共查询到20条相似文献,搜索用时 31 毫秒
1.
Jouko Rikkinen S. Kristin L. Meinke Heinrich Grabenhorst Carsten Gröhn Max Kobbert Jörg Wunderlich Alexander R. Schmidt 《Geobios》2018,51(5):469-479
Calicioid lichens and fungi are a polyphyletic grouping of tiny ascomycetes that accumulate a persistent spore mass (mazaedium) on top of their usually well-stalked ascomata (‘mazaediate fungi’). In addition to extant forms, six fossils of the group were previously known from European Paleogene amber. Here we report nine new fossils and analyze the preserved features of all fossils to assess their applicability for dating molecular phylogenies. Many fossils are extremely well preserved, allowing detailed comparisons with modern taxa. SEM investigation reveals that even fine details of ascospore wall ultrastructure correspond to those seen in extant specimens. All fossils can confidently be assigned to modern genera: three to Calicium (Caliciaceae, Lecanoromycetes), five to Chaenotheca (Coniocybaceae, Coniocybomycetes), six to Chaenothecopsis (Mycocaliciaceae, Eurotiales), and one to Phaeocalicium (Mycocaliciaceae, Eurotiales). Several Calicium and Chaenotheca fossils are assignable to specific lineages within their genera, while the Chaenothecopsis fossils demonstrate the extent of intraspecific variation within one such lineage. Some features in the morphology of Chaenotheca succina nov. sp. seem to be ancestral as they have not been reported from modern species of the genus. 相似文献
2.
A combined data set of nuclear SSU rDNA, LSU rDNA, and mitochondrial SSU rDNA sequences was analyzed in order to examine the
relationships of the major clades of euascomycetes. Partial sequences of 14 ascomycetes were determined and aligned with the
corresponding sequences of 16 other ascomycetes retrieved from Genbank. The alignment was analyzed using maximum parsimony
(MP) and a Bayesian analysis with Markov chain Monte Carlo (B/MCMC). The classification based on single-gene studies is supported,
but the confidence is enhanced in the concatenated analysis. The monophyly of the superclass Leotiomyceta, which includes
all euascomycetes with inoperculate asci, is strongly supported. The polyphyly of ascolocularous fungi is supported. The group
is divided into two groups: the Dothideomycetes basal to all other Leotiomyceta and the Chaetothyriomycetes as sister-group
to Eurotiomycetes. The Lecanoromycetes appear as a monophyletic group with strong support and form a sister-group to the Chaetothyriomycetes/Eurotiomycetes
clade, but this lacks support. The Leotiomycetes and Sordariomycetes form a strongly supported sister-group. Alternative topologies
are tested using parametric bootstrapping; a basal position of the Eurotiomycetes and Leotiomycetes in the Leotiomyceta cannot
be rejected, while such a position can be rejected for Chaetothyriomycetes, Lecanoromycetes and Sordariomycetes. The character
evolution with regard to ascoma type, ascus type and ascoma-ontogeny is examined using MP and maximum likelihood (ML). While
it appears most likely that the ancestor of the inoperculate ascomycetes had apothecia and an ascohymenial ascoma-ontogeny
using MP methods, the ML approach shows that there is some uncertainty at the current state of knowledge. The improvement
of confidence of the combined data set in comparison with single-gene studies makes us confident that analyses with additional
data sets will further improve the confidence and eventually uncover the branching order of euascomycetes. 相似文献
3.
Hofstetter V Miadlikowska J Kauff F Lutzoni F 《Molecular phylogenetics and evolution》2007,44(1):412-426
The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes. 相似文献
4.
Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens 总被引:2,自引:0,他引:2
The phylogenetic relationships of many lichen-forming perithecioid ascomycetes are unknown. We generated nuLSU and mtSSU rDNA sequences of members of seven families of pyrenocarpous lichens and used a Bayesian framework to infer a phylogenetic estimate. Members of the perithecioid Protothelenellaceae, Thelenellaceae and Thrombiaceae surprisingly cluster within the mainly discocarpous Lecanoromycetes, while Strigulaceae, Verrucariaceae and Pyrenulaceae are related to the ascolocular Chaetothyriomycetes. Micromorphological studies of the ascomata showed that the two main groups of pyrenocarpous lichen-forming fungi differ in their ascus types. The Strigulaceae, Verrucariaceae and Pyrenulaceae have apically and laterally thick-walled asci, whereas the Thelenellaceae, Protothelenellaceae and Thrombiaceae have only apically thickened asci. The latter two show ring-shaped amyloid apical structures. Based on morphological and molecular evidence we propose to reduce Thrombiaceae to synonymy with Protothelenellaceae. 相似文献
5.
