scholarly journals Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing

2017 ◽  
Vol 10 (1) ◽  
Author(s):  
Wibke J. Cramaro ◽  
Oliver E. Hunewald ◽  
Lesley Bell-Sakyi ◽  
Claude P. Muller
Keyword(s):  
Ixodes Ricinus ◽  
Single Molecule ◽  
Single Molecule Sequencing ◽  
Genome Scaffolding ◽  
Pathogen Vector

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.

scholarly journals SDS-assisted protein transport through solid-state nanopores

Nanoscale ◽  
2017 ◽  
Vol 9 (32) ◽  
pp. 11685-11693 ◽  
Author(s):  
Laura Restrepo-Pérez ◽  
Shalini John ◽  
Aleksei Aksimentiev ◽  
Chirlmin Joo ◽  
Cees Dekker
Keyword(s):  
Solid State ◽  
Sodium Dodecyl Sulfate ◽  
Single Molecule ◽  
Protein Transport ◽  
Sodium Dodecyl ◽  
Single Molecule Sequencing ◽  
Dodecyl Sulfate ◽  
Multiple Challenges

Using nanopores for single-molecule sequencing of proteins faces multiple challenges. Here, we investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore traslocations.

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