Gene Encoding ◽  
Mrna Metabolism ◽  
Carboxy Terminal

The transcriptional coactivator Sub1 has been implicated in several steps of mRNA metabolism in yeast, such as the activation of transcription, termination, and 3′-end formation. In addition, Sub1 globally regulates RNA polymerase II phosphorylation, and most recently it has been shown that it is a functional component of the preinitiation complex. Here we present evidence that Sub1 plays a significant role in transcription elongation by RNA polymerase II (RNAPII). We show that SUB1 genetically interacts with the gene encoding the elongation factor Spt5, that Sub1 influences Spt5 phosphorylation of the carboxy-terminal domain of RNAPII largest subunit by the kinase Bur1, and that both Sub1 and Spt5 copurify in the same complex, likely during early transcription elongation. Indeed, our data indicate that Sub1 influences Spt5–Rpb1 interaction. In addition, biochemical and molecular data show that Sub1 influences transcription elongation of constitutive and inducible genes and associates with coding regions in a transcription-dependent manner. Taken together, our results indicate that Sub1 associates with Spt5 and influences Spt5–Rpb1 complex levels and consequently transcription elongation rate.

Morphological characters and phylogenetic analysis reveal a new species of Phellinus with hooked hymenial setae from Vietnam

Phytotaxa ◽  
2018 ◽  
Vol 356 (1) ◽  
pp. 91 ◽  
Author(s):  
LIN ZHU ◽  
XING JI ◽  
JING SI ◽  
BAO-KAI CUI
Keyword(s):  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characters ◽  
Molecular Data ◽  
Translation Elongation ◽  
The Status ◽  
Large Subunit Rdna ◽  
Elongation Factor 1 ◽  
A New Species

Phellinus vietnamensis sp. nov. is described from Vietnam based on morphological characters and molecular data. Morphologically, it is characterized by perennial, pileate basidiomata, a dimitic hyphal system, hooked hymenial setae, and colorless, broadly subglobose to ovoid, thick-walled basidiospores 5.5–6 × 4.8–5.2 μm. Phylogenetically, the status of Phellinus vietnamensis is strongly supported based on sequences of the nuclear internal transcribed spacer (ITS) regions, the translation elongation factor 1-α gene (EF1-α) nuclear large subunit rDNA (nrLSU) and the second largest subunits of RNA polymerase II (RPB2).

A new species and a new combination in the genus Aureoboletus (Boletales, Boletaceae) from southern China

Phytotaxa ◽  
2015 ◽  
Vol 222 (2) ◽  
pp. 129 ◽  
Author(s):  
Nian-Kai Zeng ◽  
MING ZHANG ◽  
ZHI-QUN Liang
Keyword(s):  
Rna Polymerase Ii ◽  
Southern China ◽  
Large Subunit ◽  
Line Drawing ◽  
Elongation Factor ◽  
Molecular Data ◽  
New Combination ◽  
Translation Elongation ◽  
Microscopic Features ◽  
A New Species

Two lineages of Aureoboletus (Boletales, Boletaceae) from southern China were revealed by using molecular data based on combined dataset of the nuclear ribosomal large subunit RNA (nrLSU), the translation elongation factor apha-1 (tef1-a) and the largest subunit of RNA polymerase II (rpb1). One of them corresponds with the previous morphology-based taxon, viz. Boletellus longicollis, another one is different from those taxa described based on morphological features. And, thus, Auroboletus clavatus sp. nov. and A. longicollis comb. nov. were proposed. A detailed description, colour photos of fresh basidiomata, and a line-drawing of microscopic features of the two taxa were provided.

scholarly journals Trichothecene Genotype of Fusarium graminearum Isolates from Soybean (Glycine max) Seedling and Root Diseases in the United States

Plant Disease ◽  
2014 ◽  
Vol 98 (7) ◽  
pp. 1012-1012 ◽  
Author(s):  
M. L. Ellis ◽  
G. P. Munkvold
Keyword(s):  
United States ◽  
North America ◽  
Fusarium Graminearum ◽  
Root Rot ◽  
Elongation Factor ◽  
Host Shift ◽  
The United States ◽  
Sensu Stricto ◽  
Head Blight ◽  
The Third