Kanami Yoshino Kohei Yamamoto Kojiro Hara Masatoshi Sonoda Yoshikazu Yamamoto Kazunori Sakamoto 《Fungal biology》2019,123(4):318-329
In lichen symbiosis, polyol transfer from green algae is important for acquiring the fungal carbon source. However, the existence of polyol transporter genes and their correlation with lichenization remain unclear. Here, we report candidate polyol transporter genes selected from the genome of the lichen-forming fungus (LFF) Ramalina conduplicans. A phylogenetic analysis using characterized polyol and monosaccharide transporter proteins and hypothetical polyol transporter proteins of R. conduplicans and various ascomycetous fungi suggested that the characterized yeast’ polyol transporters form multiple clades with the polyol transporter-like proteins selected from the diverse ascomycetous taxa. Thus, polyol transporter genes are widely conserved among Ascomycota, regardless of lichen-forming status. In addition, the phylogenetic clusters suggested that LFFs belonging to Lecanoromycetes have duplicated proteins in each cluster. Consequently, the number of sequences similar to characterized yeast’ polyol transporters were evaluated using the genomes of 472 species or strains of Ascomycota. Among these, LFFs belonging to Lecanoromycetes had greater numbers of deduced polyol transporter proteins. Thus, various polyol transporters are conserved in Ascomycota and polyol transporter genes appear to have expanded during the evolution of Lecanoromycetes. 相似文献
6.
Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the "pattern of resolved nodes" method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade. 相似文献
7.
Lawrey JD Diederich P Nelsen MP Sikaroodi M Gillevet PM Brand AM van den Boom P 《Fungal biology》2011,115(2):176-187
Lichenicolous fungi are obligately lichen-associated organisms that have evolved many times throughout the Ascomycota and Basidiomycota. Approximately 20% of lichenicolous ascomycetes are recognized only from asexual (anamorphic) characteristics, so the phylogenetic position of many groups has never been resolved. Here we present the first molecular phylogeny of Lichenoconium, a genus of strictly asexual, obligately lichenicolous species with broad geographic distributions and diverse host ecologies. We obtained nuclear and mitochondrial rDNA sequences from fungal cultures isolated from four species in the genus, including a new species, Lichenoconium aeruginosum sp. nov., collected in France, Luxembourg and Netherlands. Our multilocus phylogeny supports the monophyly of fungi in the genus Lichenoconium, and places the genus in the Dothideomycetes, an ascomycete class made up mainly of saprobes and plant-associated endophytes and pathogens. There are only a few recognized groups of lichen-formers in the Dothideomycetes, but Lichenoconium is not supported as being closely related to any of these, nor to any other recognized order within the Dothideomycetes. Given that Lichenoconium is but one of over 100 genera of anamorphic lichenicolous fungi, most of which have never been studied phylogenetically, we suggest that asexual lichenicolous fungi may represent novel and evolutionarily significant phylogenetic groups in the Kingdom Fungi. 相似文献
8.
