rpb2 is a reliable reference gene for quantitative gene expression analysis in the dermatophyte Trichophyton rubrum

The selection of reference genes used for data normalization to quantify gene expression by real-time PCR amplifications (qRT-PCR) is crucial for the accuracy of this technique. In spite of this, little information regarding such genes for qRT-PCR is available for gene expression analyses in pathogenic fungi. Thus, we investigated the suitability of eight candidate reference genes in isolates of the human dermatophyte Trichophyton rubrum subjected to several environmental challenges, such as drug exposure, interaction with human nail and skin, and heat stress. The stability of these genes was determined by geNorm, NormFinder and Best-Keeper programs. The gene with the most stable expression in the majority of the conditions tested was rpb2 (DNA-dependent RNA polymerase II), which was validated in three T. rubrum strains. Moreover, the combination of rpb2 and chs1 (chitin synthase) genes provided for the most reliable qRT-PCR data normalization in T. rubrum under a broad range of biological conditions. To the best of our knowledge this is the first report on the selection of reference genes for qRT-PCR data normalization in dermatophytes and the results of these studies should permit further analysis of gene expression under several experimental conditions, with improved accuracy and reliability.

Unstructured N Terminus of the RNA Polymerase II Subunit Rpb4 Contributes to the Interaction of Rpb4·Rpb7 Subcomplex with the Core RNA Polymerase II of Saccharomyces cerevisiae

Two subunits of eukaryotic RNA polymerase II, Rpb7 and Rpb4, form a subcomplex that has counterparts in RNA polymerases I and III. Although a medium resolution structure has been solved for the 12-subunit RNA polymerase II, the relative contributions of the contact regions between the subcomplex and the core polymerase and the consequences of disrupting them have not been studied in detail. We have identified mutations in the N-terminal ribonucleoprotein-like domain of Saccharomyces cerevisiae Rpb7 that affect its role in certain stress responses, such as growth at high temperature and sporulation. These mutations increase the dependence of Rpb7 on Rpb4 for interaction with the rest of the polymerase. Complementation analysis and RNA polymerase pulldown assays reveal that the Rpb4 center dot Rbp7 subcomplex associates with the rest of the core RNA polymerase II through two crucial interaction points: one at the N-terminal ribonucleoprotein-like domain of Rpb7 and the other at the partially ordered N-terminal region of Rpb4. These findings are in agreement with the crystal structure of the 12-subunit polymerase. We show here that the weak interaction predicted for the N-terminal region of Rpb4 with Rpb2 in the crystal structure actually plays a significant role in interaction of the subcomplex with the core in vivo. Our mutant analysis also suggests that Rpb7 plays an essential role in the cell through its ability to interact with the rest of the polymerase.

Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex.

The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/-) mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota). In all of these fungi, the minus (-) allele features the SexM high mobility group (HMG) gene flanked by an RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.

Phylogeographie und Populationsgenetik der Arten der Gattung Fosterella (Bromeliaceae) in den südamerikanischen Anden

Die tropischen Anden sind eines der artenreichsten Gebiete der Erde. Fast die Hälfte der 45.000 in diesem Gebiet vorkommenden Gefäßpflanzenarten sind in den Anden endemisch (Myers et al. 2000). Die Gattung Fosterella (Bromeliaceae) ist eine den Anden zugeordnete Pflanzengruppe, denn die meisten ihrer 31 Arten kommen in den Anden vor. Achtzehn Arten sind kleinräumige Endemiten. Fosterella hat damit Modellcharakter für diese Region. In der vorliegenden Arbeit wurde die Evolution der Gattung in Raum und Zeit mithilfe der vergleichenden Sequenzierung von sechs plastidären Loci (atpB-rbcL, matK, psbB-psbH, rpl32-trnL, rps16-trnK, rps16-Intron) und einem nukleären Marker (PHYC) untersucht. Es wurden über 90 Akzessionen von 24 Fosterella-Arten untersucht. Mit 5,6 % informativer Merkmale innerhalb der Gattung war rpl32-trnL der informativste Chloroplastenmarker. Es wurden mit den kombinierten Sequenzdaten eine Maximum Parsimony-, eine Maximum Likelihood- und eine Bayes´sche Analyse berechnet. Weiterhin wurden biogeographische und ultrametrische Untersuchungen durchgeführt. Die 6-Locus-Phylogenie zeigt eine Aufteilung der monophyletischen Gattung Fosterella in sechs Gruppen, von denen vier – die penduliflora-, weddelliana-, weberbaueri- und micrantha-Gruppe - klar monophyletisch und gut gestützt sind. Die albicans- und die rusbyi-Gruppe bilden hingegen einen Komplex. Ultrametrische Analysen legen ein Alter der Gattung von ca. 9,6 Mio. Jahren nahe. Der geographische Ursprung von Fosterella befindet sich nach den vorliegenden biogeographischen Analysen in den Anden und nach der Biom-Analyse zu gleicher Wahrscheinlichkeit entweder in andinen Trockenwäldern (seasonally dry tropical forests, SDTFs) oder in azonalen Standorten des amazonischen Tieflands östlich der Anden. Es gab mehrere Ausbreitungsereignisse, von denen die beiden Fernausbreitungsereignisse nach Mittelamerika (F. micrantha) und in das zentrale Amazonasgebiet (F. batistana) die auffälligsten sind. Die feuchten Bergregenwälder (Yungas) der Anden wurden offenbar mehrfach unabhängig von Fosterella-Arten besiedelt. Insgesamt wurden elf nukleäre Marker (XDH, GS, RPB2, MS, ADH, MS, GLO/PI, CHS, FLO/LFY, NIAi3 und PHYC) auf ihre Anwendbarkeit für molekularsystematische Studien in Fosterella getestet. Davon konnten acht Marker erfolgreich mithilfe einer PCR amplifiziert werden. Die Fragmentgrößen lagen zwischen 350 bp und 1.500 bp. Nur für drei Loci (FLO/LFY, NIAi3 und PHYC) konnten lesbare DNA-Sequenzen in Fosterella erzeugt werden. FLO/LFY zeigte nur 1,5 % Variabilität innerhalb der Gattung. Der NIA-Locus erzeugte bei der Amplifikation mehrere Fragmente, die separat voneinander sequenziert wurden. Der Locus PHYC konnte hingegen aufgrund der guten Amplifizier- und Sequenzierbarkeit für das gesamte Probenset sequenziert werden. Dieser Marker zeigte eine Variabilität innerhalb der Gattung von 10,2 %, davon waren 6,8 % informativ. In der Phylogenie basierend auf PHYC ist Fosterella klar monophyletisch, innerhalb der Gattung zeigt sich jedoch an der Basis eine unaufgelöste Polytomie. Es lassen sich neun mehr oder weniger gut gestützte Artengruppen definieren – rusbyi-, villosula-, albicans-, weddelliana-, penduliflora-, weberbaueri-, micrantha-, robertreadii- und spectabilis-Gruppe - die sich in ihrer Zusammensetzung mit Ausnahme der weddelliana-Gruppe von den nach Chloroplastendaten definierten Gruppen unterscheiden. Viele Arten sind para- oder polyphyletisch, so z. B. F. albicans, F. penduliflora und F. rusbyi. Bei den beiden erstgenannten Arten weisen die unterschiedlichen Stellungen in Chloroplasten- und Kernphylogenie auf Hybridisierungsereignisse hin.

