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1.
The translation elongation factor-1 alpha (EF-1α) gene was used to examine the phylogenetic relationships among 30 previously
characterized isolates representing ten North American Armillaria species: A. solidipes (=A. ostoyae), A. gemina, A. calvescens, A. sinapina, A. mellea, A. gallica, A. nabsnona, North American biological species X, A. cepistipes, and A. tabescens. The phylogenetic relationships revealed clear separation of all ten North American Armillaria species, with the exception of one A. gallica isolate that perhaps represents an unnamed cryptic species. These results indicate that the EF-1α gene could potentially
serve as a diagnostic tool for distinguishing among currently recognized North American biological species of Armillaria. 相似文献
2.
Sarah L. Dodd Elke Lieckfeldt Priscila Chaverri Barrie E. Overton Gary J. Samuels 《Mycological Progress》2002,1(4):409-428
Hypocrea patella is reevaluated. Its Trichoderma anamorph is described and the phylogenetic position of the species is determined through sequences of the ITS regions of
rDNA. It is sister to a clade that includes Trichoderma longibrachiatum/H. schweinitzii. Hypocrea patella f. tropica is accepted for a Costa Rican collection. Hypocrea neorufa and its Trichoderma anamorph are described. Its phylogenetic position is determined by sequences of the ITS region of rDNA and the protein-coding
translation-elongation factor (EF-1α). It is derived from within a clade that includes T. viride/H. rufa, T. atroviride/H. atroviridis, T. koningii/H. koningii and T. asperellum.
Deceased August 2002. 相似文献
3.
Oumi Nishi Keiichi Hasegawa Kazuhiro Iiyama Chisa Yasunaga-Aoki Susumu Shimizu 《Applied Entomology and Zoology》2011,46(3):301-309
As a result of analyzing the internal transcribed spacer (ITS) and 5′ end of the EF-1α sequence of 145 isolates of Metarhizium spp. isolated from soil in Japan using selective agar medium, eight species were identified. ITS sequence analysis divided
the isolates into three clades. Two were identified as M. flavoviride var. pemphigi and M. lepidiotae, respectively. EF-1α sequence analysis identified the other clades as six species: M. anisopliae, M. brunneum, M. guizhouense, M. majus, M. pingshaense and M. robertisii. The distribution of M. flavoviride var. pemphigi was restricted to forest or wood soil, and conidial sizes of M. guizhouense and M. majus were incongruent with the phylogeny based on the sequence of the 5′ end of EF-1α. 相似文献
4.
M. B. Pildain M. P. A. Coetzee M. Rajchenberg R. H. Petersen M. J. Wingfield B. D. Wingfield 《Mycological Progress》2009,8(3):181-194
A number of species in the plant pathogen genus Armillaria are known from South America where they cause root rot disease on a wide variety of hosts. Knowledge pertaining to phylogenetic
relationships of these species with those of other Armillaria species is almost non-existent. In addition, very few cultures representing these species are available, making DNA-based
phylogenetic analyses impossible. The aim of this study was to characterise a collection of Armillaria isolates from the Patagonian Andes using DNA sequences and to determine their phylogenetic relationships with other Armillaria species. DNA sequences were obtained from the internal transcribed regions (ITS1, 5.8S and ITS4) and ribosomal large subunit
(LSU) gene and used in phylogenetic analyses. Phylogenetic trees generated from the sequences separated the Armillaria isolates into four lineages. Lineages I and II represented A. novae-zelandiae and A. luteobubalina, respectively. Isolates belonging to A. novae-zelandiae from Malaysia, New Zealand, Australia and South America showed considerable intra-clade sub-structure. Lineages III and IV
are probably distinct species and are most closely related to A. hinnulea and an unnamed species isolated from New Zealand and Kenya. This is the first comprehensive study of the phylogenetic relationships
of Armillaria species from Patagonia and it provides a foundation for future research in this region. 相似文献
5.
Dirk Redecker Philipp Raab Fritz Oehl Francisco J. Camacho Regis Courtecuisse 《Mycological Progress》2007,6(1):35-44
In the early times of taxonomy of arbuscular mycorrhizal fungi (Glomeromycota), exclusively sporocarpic species were described.
