An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing
Feb 2022
Authors:
Catherine D. Aimone, Steen Hoyer, Anna E. Dye, David O. Deppong, Siobain Duffy, Ignazio Carbone, Linda Hanley-Bowdoin
Info:
The authors provide a protocol for analyzing single stranded DNA (ssDNA) from begomoviruses, which cause significant damage to many crops (e.g. cassava and tomato), and is transmitted by whiteflies. The ssDNA is enriched from both plants and whiteflies and combined rolling circle amplification (RCA) and DNA size selection to prepare samples for sequencing and analysis of the viral genomes. The authors suggest that this method can be used to examine viral DNA as it moves from host to vector and be used for viral DNA population studies.
BluePippin was used for DNA size selection.
Author Affiliations:
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC,
Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ
Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
Journal of Virological Methods
DOI: 10.1016/j.jviromet.2021.114405
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
September 2021
Authors:
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
Info:
The authors report on a high quality genome assembly of the model plant species Arabidopsis include two telomere-to-telomere assemblies (Chr 3 and 5). PacBio’s HiFi, Oxford Nanopore ultra-long reads and Hi-C (Illumina) were used.
BluePippin was used to size select large fragments from genomic extracts and for Hi-FI library construction. The SageHLS was used to collect DNA fragments >50kb for Oxford Nanopore ultra-long library prep (Genome Center of Grandomics [Wuhan, China]). .
Author Affiliations:
Xi’an Jiaotong University, Xi’an, China
Genomics, Proteomics & Bioinformatics
DOI: 10.1016/j.gpb.2021.08.003
High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
July 2021
Authors:
Ashley Jones ,Cynthia Torkel,David Stanley,Jamila Nasim,Justin Borevitz,Benjamin Schwessinger
Info:
The authors provide a protocol for preparing high molecular weight DNA sequencing libraries with a particular focus on difficult plant and fungal tissues, and also can be used with animals and microbes. The libraries can be used for PacBio or Oxford Nanopore sequencing, includes clean up and size selection recommendations, in a manner that is economical and scalable.
The PippinHT was used for the DNA size selection recommendations.
Author Affiliations:
Australian National University, Canberra, Australian Capital Territory, Australia
PLOS ONE
DOI: 10.1371/journal.pone.0253830
Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes
June 2021
Authors:
Eric S Tvedte, Mark Gasser, Benjamin C Sparklin, Jane Michalski, Carl E Hjelmen, J Spencer Johnston, Xuechu Zhao, Robin Bromley, Luke J Tallon, Lisa Sadzewicz, David A Rasko, Julie C Dunning Hotopp
Info:
This side-by-side comparison of PacBio and Oxford Nanopore sequencing platforms for the analysis of E.coli and Drosophila assemblies. The authors provide useful guidance for which platform or approach is better suited for different areas of study, as each platform can provide certain advantages. PacBio’s Sequel II CLR, Sequel II HiFi, and RS II were evaluated as was Oxford Nanopore’s Rapid Sequencing and Ligation Sequencing. Hybrid approaches using Illumina sequencing were also evaluated.
BluePippin was used to size select libraries for both platforms.
Author Affiliations:
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
Department of Biology, Texas A&M University, College Station, TX
Department of Entomology, Texas A&M University, College Station, TX
G3 Genes|Genomes|Genetics
DOI:10.1093/g3journal/jkab083
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
April 2021
Authors:
Multiple authors, the SEQC2 Oncopanel Sequencing Working Group
Info:
A multi-site and cross-platform evaluation of circulating tumor DNA (ctDNA) NGS assays was conducted by the SEQC2 Oncopanel Sequencing Working Group and reported on in this comprehensive study. Five assays were tested for accuracy, sensitivity and reproducibility including simulations with spike-in DNA. This study is intended to report the state-of-the-art of these assays and inform best practices.
Pippin Prep was used to size select the ctDNA reference samples using 110 bp start and 190 bp end settings for an average fragment length of ~150 bp.
Nature Biotechnology
DOI: 10.1038/s41587-021-00857-z