Fusarium graminearum is an economically important pathogen that causes Fusarium head blight of wheat, barley, and oat, and Gibberella ear and stalk rot of maize. More recently, F. graminearum was reported as a soybean seedling and root pathogen in North America (1,5), causing seed decay, damping-off, and brown to reddish-brown root rot symptoms. Type B trichothecene mycotoxins are commonly produced by F. graminearum, which can be categorized into three trichothecene genotypes; those that produce 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), or nivalenol (NIV). The 15-ADON genotype is dominant in populations from small grains and maize in North America (4), but the 3-ADON genotype has recently been found (4). F. graminearum was known as a pathogen of wheat and maize in North America for over a century before it was reported as a soybean pathogen. Therefore, we hypothesized that recent reports on soybean could be associated with the appearance of the 3-ADON genotype. The objective of this research was to determine the trichothecene genotype of F. graminearum isolates from soybean in the United States. Thirty-eight isolates from soybean were evaluated. Twenty-seven isolates came from a 3-year survey for Fusarium root rot from 2007 to 2009 in Iowa. Other isolates (Ahmad Fakhoury, Southern Illinois University, Carbondale) were collected from soybean seedlings during a multi-state survey in 2012, and included three isolates from Illinois, three from Indiana, and five from Nebraska. Species identification and lineage of F. graminearum were confirmed by sequencing the translation elongation factor gene (EF1-α) using EF-1H and EF-2T primers. A maximum likelihood analysis of the EF1-α, including voucher strains from nine lineages of F. graminearum (2), placed all 38 isolates into lineage 7, F. graminearum sensu stricto (representative GenBank accessions KJ415349 to KJ415352). To determine the trichothecene genotype of each isolate we used three multiplex PCR assays. The first two assays targeted a portion of trichothecene biosynthesis genes Tri3 and Tri12 (4), while the third assay targeted portions of the Tri3, Tri5, and Tri7 genes (3). The PCR for the first two assays was conducted as described by Ward et al. (4) using four sets of primers: 3CON, 3NA, 3D15A, and 3D3A; and 12CON, 12NF, 12-15F, and 12-3F for the Tri3 and Tri12 genes, respectively. The PCR for the third assay was conducted as described by Quarta et al. (3) using the following primers: Tri3F971, Tri3F1325, Tri3R1679, Tri7F340, Tri7R965, 3551H, and 4056H. The amplification products were analyzed by gel electrophoresis. All 38 isolates produced amplicons consistent with the 15-ADON genotype; ~610 and 670 bp for the Tri3 and Tri12 genes, respectively (4), and two amplicons of ~708 and 525 bp for the Tri3/Tri5 genes (3). Our results indicated that the dominant trichothecene genotype among isolates of F. graminearum from soybean is 15-ADON, and the introduction of 3-ADON isolates does not explain the recent host shift of F. graminearum to soybean in North America. To our knowledge, this is the first assessment of trichothecene genotypes in F. graminearum populations from soybean from the United States. References: (1) K. E. Broders et al. Plant Dis. 91:1155, 2007. (2) K. O'Donnell et al. Fungal Gen. Biol. 41:600, 2004. (3) A. Quarta et al. FEMS Microbiol. Lett. 259:7, 2006. (4) T. D. Ward et al. Fungal Gen. Biol. 45:473, 2008. (5) A. G. Zue et al. Can. J. Plant Pathol. 29:35, 2007.

scholarly journals Four new species in the Tremella fibulifera complex (Tremellales, Basidiomycota)

MycoKeys ◽  
2021 ◽  
Vol 82 ◽  
pp. 33-56
Author(s):  
Long-Fei Fan ◽  
Renato Lúcio Mendes Alvarenga ◽  
Tatiana Baptista Gibertoni ◽  
Fang Wu ◽  
Yu-Cheng Dai
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Small Subunit ◽  
Molecular Evidence ◽  
Rrna Gene

Samples of species close to Tremella fibulifera from China and Brazil are studied, and T. fibulifera is confirmed as a species complex including nine species. Five known species (T. cheejenii, T. fibulifera s.s., T. “neofibulifera”, T. lloydiae-candidae and T. olens) and four new species (T. australe, T. guangxiensis, T. latispora and T. subfibulifera) in the complex are recognized based on morphological characteristics, molecular evidence, and geographic distribution. Sequences of eight species of the complex were included in the phylogenetic analyses because T. olens lacks molecular data. The phylogenetic analyses were performed by a combined sequence dataset of the internal transcribed spacer (ITS) and the partial nuclear large subunit rDNA (nLSU), and a combined sequence dataset of the ITS, partial nLSU, the small subunit mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α (TEF1), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). The eight species formed eight independent lineages with robust support in phylogenies based on both datasets. Illustrated description of the six species including Tremella fibulifera s.s., T. “neofibulifera” and four new species, and discussions with their related species, are provided. A table of the comparison of the important characteristics of nine species in the T. fibulifera complex and a key to the whitish species in Tremella s.s. are provided.

