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Comparison of rDNA regions (ITS, LSU, and SSU) of some Aspergillus, Penicillium, and Talaromyces spp.
Aspergillus, Penicillium, and Talaromyces spp. are commonly found worldwide and include industrially and medicinally important members. These genera are deeply related with life from soil to health hazards via their industrial products, surface proteins, biodiversity, food spoilage, mycotoxins, etc. These three genera progressively encounter important taxonomic revisions, such as the one fungus-one name concept, and various methods are available to establish their evolutionary and phylogenetic relationships. Besides morphological, microscopic, and extrolite analyses, nucleotide sequence analysis is the most preferred method. In particular, rDNA regions, such as the internal transcribed spacer (ITS), large subunit (LSU), and small subunit (SSU), are commonly used for taxonomic and phylogenetic studies. Although the ITS locus is accepted as the barcode gene for fungal identification, it has some limitations. Therefore, the aim of the present study was to compare ITS, LSU, and SSU loci in terms of ease of application, discrimination of species, and phylogeny by using 43 strains belonging to the above-mentioned three genera of fungi. The results indicated that the ITS and LSU loci were the most effective, exhibiting identical topology and species discrimination, while the SSU locus was the least effective, demonstrating lower species discrimination and the worst topology. Furthermore, the long and high-quality ITS, LSU, and SSU sequences obtained in the present study, which belong to the above-mentioned three genera of fungi, have been deposited in the NCBI database. [ABSTRACT FROM AUTHOR]
Genome-wide analysis of response to low sulfur (LSU) genes in grass species and expression profiling of model grass species Brachypodium distachyon under S deficiency.
Sulfur (S) affects the plant life cycle and crop yield and has nutritional importance for human and animal diet. Its deficiency is one of the major problems in agriculture. However, the plant-specific LSU (response to Low SUlfur) gene family has not been extensively analyzed in major plant species such as grasses. In this study, we have performed in silico genome-wide analysis of LSU genes in 6 grass species, including Brachypodium distachyon, Sorghum bicolor, Oryza sativa, Zea mays, Triticum aestivum, and Panicum virgatum. All identified LSU genes contained one exon encoding proteins of acidic character with cytoplasmic localization. In silico analysis of ciselements revealed that sulfur-responsive elements (SURE boxes, SUlfur Response Element, GAGAC motif) were present in all LSU genes. In phylogenetic analysis, dicot and monocot LSU genes were separated. Expression profiles of B. distachyon BdLSU1 and BdLSU2 genes were analyzed by qRT-PCR method. Two Brachypodium LSU genes demonstrated different expression patterns when subjected to 48 h of S-depletion treatment. In roots, the BdLSU2 gene was upregulated, while BdLSU1 was downregulated. In leaves, expression levels were decreased for both genes. Analysis of the BdLSU expression under drought, cold, salt, and heat stresses was carried out based on the Brachypodium stress atlas. Results showed that BdLSU genes are not specific to S limitation; indeed, they may be involved in different stress conditions by cooperating with their interacting partner proteins. The results of this study could significantly contribute to the understanding of LSU genes in plants, particularly in grass species. These results may also support plant molecular studies by aiding the understanding of the sulfur assimilation pathway. [ABSTRACT FROM AUTHOR]

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