scholarly journals Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

2017 ◽  
Vol 27 (5) ◽  
pp. 709-721 ◽  
Author(s):  
Daniel E. Khost ◽  
Danna G. Eickbush ◽  
Amanda M. Larracuente
Keyword(s):  
Drosophila Melanogaster ◽  
Single Molecule ◽  
Satellite Dna ◽  
Detailed Structure ◽  
Single Molecule Sequencing

scholarly journals Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

2016 ◽  
Author(s):  
D. E. Khost ◽  
D. G. Eickbush ◽  
A. M. Larracuente
Keyword(s):  
Drosophila Melanogaster ◽  
Single Molecule ◽  
Satellite Dna ◽  
Genome Stability ◽  
Tandem Repeats ◽  
Genomic Structure ◽  
Large Fraction ◽  
Pericentric Heterochromatin ◽  
Repetitive Nature ◽  
Long Read

ABSTRACTSatellite DNA (satDNA) repeats can make up a large fraction of eukaryotic genomes. These blocks of tandem repeats are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses genome assembly challenges and has stymied progress on the detailed study of satDNA structure. Here we use single molecule real-time sequencing reads to assemble and study the genomic structure of two complex satDNA loci in Drosophila melanogaster—260-bp and Responder—with unprecedented resolution. We find that complex satDNAs are organized into large tandem arrays interrupted by transposable elements. The homogenized repeats in the array center suggest that gene conversion and unequal crossovers drive the concerted evolution of repeats, the degree to which differs among satDNA loci. Both satDNA arrays have a higher order organization that suggests recent structural rearrangements. These assemblies provide a platform for the evolutionary and functional genomics of satDNAs in pericentric heterochromatin.

scholarly journals A DNA-binding protein from Ustilago maydis prefers duplex DNA without chain interruptions.

1983 ◽  
Vol 3 (4) ◽  
pp. 605-612 ◽  
Author(s):  
J R Rusche ◽  
W K Holloman
Keyword(s):  
Drosophila Melanogaster ◽  
Satellite Dna ◽  
Binding Assay ◽  
Ustilago Maydis ◽  
Dna Binding Protein ◽  
Double Strand Breaks ◽  
Duplex Dna ◽  
Plasmid Pbr322 ◽  
Strand Breaks ◽  
Dna Strand

Using a nitrocellulose filter binding assay, we have partially purified a protein from mitotic cells of Ustilago maydis that binds preferentially to covalently closed circular duplex DNA. DNA containing single- or double-strand breaks is bound poorly by the protein. Once formed, the DNA-protein complex is stable, resisting dissociation in high salt. However, when a DNA strand is broken, the complex appears to dissociate. The protein binds equally well to form I DNA of phi X174 or the plasmid pBR322, but has a higher affinity for a hybrid plasmid containing a cloned region of Drosophila melanogaster satellite DNA.

scholarly journals Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

2021 ◽  
Author(s):  
Fei Ge ◽  
Jingtao Qu ◽  
Peng Liu ◽  
Lang Pan ◽  
Chaoying Zou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Inbred Line ◽  
Genome Mapping ◽  
Maize Inbred Line ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Maize Genetic ◽  
Induction Ratio ◽  
Phenotypic Variations

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

2. How to read the book of life

2018 ◽  
pp. 12-27
Author(s):  
John Archibald
Keyword(s):  
Dna Sequencing ◽  
Human Genome ◽  
Single Molecule ◽  
Human Genome Project ◽  
Genome Project ◽  
Chain Termination ◽  
Single Molecule Sequencing ◽  
Semiconductor Sequencing ◽  
The Cost ◽  
The Human Genome Project

For all its biological importance, DNA is a fragile molecule so extracting it is a difficult process. ‘How to read the book of life’ explains the techniques required to sequence DNA. It begins by explaining the techniques developed for protein and RNA sequencing by Frederick Sanger, Robert Holley, and Carl Woese that were then developed further for DNA sequencing. Following the success of the Human Genome Project, the next generation of DNA sequencing was developed in the mid-2000s. Pyrosequencing was capable of generating orders of magnitude more data at a fraction of the cost, but was superceded within a decade by semiconductor sequencing, reversible chain-termination sequencing, and single-molecule sequencing.

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