Optimising ddRAD sequencing for population genomic studies with ddgRADer
October 2022
Authors:
Aparna Lajmi, Felix Glinka, Eyal Privman
Info:
In this preprint, the authors describe an online webtool that they have developed for designing ddRAD-seq experiments. This webtool assists in the recommendation of restriction enzyme pairs and size-selection criteria. This can assist in make the size selection process more robust, leading to higher sequencing efficiency.
ddgRADer can be accessed here: http://ddgrader.haifa.ac.il/
Author Affiliations:
Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Israel
BioRxiv Preprint
DOI: 10.1101/2022.10.08.508655
Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients
September 2022
Authors:
Elsie Cheruba, Ramya Viswanathan, Pui-Mun Wong, Howard John Womersley,
Shuting Han, Brenda Tay, Yiting Lau, Anna Gan, Polly S. Y. Poon, Anders Skanderup,
Sarah B. Ng, Aik Yong Chok, Dawn Qingqing Chong, Iain Beehuat Tan, Lih Feng Cheow
Info:
The authors outline a method (Heatrich-BS) for enriching GC-rich regions (CpG islands) in cell free DNA by heating the sequencing libraries prior to performing bisulfite sequencing. Since methylation profiles are key biomarkers for many cancers, this method provides a low cost and scalable method for clinical assays. The authors also provide an algorithm for monitoring response to colorectal cancer treatment in patients.
BluePippin was used size select the libraries prior to sequencing.
Author Affiliations:
Department of Biomedical Engineering, National University of Singapore
Institute for Health Innovation and Technology, National University of Singapore
Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore
Division of Medical Oncology, National Cancer Centre Singapore,
Department of Colorectal Surgery, Singapore General Hospital, Singapore
Medical School, National University of Singapore, Singapore
Science Advances
DOI: 10.1126/sciadv.abn4030
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