scholarly journals Characterization of Fusarium and Neocosmospora Species Associated With Crown Rot and Stem Canker of Pistachio Rootstocks in California

Plant Disease ◽  
2019 ◽  
Vol 103 (8) ◽  
pp. 1931-1939 ◽  
Author(s):  
Maria Crespo ◽  
Daniel P. Lawrence ◽  
Mohamed T. Nouri ◽  
David A. Doll ◽  
Florent P. Trouillas
Keyword(s):  
Rna Polymerase Ii ◽  
Fusarium Species ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Stem Canker ◽  
The United States ◽  
Fungal Species ◽  
Crown Rot ◽  
Pathogenicity Tests ◽  
Pistachio Trees

California produces 99.1% of pistachios grown in the United States, and diseases affecting pistachio rootstocks represent a constant challenge to the industry. Field surveys of fungi associated with pistachio rootstocks with symptoms of crown rot and stem canker in three central California counties followed by phylogenetic analyses of translation elongation factor 1-α and second largest subunit of RNA polymerase II gene fragments identified three Fusarium species (Fusarium equiseti, Fusarium oxysporum, and Fusarium proliferatum) and two Neocosmospora species (Neocosmospora falciformis and Neocosmospora solani). F. oxysporum and N. falciformis were the fungal species most frequently recovered from symptomatic pistachio trees. Inoculations of detached twigs of cultivar Kerman pistachio Pioneer Gold I and clonal University of California, Berkeley I (UCBI) rootstocks showed that all five species could colonize pistachio wood and cause vascular discolorations. Pathogenicity tests in potted pistachio trees completed Koch’s postulates and confirmed that F. oxysporum, F. proliferatum, N. falciformis, and N. solani were capable of producing rot and discoloration in stems of clonal UCBI rootstocks, the most widely planted pistachio rootstock in California. To our knowledge, this study is the first to present insights into the biodiversity and biology of Fusarium and Neocosmospora species associated with pistachio trees in California.

scholarly journals From Phenology and Habitat Preferences to Climate Change: Importance of Citizen Science in Studying Insect Ecology in the Continental Scale with American Red Flat Bark Beetle, Cucujus clavipes, as a Model Species

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 369
Author(s):  
Radomir Jaskuła ◽  
Marta Kolanowska ◽  
Marek Michalski ◽  
Axel Schwerk
Keyword(s):  
Climate Change ◽  
North America ◽  
Bark Beetle ◽  
Habitat Preferences ◽  
Molecular Data ◽  
Negative Influence ◽  
Future Climate Change ◽  
Separate Species ◽  
Continental Scale ◽  
Body Coloration

The American red flat bark beetle, Cucujus clavipes, is a wide distributed saproxylic species divided into two subspecies: ssp. clavipes restricted to eastern regions of North America and ssp. puniceus occurring only in western regions of this continent. Unique morphological features, including body shape and body coloration, make this species easy to recognize even for amateurs. Surprisingly, except some studies focused on physiological adaptations of the species, the ecology of C. clavipes was almost unstudied. Based on over 500 records collected by citizen scientists and deposited in the iNaturalist data base, we studied phenological activity of adult beetles, habitat preferences and impact of future climate change for both subspecies separately. The results clearly show that spp. clavipes and ssp. puniceus can be characterized by differences in phenology and macrohabitat preferences, and their ranges do not overlap at any point. Spp. clavipes is found as more opportunistic taxon occurring in different forests as well as in urban and agricultural areas with tree vegetation always in elevations below 500 m, while elevational distribution of ssp. puniceus covers areas up to 2300 m, and the beetle was observed mainly in forested areas. Moreover, we expect that climate warming will have negative influence on both subspecies with the possible loss of proper niches at level even up to 47–70% of their actual ranges during next few decades. As the species is actually recognized as unthreatened and always co-occurs with many other species, we suggest, because of its expected future habitat loss, to pay more attention to conservationists for possible negative changes in saproxylic insects and/or forest fauna in North America. In addition, as our results clearly show that both subspecies of C. clavipes differ ecologically, which strongly supports earlier significant morphological and physiological differences noted between them, we suggest that their taxonomical status should be verified by molecular data, because very probably they represent separate species.