Since then the focus has mainly shifted to species forming spores singly. For many of the sporocarpic species, no molecular
data have been made available, and their phylogenetic position has remained unclear. We obtained small subunit ribosomal rDNA
and internal transcribed spacer data from specimens of glomeromycotan sporocarps from tropical areas that were assigned to
three morphospecies. The complete sequence of the 18S small rDNA subunit sequence, internal transcribed spacers (ITS) 1 and
2 and 5.8S rDNA subunit, was determined from a sporocarp of Glomus fulvum. Partial sequences of the small subunit and the other regions were obtained from Glomus pulvinatum and the newly described species Glomus megalocarpum. Molecular phylogenetic analyses placed all species analyzed as a monophyletic sister group to the Diversispora spurca/Glomus versiforme clade group (“Glomus group C”) within the Diversisporales. The phylogenetic divergence from other known species suggests that this clade may constitute
a new genus. These findings will have important consequences for taxon definition in the Diversisporales. They will facilitate
identification of these fungi using rDNA sequences within colonized roots or the environment.
Taxonomic novelties: Glomus megalocarpum D. Redecker 相似文献
6.
Tomohiko Kiyuna Kwang-Deuk An Rika Kigawa Chie Sano Sadatoshi Miura Junta Sugiyama 《Mycoscience》2008,49(5):298-311
In an effort to clarify the cause of the deterioration of the colorfully painted murals that adorn the inner walls of the
small stone chambers in the Takamatsuzuka and Kitora Tumuli in Japan, we enumerated the fungi that were isolated from moldy
spots on the plaster walls collected between May 2004 and April 2005. The 262 fungal isolates from 79 samples of both tumuli
were identified as approximately 100 species based on their phenotypic characters. Fusarium, Trichoderma, and Penicillium species were the predominant colonizers in the stone chamber interior and adjacent areas of both tumuli. In addition to the
28S phylogeny, neighbor-joining and Bayesian phylogenies of partial EF-1-alpha gene sequences revealed 24 genetically diverse fusaria in the Takamatsuzuka and Kitora Tumuli. Most of the fusaria
were nested in clade 3 of the Fusarium solani species complex (FSSC); however, a few isolates were members of the F. oxysporum species complex (FOSC) clade or the F. avenaceum/F. tricinctum species complex clade. The FSSC isolates were compared with those detected in the Lascaux cave in France. In addition, a
partial EF-1α gene phylogeny indicated that 13 Trichoderma isolates clustered in the Harzianum-Virens clade and 5 isolates in the Viride clade or Trichoderma sect. Longibrachiatum. Our analyses suggest that most of the fungi recovered from both tumuli are typically soil dwellers.
First two authors contributed equally to this work 相似文献
7.
Ayako Yamamoto Tetsuo Hashimoto Emiko Asaga Masami Hasegawa Nobuichi Goto 《Journal of molecular evolution》1997,44(1):98-105
Major parts of amino-acid-coding regions of elongation factor (EF)-1α and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones
from each of the products of the EF-1α and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1α
coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of
the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long,
and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1α and EF-2 gene per chromosome were
estimated as four and two, respectively.
The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1α and 761 and 762 residues
from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1αs and EF-2s, respectively.
The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1α and EF-2 data sets. The EF-1α analysis suggested that
three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the
divergence of T. tenax to be immediately next to G. lamblia.
Received: 15 February 1996 / Accepted: 28 June 1996 相似文献
8.
Morphology and phylogeny of <Emphasis Type="Italic">Botryosphaeria dothidea</Emphasis> causing fruit rot of olives 总被引:1,自引:0,他引:1
The taxonomic position of the causal agent of fruit rot of olives was determined from fresh collections of the fungus from central Greece. In culture it formed two types of conidia, namely fusiform, hyaline, aseptate conidia typical of the genus Fusicoccum, and dark-walled, ovoid, ellipsoid or fusiform, 1–2 septate conidia that are not typically observed in Fusicoccum. A phylogenetic analysis based on ITS and EF1- sequences placed the fungus within the same clade as Fusicoccum aesculi, which is the anamorph of Botryosphaeria dothidea, and the type of the genus Fusicoccum. 相似文献
9.
The internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were amplified and sequenced from 19 samples representing
all species of the genus Mercurialis and two outgroup species, Ricinus communis and Acalypha hispida. The length of ITS1 in the ingroups ranged from 223 to 246 bp and ITS2 from 210 to 218 bp. Sequence divergence between pairs
of species ranged from 1.15% to 25.88% among the ingroup species in the combined data of ITS1 and ITS2. Heuristic phylogenetic
analyses using Fitch parsimony on the combined data of ITS1 and ITS2 with gaps treated as missing generated 45 equally parsimonious
trees. The strict consensus tree was principally concordant with morphological classification. Within the genus, the ITS sequences
recognised two main infrageneric clades: the M. perennis complex including three Eurasian stoloniferous species (M.␣leiocarpa, M. ovata and M. perennis) and the western Mediterranean group including eight both annual and perennial species. Of the western Mediterranean clade,
the annual and perennial species grouped respectively into two different groups, and the annual life form is revealed as a
synapomorphic character derived from perennial, whereas in the Eurasian clade ITS phylogeny suggested M. leiocarpa as basal clade sister to M.␣perennis and M. ovata. ITS phylogeny failed to resolve the relationships among the different cytotypes of M. ovata and M. perennis. ITS phylogeny also suggested rapid karyotypic evolution for the genus. The karyotypic divergence among the perennial species
of western Mediterranean region did not corroborate the nucleotide sequence divergence among the species. Optimisation of
chromosome numbers onto the ITS phylogeny suggested x=8 to be the ancestral basic chromosome number of the genus. ITS phylogeny
confirmed that the androdioecy of M. ambigua is derived from dioecy. The nucleotide heterozygosity and additivity in ITS sequences clearly confirm the interspecific hybridisation
in the genus Mercurialis.
Received December 22, 2001; accepted May 21, 2002?Published online: November 14, 2002
Address of the authors: Martin Kr?henbühl, Yong-Ming Yuan (correspondence) and Philippe Küpfer, Institut de Botanique, Laboratoire
de botanique évolutive, Université de Neuchatel, Emile-Argand 11, CH-2007 Neuchatel, Suisse. (e-mail: yong-ming.yuan@unine.ch) 相似文献
10.
Two new species of the fungal genus Trichoderma, Trichoderma compactum and Trichoderma yunnanense, isolated from rhizosphere of tobacco in Yunnan Province, China are described based on morphological characters and phylogenetic
analyses of nucleotide sequences. Our DNA sequences included the internal transcribed spacer (ITS) regions of the rDNA cluster
(ITS1 and ITS2), and partial sequences of the translation elongation factor 1-alpha (tef1) and a fragment of the gene coding for endochitinase 42 (ech42). The analyses show that T. compactum belongs to the Harzianum clade, and T. yunnanense belongs to the Hamatum clade. 相似文献
11.
The three chthamalids Chthamalus stellatus , C. montagui and Euraphia depressa are common inhabitants of the intertidal zone in the Eastern Atlantic, Mediterranean Sea and Black Sea. In this study, we investigated the occurrence of these barnacles in a wide range of their distribution. Population divergences of these two species have been inferred using three molecular markers — internal transcribed spacer (ITS), elongation factor 1α (EF-1α) and cytochrome oxidase subunit I (COI). ITS sequences of C. stellatus were identical throughout the species range, whereas ITS sequences of C. montagui indicated that the Black Sea and Mediterranean populations are isolated from the Atlantic population. The COI and EF-1α sequences were the most variable and informative. They indicated a high genetic divergence between Atlantic, Mediterranean and Black Sea populations for C. montagui . In addition significant genetic structure was found among the populations of C. stellatus based on EF-1α but not COI. Interestingly, our molecular dating analysis correlated the pattern of diversification in C. montagui to major geological changes that occurred in the Mediterranean during the end of the Messinian and Pleiocene periods. We suggest that palaeohistory shaped the divergences between Chthamalus populations that have probably been maintained by current hydrographic conditions. Finally, COI phylogenetic analysis placed the genus Euraphia within the Chthamalus clade, suggesting the need for a taxonomic revision of Euraphia . This study represents the most detailed phylogeographical analysis of intertidal Mediterranean species to date, and shows that geological events have strongly shaped the current diversity pattern of this fauna. 相似文献
12.
