Extraction of total cellular DNA from plants, algae and fungi

Rogers, Scott O.; Bendich, Arnold J.

doi:10.1007/978-94-011-0511-8_12

Cited by 468 publications

(338 citation statements)

References 16 publications

Supporting

Mentioning

332

Contrasting

Unclassified

Order By: Relevance

“…Ustilaginoidea virens strains UV-8b, FJ1-1a, HB3-1a, LN10-16-1 and LN2010-1-1 were collected from different rice cultivars at different provinces in China, and used for sequencing (Supplementary Table 8). Total DNA was isolated from the mycelium of U. virens using a CTAB (cetyl trimethyl ammonium bromide) method 51 . Nuclear DNA was purified through a CsCl density-gradient centrifugation to remove mitochondrial DNA using standard procedures 52 .…”

Section: Methodsmentioning

confidence: 99%

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

et al. 2014

View full text Add to dashboard Cite

Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has B25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. virens is close to the entomopathogenic Metarhizium spp., suggesting potential host jumping across kingdoms. U. virens possesses reduced gene inventories for polysaccharide degradation, nutrient uptake and secondary metabolism, which may result from adaptations to the specific floret infection and biotrophic lifestyles. Consistent with their potential roles in pathogenicity, genes for secreted proteins and secondary metabolism and the pathogen-host interaction database genes are highly enriched in the transcriptome during early infection. We further show that 18 candidate effectors can suppress plant hypersensitive responses. Together, our analyses offer new insights into molecular mechanisms of evolution, biotrophy and pathogenesis of U. virens.

show abstract

Section: Methodsmentioning

confidence: 99%

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

et al. 2014

View full text Add to dashboard Cite

show abstract

“…High molecular weight genomic DNA was extracted from the fungus according to the CTAB method of Rogers & Bendich (Rogers and Bendich 1994) with minor modifications. Total RNA extraction was done according to the manual of TRI REAGENT TM (Sigma-Aldrich, St. Louis, USA) and RNA was stored at -70°C.…”

Section: Isolation and Manipulation Of Nucleic Acidsmentioning

confidence: 99%

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

Corso

Chellappan

Sukumaran

et al. 2010

World J Microbiol Biotechnol

View full text Add to dashboard Cite

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca 2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.Keywords Engyodontium album Á Alkaline serine protease Á Subtilases Á Homology modelling Abbreviations E. album Engyodontium album EAPEngyodontium album protease (deduced protein) Eap Engyodontium album protease (gene)

show abstract

“…The DNA was isolated from frozen plant material of individual plants using the cetyltriammonium bromide (CTAB) method (Rogers and Bendich, 1994) adapted as follows. Approximately 40-60 mg leaf material was ground in liquid nitrogen in a 1.5 ml Eppendorf tube followed by addition of 700 ml extraction buffer (100 mM Tris-HCl, pH 9.5; 20 mM EDTA, pH 8.0; 1.4 M NaCl; 1% PEG; 2% CTAB; 2.5 ml/ml b-mercaptoethanol).…”

Section: Dna Isolationmentioning

confidence: 99%

Genetic differentiation among populations of Sesleria albicans Kit. ex Schultes (Poaceae) from ecologically different habitats in central Europe

2003

View full text Add to dashboard Cite

As observed for many other plant species, the populations of Sesleria albicans in Central Europe are located in habitats, which differ to a high degree from each other with regard to ecological factors such as nutrients, light and water as well as in type of land use. The species colonizes limestone cliffs, pavements, screes, grazed and mown grasslands, heaths, fens and open woodlands. In this study, we used random amplified polymorphic DNA (RAPD) analysis to investigate the genetic differentiation among 25 populations of S. albicans from six different types of habitat (beech forests, alpine and lowland rocky ridges, lowland screes, fens, calcareous grasslands). With RAPD analysis, 344 fragments could be amplified, of which 95.9% were polymorphic. The level of polymorphism ranged from 29.7 to 56.7% polymorphic bands per population and was correlated with population size. In an analysis of molecular variance (AMOVA), used to detect variation among individuals within populations, among populations from the same habitat and among different habitats, most of the genetic variation was found within populations (62.06%) and among populations from the same habitat (33.36%). In contrast, only a very low level of differentiation could be observed among different habitats (4.58%). The results of our study give only little evidence for an ecotypic differentiation of Sesleria albicans. This differentiation is principally conceivable, but obviously not related to the investigated RAPD loci.

show abstract

Extraction of total cellular DNA from plants, algae and fungi

Cited by 468 publications

References 16 publications

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

Genetic differentiation among populations of Sesleria albicans Kit. ex Schultes (Poaceae) from ecologically different habitats in central Europe

Contact Info

Product

Resources

About