R Gazis J Miadlikowska F Lutzoni AE Arnold P Chaverri 《Molecular phylogenetics and evolution》2012,65(1):294-304
Through a culture-based survey of living sapwood and leaves of rubber trees (Hevea spp.) in remote forests of Peru, we discovered a new major lineage of Ascomycota, equivalent to a class rank. Multilocus phylogenetic analyses reveal that this new lineage originated during the radiation of the 'Leotiomyceta', which resulted not only in the evolution of the Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, and Sordariomycetes, but also of the majority of hyperdiverse foliar endophytes. Because its origin is nested within this major burst of fungal diversification, we could not recover strong support for its phylogenetic relationship within the 'Leotiomyceta'. Congruent with their long phylogenetic history and distinctive preference for growing in sapwood, this new lineage displays unique morphological, physiological, and ecological traits relative to known endophytes and currently described members of the 'Leotiomyceta'. In marked contrast to many foliar endophytes, the strains we isolated fail to degrade cellulose and lignin in vitro. Discovery of the new class, herein named Xylonomycetes and originally mis-identified by ITSrDNA sequencing alone, highlights the importance of inventorying tropical endophytes from unexplored regions, using multilocus data sets to infer the phylogenetic placement of unknown strains, and the need to sample diverse plant tissues using traditional methods to enhance efforts to discover the evolutionary, taxonomic, and functional diversity of symbiotrophic fungi. 相似文献
9.
A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors. 相似文献
10.
Assessment of soil fungal communities using pyrosequencing 总被引:1,自引:0,他引:1
Young Woon Lim Byung Kwon Kim Changmu Kim Hack Sung Jung Bong-Soo Kim Jae-Hak Lee Jongsik Chun 《Journal of microbiology (Seoul, Korea)》2010,48(3):284-289
Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in
soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived
from the 5′ region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number
of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and
95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa
were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa
in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have
been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporicAscomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including
species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales,
Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high
diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities
in soils. 相似文献
11.
Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit 总被引:1,自引:0,他引:1
In an effort to establish a suitable alternative to the widely used 18S rRNA system for molecular systematics of fungi, we examined the nuclear gene RPB2, encoding the second largest subunit of RNA polymerase II. Because RPB2 is a single-copy gene of large size with a modest rate of evolutionary change, it provides good phylogenetic resolution of Ascomycota. While the RPB2 and 18S rDNA phylogenies were highly congruent, the RPB2 phylogeny did result in much higher bootstrap support for all the deeper branches within the orders and for several branches between orders of the Ascomycota. There are several strongly supported phylogenetic conclusions. The Ascomycota is composed of three major lineages: Archiascomycetes, Saccharomycetales, and Euascomycetes. Within the Euascomycetes, plectomycetes, and pyrenomycetes are monophyletic groups, and the Pleosporales and Dothideales are distinct sister groups within the Loculoascomycetes. We confirm the placement of Neolecta within the Archiascomycetes, suggesting that fruiting body formation and forcible discharge of ascospores were characters gained early in the evolution of the Ascomycota. These findings show that a slowly evolving protein-coding gene such as RPB2 is useful for diagnosing phylogenetic relationships among fungi. 相似文献
12.
Xunbiao Liu Qianqian Zhang Xinyao Xia Xiuyuan Liu Lei Ge Long Yang 《Genes & genomics.》2017,39(12):1307-1316
The relationship between ascomycetes and basidiomycetes, the two main phyla of non-flagellated fungi, has rarely been investigated. In this study, we performed a comparative genomics analysis of genome sequences of 55 ascomycetes and 26 basidiomycetes species and detected 81 universal markers, 875 homologous genes and a conserved contig in the glucose-regulated protein gene. In dendrograms based on simple sequence repeat markers and homologous genes, ascomycetes and basidiomycetes formed distinct clusters, with each set of taxa having a high coefficient of relatedness. Ascomycetes and basidiomycetes also constituted distinct groups in a phylogenetic tree based on a conserved contig in the glucose-regulated protein gene. These results provide evidence that basidiomycetes may be derived from ascomycetes but are definitely genetically differentiated at the genomic level. The phylogenetic relationships of ascomycetes and basidiomycetes uncovered in this study provide new insights for future research related to fungal classification and evolution. 相似文献
13.
14.