To determine a suitable DNA barcode for the genus Neonectria, the internal transcribed spacer rDNA, β-tubulin, EF-1α, and RPB2 genes were selected as candidate markers. A total of 205
sequences from 19 species of the genus were analyzed. Intra- and inter-specific divergences and the ease of nucleotide sequence
acquisition were treated as criteria to evaluate the feasibility of a DNA barcode. Our results indicated that any single gene
among the candidate markers failed to serve as a successful barcode, while the combination of the partial EF-1α, and RPB2
genes recognized all species tested. We tentatively propose the combined partial EF-1α and RPB2 genes as a DNA barcode for
the genus. During this study, two cryptic species were discovered, based on the combined data of morphology and DNA barcode
information. We described and named these two new species N. ditissimopsis and N. microconidia. 相似文献
13.
Meherun Naher Keiichi Motohash Hideki Watanabe Yoshiaki Chikuo Masako Senda Haruhisa Suga Clive Brasier Koji Kageyama 《Mycological Progress》2011,10(1):21-31
A new species of Phytophthora was isolated from stem and root rot of chrysanthemum in the Gifu and Toyama prefectures of Japan. The species differs from
other Phytophthora species morphologically, and is characterized by nonpapillate, noncaducous sporangia with internal proliferation, formation
of both hyphal swellings and chlamydospores, homothallic nature, distinctive intercalary antheridia, and funnel-shaped oogonia.
The new species can grow even at 35°C, with an optimum growth temperature of 30°C in V8 juice agar medium. In phylogenetic
analyses based on five nuclear regions (LSU rDNA; genes for translation elongation factor 1α, β-tubulin, 60 S ribosomal protein
L10, and heat shock protein 90), the isolates formed a monophyletic clade. Although the rDNA ITS region shows a high resolution
and has proven particularly useful for the separation of Phytophthora species, it was difficult to align the sequences for phylogenetic analysis. Therefore, ITS region analysis using related
species as defined by the multigene phylogeny was performed, and the topology of the resulting tree also revealed a monophyletic
clade formed by the isolates of the species. The morphological characteristics and phylogenetic relationships indicate that
the isolates represent a new species, Phytophthora chrysanthemi sp. nov. In pathogenicity tests, chrysanthemum plants inoculated with the isolates developed lesions on stems and roots within
3 days, and the symptoms resembled the ones originally observed. Finally, the pathogen’s identity was confirmed by re-isolation
from lesions of infected plants. 相似文献
14.
The phylogeny of the cetrarioid lichens with bifusiform spermatia and dorsiventral thalli which contain usnic acid is reanalysed
using three parts of the genome, ITS rDNA, β-tubulin and GAPDH sequences. Molecular data from five cetrarioid species are
presented for the first time, and 13 new sequences are combined with sequences from the gene bank to delimit the genus Nephromopsis. A monophyletic clade of Nephromopsis, Tuckneraria, ‘Cetraria’ leucostigma and ‘C.’ melaloma is identified and circumscribed as one genus, Nephromopsis, which now includes 19 species. Four new combinations are presented. A key to the species is provided. 相似文献
15.
The ribosomal protection proteins (RPPs) mediate the resistance to tetracycline (TC) in Gram-positive and Gram-negative bacteria.
