Analysis of part of the<Emphasis Type="Italic">Trichophyton rubrum</Emphasis> ESTs

Trichophyton rubrum (T. rubrum) is the most common of the superficial fungi. In an effort to better understand the genetic and biochemical makeup ofT. rubrum, we generated cDNA libraries from 3 growth stages and used these to isolate 4002 unique expressed sequence tags (ESTs). Sequence comparisons with the Genbank database allowed 1226 of the ESTs to be assigned putative functions or matched with homologs from other organisms. Of the remaining ESTs, 989 were only weakly similar to known sequences and 1787 had no identifiable functions, suggesting that they represent novel genes. We further analyzed the presence of several important genes involved in the growth, metabolism, signal transduction, pathogenesis and drug resistance inT. rubrum. This information was used to newly elucidate important metabolic pathways inT. rubrum. Taken together, our results should form the molecular basis for continued research on the physiological processes and pathogenic mechanisms ofT. rubrum, and may lead to a better understanding of fungal drug resistance and identification of new drug targets.     

Expression profile of calcium-dependent protein kinase (CDPKs) genes during the whole lifespan and under phytohormone treatment conditions in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L. ssp. <Emphasis Type="Italic">indica</Emphasis>)

Calcium-dependent protein kinases (CDPKs) control plant development and response to various stress environments through the important roles in the regulation of Ca²⁺ signaling. Thirty-one CDPK genes have been identified in the rice genome by a complete search of the genome based upon HMM profiles. In this study, the expression of this gene family was analyzed using the Affymetrix rice genome array in three rice cultivars: Minghui 63, Zhenshan 97, and their hybrid Shanyou 63 independently. Twenty-seven tissues sampled throughout the entire rice life-span were studied, along with three hormone treatments (GA3, NAA and KT), applied to the seedling at the trefoil stage. All 31 genes were found to be expressed in at least one of the experimental stages studied and revealed diverse expression patterns. We identified differential expression of the OsCPK genes in the stamen (1 day before flowering), the panicle (at the heading stage), the endosperm (days after pollination) and also in callus, in all three cultivars. Eight genes, OsCPK2, OsCPK11, OsCPK14, OsCPK22, OsCPK25, OsCPK26, OsCPK27 and OsCPK29 were found dominantly expressed in the panicle and the stamen, and five genes, OsCPK6, OsCPK7, OsCPK12, OsCPK23 and OsCPK31 were up-regulated in the endosperm stage. The OsCPK genes were also found to be regulated in rice seedlings subjected to different hormone treatment conditions, however their expression were not the same for all varieties. These diverse expression profiles trigger the functional analysis of the CDPK family in rice. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

High-resolution mapping of the <Emphasis Type="Italic">S</Emphasis>-locus in <Emphasis Type="Italic">Turnera</Emphasis> leads to the discovery of three genes tightly associated with the <Emphasis Type="Italic">S</Emphasis>-alleles

While the breeding system known as distyly has been used as a model system in genetics, and evolutionary biology for over a century, the genes determining this system remain unknown. To positionally clone genes determining distyly, a high-resolution map of the S-locus region of Turnera has been constructed using segregation data from 2,013 backcross progeny. We discovered three putative genes tightly linked with the S-locus. An N-acetyltransferase (TkNACE) flanks the S-locus at 0.35 cM while a sulfotransferase (TkST1) and a non-LTR retroelement (TsRETRO) show complete linkage to the S-locus. An assay of population samples of six species revealed that TsRETRO, initially discovered in diploid Turnera subulata, is also associated with the S-allele in tetraploid T. subulata and diploid Turnera scabra. The sulfotransferase gene shows some level of differential expression in long versus short styles, indicating it might be involved in some aspect of distyly. The complete linkage of TkST1 and TsRETRO to the S-locus suggests that both genes may reside within, or in the immediate vicinity of the S-locus. Chromosome walking has been initiated using one of the genes discovered in the present study to identify the genes determining distyly. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

<Emphasis Type="Italic">Trichophyton rubrum</Emphasis> and <Emphasis Type="Italic">Trichophyton interdigitale</Emphasis>: Genetic Diversity Among Species and Strains by Random Amplified Polymorphic DNA Method

Onychomycosis is a common condition that represents up to 50% of all nail problems and 30% of all cases of dermatophytoses. Trichophyton rubrum and Trichophyton interdigitale are the most common agents involved in this condition. In cases of recurrent post-treatment onychomycosis, strain fingerprinting could reveal whether the original isolate is responsible, a new strain has been acquired or if multiple strains are involved. The aim of this study was to evaluate the efficacy of the RAPD method for species and strain differentiation of T. rubrum and T. interdigitale obtained from patients with subungeal distal-lateral onychomycosis. A set of 86 strains of onychomycosis causative dermatophytes were submitted to species differentiation and strain typing by RAPD method with two previously described primers. Both primers proved capable of strain differentiation when tested for each species. Nineteen molecular profiles were configured for T. rubrum isolates with primers 1 and 6. For T. mentagrophytes, ten molecular profiles were configured with primer 1 and twenty-one with primer 6. We found that T. interdigitale and T. rubrum species were grouped in different clusters when both primers were analyzed together. This study shows that these primers are valuable tools for strain differentiation with T. rubrum and T. intedigitale.     

Phylogeny of the genera Trichophyton using mitochondrial DNA analysis

Diversity of mitochondrial DNA (mtDNA) was investigated in 92 Trichophyton rubrum strains, 2 T. mentagrophytes var. mentagrophytes, 2 T. m. vor. interdigitale, 2 T. m. var. goetzii, 1 T. m. var. erinacei, 2 T. quinckeanum, 2 T. schoenleinii, 1 T. tonsurans, 2 T. verrucosum var. album, 2 T. v. var. discoides, 1 T. violaceum var. violaceum, 1 Arthroderma benhamiae, and 1 A. vanbreuseghemii using endonucleases, Hae III, Msp I, Hind III, Xba I, and Bgl II. Trichophyton species were divided into 7 groups, and a phylogenetic tree was produced based on sequence divergence within mtDNA. The following results were obtained: (1) T. rubrum was divided into 2 groups Type I and Type II, and was suggested to be a complex. (2) A. benhamiae was closely related to T. m. var. erinacei. (3) T. rubrum Type II, T. tonsurans, and A. vanbreuseghemii showed identical restriction profiles, and were suggested to be closely related to each other or identical. (4) T. quinckeanum and T. schoenlenii showed identical restriction profiles, which differed slightly from those of A. vanbreuseghemii. (5) mtDNA analysis was useful in identifying pleomorphic strains.