The phylogenetic relationships of the cyanobacterial lichens in the Lecanorales suborder Peltigerineae 总被引:1,自引:0,他引:1
Elisabeth Wiklund Mats Wedin 《Cladistics : the international journal of the Willi Hennig Society》2003,19(5):419-431
We present major cladistic analyses of the Lecanoromycetes (Ascomycota, Fungi) focusing on the Lecanorales suborder Peltigerineae, a group including the majority of the cyanobacterial lichens. DNA sequence datasets from the mtSSU and nLSU rDNA were produced and analyzed with maximum parsimony and parsimony jackknifing. The results suggest that the Lecanorales is monophyletic. The Peltigerineae (including Placynthiaceae, Peltigeraceae, Lobariaceae, Nephromataceae, Collemataceae, Coccocarpiaceae, Pannariaceae, and Massalongia) is likewise a monophyletic group. The Lobariaceae, and Lobaria in the traditional sense, are strongly supported as monophyletic, in contrast to results of other investigations based on nITS rDNA data. Pseudocyphellaria may be paraphyletic. Placynthiaceae is the sister group to the Collemataceae and Collema may be nested within Leptogium. Pannariaceae in the traditional sense is not a monophyletic group. Finally, the Lecanorineae is nonmonophyletic in all analyses, and the Cladoniineae and Teloschistineae are nested within the Lecanorineae in the combined analysis. 相似文献
15.
To determine the phylogenetic placement of the major groups of higher
fungi, we sequenced the DNA sequences from the small-subunit ribosomal RNA
(18S rRNA) coding regions from Taphrina wiesneri (synonym: T. cerasi) and
Saitoella complicata and compared them to 18S rRNA sequences from the
oomycetes, chytridiomycetes, zygomycetes, ascomycetes, and basidiomycetes.
Here we demonstrate that the ascomycetes have at least two major
evolutionary lineages. Taphrina wiesneri and Saitoella complicata form a
monophyletic branch that diverged prior to the separation of other
ascomycetes. The same treatment could be accorded to Schizosaccharomyces
pombe.
相似文献
16.
Abstract Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts, traditionally included in the family Clavicipitaceae of Ascomycota. Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co‐evolution of parasites and hosts in entomopathogenic ascomycetes. To this end, we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses. Based on the phylogenetic tree, we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character. The phylogenetic analyses revealed two important points. (i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps. The vertically immersed perithecia form was the ancestral state, superficial and obliquely immersed perithecia were derived characters, obliquely immersed was irreversible. Species with obliquely immersed perithecia were in a closely related group and were the derived group. (ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats. Based on the results of these analyses, host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps. 相似文献
17.
Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various ‘relaxed clock’ scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen–forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non–lichenized Ascomycota, many of which had not been previously dated. 相似文献
18.
A. V. Kurakov S. A. Gevorkyan V. B. Goginyan S. M. Ozerskaya 《Applied Biochemistry and Microbiology》2008,44(2):210-212
We summarized experimental data on species diversity of fungi decomposing synthetic polymeric materials. Most of the fungi were anamorphs of the phylum Ascomycota, class Ascomycetes (231 species and 85 genera). Teleomorphs of ascomycetes were represented by 18 species and 7 genera. We revealed a smaller number of fungi belonging to the phylum Zygomycota, class Zygomycetes (31 species and 15 genera), or the phylum Basidiomycota, class Basidiomycetes (5 species and 5 genera). The specific composition of fungi was assessed on polymeric materials of various classes. 相似文献
19.
The depiction of evolutionary relationships within phylum Ascomycota is still controversial because of unresolved branching orders in the radiation of major taxa. Here we generated a dataset of 166 small subunit (18S) rDNA sequences, representative of all groups of Fungi and used as input in a Bayesian phylogenetic analysis. This phylogeny suggests that Discomycetes are a basal group of filamentous Ascomycetes and probably maintain ancestor characters since their representatives are intermingled among other filamentous fungi. Also, we show that the evolutionary rate heterogeneity within Ascomycota precludes the assumption of a global molecular clock. Accordingly, we used the penalized likelihood method, and for calibration we included a 400 million-year-old Pyrenomycete fossil considering two distinct scenarios found in the literature, one with an estimated date of 1576 Myr for the plant–animal–fungus split and the other with an estimated date of 965 Myr for the animal–fungus split. Our data show that the current classification of the fossil as a Pyrenomycete is not compatible with the second scenario. Estimates under the first scenario are older than dates proposed in previous studies based on small subunit rDNA sequences but support estimates based on multiprotein analysis, suggesting that the radiation of the major Ascomycota groups occurred into the Proterozoic era.
Reviewing Editor: Dr. Nicolas Galtier 相似文献
20.