scholarly journals EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments

2006 ◽  
Vol 34 (Web Server) ◽  
pp. W459-W462 ◽  
Author(s):  
A. Masoudi-Nejad ◽  
K. Tonomura ◽  
S. Kawashima ◽  
Y. Moriya ◽  
M. Suzuki ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Large Scale ◽  
Dna Fragments

Enzymatic amplification and characterization of large DNA fragments from genomic DNA

Gene ◽  
1988 ◽  
Vol 71 (1) ◽  
pp. 211-216 ◽  
Author(s):  
Phouthone Keohavong ◽  
Cindy C. Wang ◽  
Rita S. Cha ◽  
William G. Thilly
Keyword(s):  
Genomic Dna ◽  
Dna Fragments ◽  
Enzymatic Amplification

Development of a fungal transformation system based on selection of sequences with promoter activity

1987 ◽  
Vol 7 (9) ◽  
pp. 3297-3305
Author(s):  
B G Turgeon ◽  
R C Garber ◽  
O C Yoder
Keyword(s):  
Genomic Dna ◽  
Pathogenic Fungus ◽  
Low Frequency ◽  
Hygromycin B ◽  
Fungal Transformation ◽  
Dna Fragments ◽  
Transformation System ◽  
Chromosomal Dna ◽  
General Utility ◽  
Novel Strategy

A novel strategy was used to develop a transformation system for the plant pathogenic fungus Cochliobolus heterostrophus. Sequences capable of driving the expression of a gene conferring resistance to the antibiotic hygromycin B in C. heterostrophus were selected from a library of genomic DNA fragments and used, with the selectable marker, as the basis for transformation. The library of random 0.5- to 2.0-kilobase-pair fragments of C. heterostrophus genomic DNA was inserted at the 5' end of a truncated, promoterless Escherichia coli hygromycin B phosphotransferase gene (hygB) whose product confers resistance to hygromycin B. C. heterostrophus protoplasts were transformed with the library and selected for resistance. Resistant colonies arose at low frequency. Each colony contained a transformation vector stably integrated into chromosomal DNA. When the transforming DNA was recovered from the genome and introduced into C. heterostrophus, resistant colonies appeared at higher frequency. We determined the sequences of two of the C. heterostrophus DNA fragments which had been inserted at the 5' end of hygB in the promoter library and found that both made translational fusions with hygB. One of the two fusions apparently adds 65 and the other at least 86 amino acids to the N-terminus of the hygB product. Plasmids containing hygB-C. heterostrophus promoter fusions can be used unaltered to drive hygB expression in several other filamentous ascomycetes. This approach to achieving transformation may have general utility, especially for organisms with relatively undeveloped genetics.

Identification of developmental regulatory genes in Aspergillus nidulans by overexpression.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 537-547 ◽  
Author(s):  
J F Marhoul ◽  
T H Adams
Keyword(s):  
Growth Inhibition ◽  
Aspergillus Nidulans ◽  
Genomic Dna ◽  
Regulatory Gene ◽  
Regulatory Genes ◽  
Dna Fragments ◽  
Expression Library ◽  
Phenotypic Changes ◽  
Inhibition Of Growth ◽  
Induction Sequence

Abstract Overexpression of several Aspergillus nidulans developmental regulatory genes has been shown to cause growth inhibition and development at inappropriate times. We set out to identify previously unknown developmental regulators by constructing a nutritionally inducible A. nidulans expression library containing small, random genomic DNA fragments inserted next to the alcA promoter [alcA(p)] in an A. nidulans transformation vector. Among 20,000 transformants containing random alcA(p) genomic DNA fusion constructs, we identified 66 distinct mutant strains in which alcA(p) induction resulted in growth inhibition as well as causing other detectable phenotypic changes. These growth inhibited mutants were divided into 52 FIG (Forced expression Inhibition of Growth) and 14 FAB (Forced expression Activation of brlA) mutants based on whether or not alcA(p) induction resulted in accumulation of mRNA for the developmental regulatory gene brlA. In four FAB mutants, alcA(p) induction not only activated brlA expression but also caused hyphae to differentiate into reduced conidiophores that produced viable spores from the tips as is observed after alcA(p)::brlA induction. Sequence analyses of the DNA fragments under alcA(p) control in three of these four sporulating strains showed that in two cases developmental activation resulted from overexpression of previously uncharacterized genes, whereas in the third strain, the alcA(p) was fused to brlA. The potential uses for this strategy in identifying genes whose overexpression results in specific phenotypic changes like developmental induction are discussed.

scholarly journals Precision nomenclature for the new genomics

GigaScience ◽  
2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Harris A Lewin ◽  
Jennifer A Marshall Graves ◽  
Oliver A Ryder ◽  
Alexander S Graphodatsky ◽  
Stephen J O'Brien
Keyword(s):  
Large Scale ◽  
Genomic Analysis ◽  
End Users ◽  
Dna Fragments ◽  
Current State ◽  
Scientific Disciplines ◽  
Genome Assemblies

Abstract The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images of all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclature will assist end users to properly classify genome assemblies, thus facilitating genomic analysis.

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