Filogenia molecular de fungos gasteroides das ordens Phallales e Geastrales (Phallomycetidae)

Gasteroids fungi are characterized by the basidiospores maturation inside the basidioma, from which spores liberation occurs in a passive manner. These fungi were once seen as a well definite class of Basidiomycota, but nowadays they are considered an artificial assemblage, because the organisms have independent evolutionary histories forming a polyphyletic group with a vast morphological variety. Despite their diversity, studies with this group in the tropics are incipient, and the phylogenetic relationships of the species from temperate climate remain unknown. Thus, this work aimed to elucidate the phylogenetic relationships of gasteroids fungi from the Geastrales and Phallales orders, with the inclusion of tropical and temperate species, and with these analyses suggest a systematic position of species like Aseroë floriformis and Phallus roseus, as well as to verify if the lignicolous habit can indicate parental relationship in the Geastrum genus. For this, basidiomata were collected at Atlantic rain forest areas, during the rainy season, and the specimen identification followed specific literature for gasteroid fungi. The phylogenetic analyses were performed with Maximum Parsimony and Bayesian Analysis, making use of RPB2 and 28S nuclear genes and atp6 mitochondrial gene. It could be observed on the Phallales dendogram, that Aseroë floriformis did not cluster with A. rubra, and that it has an anterior divergence from all others species of the family Clathraceae used in this analysis, assuming a basal position in the clade. Phallus roseus, which once was recognized as Itajahya, has previous divergence from the group formed by Phallus species. At the Geastrales dendogram, in the group corresponding to Geastrum genus, it could be observed that species with lignicolous habitat clustered in a clade with high support values. So, the results suggest the creation of a new genus to accommodate A. floriformis, and the revalidation of Itajahya, as well as it can be affirmed that the lignicolous habitat on the Geastrum genus in fact indicates parental relationships, and that it has arised only once at the evolutionary history of the genus

Diversidade genética de Rhizoctonia spp. e análise de sequência multilocos

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Unraveling Trichoderma species in attine ant environment: description of three new taxa

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

First report of Didymella americanaon baby lima bean (Phaseolus lunatus)

A new foliar disease was observed on baby lima bean (Phaseolus lunatus) in fields across western New York State, USA. The disease occurred in 10 fields with variable incidence and severity. Symptoms were initially necrotic, tan spots on leaves with red to reddish brown irregular margins that coalesced to encompass the entire leaf and cause abscission. Pycnidia were observed within the lesions. Isolations from diseased leaves yielded several pycnidial forming fungi, including a Didymella species. These isolates were characterized by morphology and sequencing of multiple reference genes (internal transcribed spacer (ITS), partial actin, β- tubulin (tub2), translation elongation factor 1-α (TEF), 28S rDNA large subunit (LSU), rpb2, and calmodulin). A four gene phylogeny (ITS, tub2, LSU, and rpb2) showed that the isolates from baby lima bean belonged to a well-supported clade that contained the type culture of Didymella americana. Pathogenicity of the isolates on three commonly grown cultivars of baby lima bean was confirmed. Symptoms that developed on inoculated plants were similar to those observed on diseased plants in the field. This is the first report of D. americana on baby lima bean.