The RPPs display sequence similarity to translation elongation factors, EF-G/EF-2 and EF-Tu/EF-1α. To determine the evolutionary
origin of the RPPs, we constructed a composite phylogenetic tree of the RPPs, EF-G/EF-2 and EF-Tu/EF-1α. This tree includes
two universal trees for the EF-G/EF-2 and EF-Tu/EF-1α, which form clusters corresponding to the respective two groups of proteins
from three superkingdoms. The cluster of RPPs was placed at a point between the EF-G/EF-2 and EF-Tu/EF-1α clusters. The branch
length (substitutions/site) between the node for the RPP cluster and the primary divergence of the RPPs was statistically
shorter than that between the node for this cluster and the primary divergence in the EF-G/EF-2 cluster. This indicates that
the RPPs derived through duplication and divergence of the ancient GTPase before the divergence of the three superkingdoms.
Furthermore, this suggests the RPPs’ extant function occurred before the streptomycetes that include the TC-producing strains.
Therefore, the RPPs evolved independent of the presence of TCs and serve a function other than antibiotic resistance. The
RPPs may provide ribosomal protection against other chemical substances in the environment.
Reviewing
Editor: Dr. Margaret Riley
Takeshi Kobayashi, Lisa Nonaka have contributed significantly to the research and preparation of this article. 相似文献
16.
We describe a new cliff-dwelling species within Sonchus (Asteraceae): Sonchus boulosii and analyze its systematic position and evolutionary significance; in addition, we provide a key to the species of Sonchus in Morocco. Both morphological and ecological characteristics suggest a close relationship of S. boulosii with taxa of section Pustulati. However, ITS nrDNA and cpDNA matK markers indicate its uncertain position within the genus, but clear genetic differentiation from the remaining major clades. ITS phylogenetic trees show that likely evolutionary shifts to rocky habitat took place at least five times within genus Sonchus and that sect. Pustulati and S. boulosii clades have a clearly independent evolutionary origin. We postulate that the strong resemblance of S. boulosii to other rocky species reflects a phenomenon of homoplasy, probably driven by parallel evolutionary adaptations to the severe ecological constraints of its cliff face habitat. Therefore, a new section is also described, which includes S. boulosii as its sole representative: section Pulvinati. According to phylogenetic trees, the new clade may share its common ancestor with the clade comprising sections Maritimi and Arvenses, from which it is widely divergent in morphology and ecology, with the exception of Sonchus novae-zelandiae. However, the latter is a derived taxon, with high level of polyploidy unlike S. boulosii that shows 2n?=?18, basal chromosome number of the genus. Since sections Pulvinati and Pustulati seem to be quite old in Sonchus, we also hypothesize that some similarities, such as fruit morphology, may reflect the persistence of some primitive characteristics. 相似文献
17.
O. V. Kalyuzhnaya A. G. Krasko V. A. Grebenyuk V. B. Itskovich N. A. Semiturkina I. S. Solovarov W. E. G. Mueller S. I. Belikov 《Molecular Biology》2011,45(4):567-575
Silicateins found in spicules of siliceous sponges are proteins that take part in biogenic silica precipitation and determine
the morphological features of spicules. The exon-intron structure of the genes encoding four silicatein-α isoforms (−α1, −α2,
−α3, and −α4) from an endemic Baikalian sponge Lubomirskia baicalensis was studied. For eight sponge species, including both cosmopolitan (Spongilla lacustris, Ephydatia muelleri, E. fluviatilis) and endemic Baikalian (L. baicalensis, L. incrustans, Baikalospongia intermedia, B. fungiformis, Sw. papyracea) species, seventeen partial sequences of different silicatein isoform genes were determined. It was shown that cosmopolitan
and endemic Baikalian sponges differ from each other in gene structure, in particular, in intron length. Among Baikalian sponges,
silicatein-α1 genes had the highest variation of intron length, and silicatein-α4 genes were the most conservative. A phylogenetic
analysis based on amino acid sequences of different silicatein isoforms identified four distinct clusters within the freshwater
sponge clade. An analysis based on exon-intron gene sequences enables discrimination between different sponge species within
the clusters. 相似文献
18.
