Bioinformatics analysis of the promoter sequence of the 9f-2.8 gene encoding germin

Bioinformatics is a field of study having an enormous potential, allowing to solve a number of problems arising as a result of dynamic development of natural sciences with the use of computer science methodologies. It is widely used and constitutes a basis for most scientific research conducted in the field of molecular biology. The aim of this study was in silico analysis of the promoter sequence of the 9f-2.8 gene encoding isoform of the germin protein considered as a germination marker in common wheat’s (Triticum aestivum L.). The gene mentioned above has already been characterized, however, with the use of experimental methods instead of bioinformatics. Analysis with the use of TSSP and TSSPlant software identified the promoter region and classified it as the TATA-box containing promoter. For 9f-2.8 gene including 2.8 kbp, the TSSP software indicated that the TATA-box sequence was located in the position 1665 nt, while the TSSPlant tool showed that TSS [+1] was located in the position 1699 nt. At the second stage, transcription factors were analyzed. Four main families of transcription factors were detected within the analyzed region: MADS, AP2, bZIP and NAC. The most common were MADS-box and bZIP motifs. In the final step of analysis the presence of CpG islands have been checked using the PlantPAN software. The region which could be potentially considered as CpG island have been detected and localized. Software used in analysis above is free online tool.Bioinformatyka jest dyscypliną nauki, w której tkwi olbrzymi potencjał. Dyscyplina ta rozwiązuje wiele problemów powstałych w wyniku dynamicznego rozwoju nauk przyrodniczych przy użyciu metodologii nauk informatycznych. Ma szerokie zastosowanie i jest bazą dla prowadzenia większości badań naukowych z dziedziny biologii molekularnej. Celem artykułu jest analiza in silico promotora genu 9f-2.8 kodującego izoformę (9f-2.8) białka germiny uważaną za marker kiełkowania u pszenicy zwyczajnej (Triticum aestivum L.). Gen ten był już wcześniej scharakteryzowany, jednak do jego analizy korzystano z metod eksperymentalnych, nie obliczeniowych. Analiza bioinformatyczna za pomocą programów TSSP i TSSPlant pozwolila zidentyfikować promotor i potwierdziła jego klasyfikacje do grupy promotorów z motywem TATA-box. W genie 9f-2.8 liczącym 2.8 kpz program TSSP wykazał, że sekwencja TATA-box znajduje się w pozycji 1665 nt, zaś narzędzie TSSPlant wskazało, że TSS [+1] znajduje się w pozycji 1699 nt. Drugim etapem była analiza czynników transkrypcyjnych. W analizowanym obszarze wyróżniono cztery główne rodziny czynników transkrypcyjnych: MADS, AP2, bZIP oraz NAC, z których najliczniejsze były motywy MADS-box oraz bZIP. Ostatnią częścią analiz była kontrola obecności wysp CpG. Zastosowano program PlantPAN, dzięki któremu zlokalizowano region spełniający warunki, pozwalające uznać go za wyspę CpG. Programy, których użyto do scharakteryzowania tych sekwencji są darmowe i ogólnodostępne online

Characteristic and applications of SSR and ISSR in study of plant genomes

W badaniach roślin markery DNA stanowią odpowiednie narzędzie pozwalające na szczegółową genetyczną analizę, mapowanie genów oraz określenie genetycznego zróżnicowania. Sekwencje mikrosatelitarne i obszary znajdujące się między nimi okazały się ważnym źródłem markerów DNA i były z powodzeniem stosowane przy badaniach genetycznego zróżnicowania, mapowaniu genomów, selekcji cech pożądanych w rolnictwie oraz przy rozróżnianiu genotypów. Markery SSR (ang simple sequence repeat) i ISSR (ang. inter simple sequence repeat) wykazują wiele zalet w porównaniu do innych markerów stosowanych w badaniach genetycznych. Charakteryzują się one wysokim polimorfizmem i dużą częstością występowania. Niniejszy przegląd przedstawia cechy i zastosowanie markerów SSR i ISSR w badaniach genomów roślinnych.In plant investigations, DNA based markers are suitable tools for detailed genetic analysis, gene mapping and estimation of genetic diversity. Microsatellites and regions between them are important source of DNA markers and have been successfully applied for detection of genetic diversity, genome mapping, marker assisted selection of agronomically important traits and genotype differentiation. Simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers have many advantages for genetic studies over other markers. They are highly polymorphic and abundant. This review aimed to characterize and present possible applications of SSR and ISSR in plant genome research

Natural Molecular Mechanisms of Plant Hyperaccumulation and Hypertolerance towards Heavy Metals

The main mechanism of plant tolerance is the avoidance of metal uptake, whereas the main mechanism of hyperaccumulation is the uptake and neutralization of metals through specific plant processes. These include the formation of symbioses with rhizosphere microorganisms, the secretion of substances into the soil and metal immobilization, cell wall modification, changes in the expression of genes encoding heavy metal transporters, heavy metal ion chelation, and sequestration, and regenerative heat-shock protein production. The aim of this work was to review the natural plant mechanisms that contribute towards increased heavy metal accumulation and tolerance, as well as a review of the hyperaccumulator phytoremediation capacity. Phytoremediation is a strategy for purifying heavy-metal-contaminated soils using higher plants species as hyperaccumulators

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species

Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis.

The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated