rDNA array length is a major determinant of replicative lifespan in budding yeast
April 2022
Authors:
Manuel Hotz, Nathaniel H. Thayer, David G. Hendrickson, Elizabeth L. Schinski, Jun Xu, and Daniel E. Gottschling
Info:
The authors propose a new mechanism for aging and lifespan determination in budding yeast.
The researchers “discovered a previously unappreciated relationship between the number of copies of the ribosomal RNA gene present in its chromosomal array and replicative lifespan (RLS). Specifically, the chromosomal ribosomal DNA (rDNA) copy number (rDNA CN) positively correlated with RLS and this interaction explained over 70% of variability in RLS among a series of wild-type strains. In strains with low rDNA CN, SIR2 expression was attenuated and extra chromosomal rDNA circle (ERC) accumulation was increased, leading to shorter lifespan.”
Pippin Prep was used for DNA size selection for ATAC-seq analysis.
Author Affiliations:
Calico Life Sciences LLC, South San Francisco, CA
PNAS Genetics
DOI: 10.1073/pnas.2119593119
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