Nicolas Puillandre Maren Watkins Baldomero M. Olivera 《Journal of molecular evolution》2010,70(2):190-202
A remarkable diversity of venom peptides is expressed in the genus Conus (known as “conotoxins” or “conopeptides”). Between 50 and 200 different venom peptides can be found in a single Conus species, each having its own complement of peptides. Conopeptides are encoded by a few gene superfamilies; here we analyze
the evolution of the A-superfamily in a fish-hunting species clade, Pionoconus. More than 90 conopeptide sequences from 11 different Conus species were used to build a phylogenetic tree. Comparison with a species tree based on standard genes reveals multiple gene
duplication events, some of which took place before the Pionoconus radiation. By analysing several A-conopeptides from other Conus species recorded in GenBank, we date the major duplication events after the divergence between fish-hunting and non-fish-hunting
species. Furthermore, likelihood approaches revealed strong positive selection; the magnitude depends on which A-conopeptide
lineage and amino-acid locus is analyzed. The four major A-conopeptide clades defined are consistent with the current division
of the superfamily into families and subfamilies based on the Cys pattern. The function of three of these clades (the κA-family,
the α4/7-subfamily, and α3/5-subfamily) has previously been characterized. The function of the remaining clade, corresponding
to the α4/4-subfamily, has not been elucidated. This subfamily is also found in several other fish-hunting species clades
within Conus. The analysis revealed a surprisingly diverse origin of α4/4 conopeptides from a single species, Conus bullatus. This phylogenetic approach that defines different genetic lineages of Conus venom peptides provides a guidepost for identifying conopeptides with potentially novel functions. 相似文献
19.
A multigene phylogeny of theGibberella fujikuroi species complex: Detection of additional phylogenetically distinct species 总被引:2,自引:0,他引:2
Phylogenetic relationships within theGibberella fujikuroi species complex were extended to newly discovered strains using nucleotide characters obtained by sequencing polymerase chain
reaction (PCR) amplified DNA from 4 loci used in a previous study [nuclear large subunit 28S rDNA, nuclear ribosomal internal
transcribed spacer (ITS) region, mitochondriaal small subunit (mtSSU) ribosomal DNA, and β-tubulin] together with two newly
sampled protein-encoding nuclear genes, translation elongation factor EF-1α and calmodulin. Sequences from the ribosomal ITS
region were analyzed separately and found to contain of two highly divergent, nonorthologous ITS2 types. Phylogenetic analysis
of the individual and combined datasets identified 10 new phylogenetically distinct species distributed among the following
three areas: 2 within Asia and 4 within both Africa and South America. Hypotheses of the monophyly ofFusarium subglutinans and its two formae speciales, f. sp.pini and f. sp.ananas, were strongly rejected by a likelihood analysis. Maximum parsimony results further indicate that the protein-encoding nuclear
genes provide considerably more phylogenetic signal that the ribosomal genes sequenced. Relative apparent synapomorphy analysis
was used to detect long-branch attraction taxa and to obtain a statistical measure of phylogenetic signal in the individual
and combined datasets. 相似文献
20.
Using a combined set of sequences of SSU and ITS regions of nuclear‐encoded ribosomal DNA, the concept of the experimental algal genus Chlorella was evaluated. Conventionally in the genus Chlorella, only coccoid, solitary algae with spherical morphology that do not possess any mucilaginous envelope were included. All Chlorella species reproduce asexually by autospores. However, phylogenetic analyses showed that within the clade of ‘true’Chlorella species (Chlorella vulgaris, C. lobophora, and C. sorokiniana), taxa with a mucilaginous envelope and colonial lifeform have also evolved. These algae, formerly designated as Dictyosphaerium, are considered as members of the genus Chlorella. In close relationship to Chlorella, five different genera were supported by the phylogenetic analyses: Micractinium (spherical cells, colonial, with bristles), Didymogenes (ellipsoidal cells, two‐celled coenobia, with or without two spines per cell), Actinastrum (ellipsoidal cells within star‐shaped coenobia), Meyerella (spherical cells, solitary, without pyrenoids), and Hegewaldia (spherical cells, colonial, with or without bristles, oogamous propagation). Based on the secondary structures of SSU and ITS rDNA sequences, molecular signatures are provided for each genus of the Chlorella clade. 相似文献