Agrilus Curtis (Coleoptera: Buprestidae) of the Baja California peninsula, México

Zootaxa ◽  
2011 ◽  
Vol 2805 (1) ◽  
pp. 36 ◽  
Author(s):  
HENRY A. HESPENHEIDE ◽  
RICHARD L. WESTCOTT ◽  
CHARLES L. BELLAMY
Keyword(s):  
United States ◽  
New Species ◽  
Baja California ◽  
The United States ◽  
Baja California Peninsula ◽  
Separate Species ◽  
Additional Species ◽  
First Time ◽  
Agrilus Auroguttatus

The genus Agrilus Curtis 1825 is reviewed for the Baja California peninsula of Mexico. Of the 25 species included, 11 are recorded here for the first time and four are previously unknown to science and described as new: Agrilus barri new species, A. interstitialis new species, A. vescivittatus new species, and A. argythamniae new species. Four additional species may be expected based on their occurrence just north of the border in the United States. Upon further study Agrilus auroguttatus Schaeffer 1905, revalidated status, is judged to be a separate species from A. coxalis Waterhouse 1889. Figures and a key to known and expected species are given, as well as a summary checklist.

scholarly journals Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Wen-Tao Qin ◽  
Wen-Ying Zhuang
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Elongation Factor ◽  
Molecular Data ◽  
Translation Elongation ◽  
Elongation Factor 1 Alpha ◽  
Trichoderma Fungi ◽  
Close Relatives ◽  
Subunit B ◽  
Elongation Factor 1

Abstract More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed.

Separation of Pleuroxus laevis Sars, 1861 from two resembling species in North America: Pleuroxus straminius Birge, 1879 and Pleuroxus chiangi n.sp. (Cladocera, Chydoridae)

1988 ◽  
Vol 66 (11) ◽  
pp. 2534-2563 ◽  
Author(s):  
David G. Frey
Keyword(s):  
North America ◽  
Atlantic Coast ◽  
Relative Size ◽  
The United States ◽  
Shell Shape ◽  
Eastern Canada ◽  
Separate Species ◽  
Closely Related Species ◽  
The North ◽  
Surface Ornamentation

E. A. Birge, in his Ph.D. dissertation (1878. Harvard University, Cambridge, MA) and in his first published paper (E. A. Birge. 1879. Trans. Wis. Acad. Sci. Arts. Lett. 4: 77–109), described a species of Pleuroxus from North America and named it P. straminius, then later (E. A. Birge. 1893. Trans. Wis. Acad. Sci. Arts. Lett. 9: 275–317) decided the organism was the same as P. laevis of Scandinavia and hence gave it that name, or rather the invalid, newer name P. hastatus. Detailed study of these two taxa has shown that they are completely different from each other in size, shape, surface ornamentation, nature and color of the carapace, structure of the posterior-ventral corner of the shell, shape and denticulation of the postabdomen, and especially armament of the male postabdomen, that of P. straminius having essentially the same denticulation as the female, whereas in P. laevis all of the marginal denticles are replaced by oblique short rows of spines. Perhaps more significant is the occurrence of a second species in North America, Pleuroxus chiangi n.sp., which is much more closely related to P. laevis than is P. straminius. It differs somewhat vaguely in the relative size of various parts, but it also differs in a number of specific characters, all of which demonstrate that it is a valid separate species. Thus, the posterior-ventral angle of the shell is rounded, with the shell tooth some distance anterior and with several setae immediately posterior being long and projecting well beyond the margin; the postanal portion of the postabdomen is shorter and has about two fewer denticles; and, most important, the male postabdomen retains the two large distalmost denticles and has the oblique rows of setae substituting for the others. Pleuroxus straminius is widely distributed in glaciated North America from Newfoundland to northern Wisconsin and Minnesota, then south along the Atlantic Coast into northern Florida. One suspects that because of species differences already demonstrated between northern and southern populations of Eurycercus and of Pleuroxus denticulatus, P. straminius might also be so differentiated. However, no decision can be made without having males and ephippial females from the southern populations. Pleuroxus chiangi presently seems much less frequent and less abundant than P. straminius. It occurs from Nova Scotia westward to British Columbia, including northern Wisconsin and possibly northern Minnesota, and northward into the Northwest Territories. It seems similar to a number of species, such as Alonopsis americana and Chydorus canadensis, whose distributions barely reach the United States at all but which are well distributed northward in eastern Canada. We need many more data on the occurrence of various taxa in the north. Thus, here is still another example of noncosmopolitanism in the chydorids. The presence of closely related species in North America and Europe might have derived vicariously from the splitting of North America from Europe as the Atlantic Ocean developed. The other species, P. straminius, does not seem to have any counterpart in Europe, although possibly P. sinkiangensis of China is related to it. This and other taxa presently called P. laevis must be studied to work out the degrees of relationship and to develop ideas as to when and how the species evolved. Neotypes have been selected for P. laevis and for P. straminius. These and diverse samples of all three taxa have been deposited in major museums in North America and Europe.

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