Long and ultra-long read DNA sequencing technologies require high molecular weight DNA with high quality and sufficient quantity, which could be challenging to obtain from recalcitrant plant tissues. We describe a protocol to isolate ultra-long DNA from 12 species for ultra-long read genome sequencing. A suitable nuclei lysis buffer is critical for DNA quality and yield. This protocol will enable individual labs to isolate high molecular weight DNA at a rapid pace with low cost from a variety of plant species. For complete information on the use and execution of this protocol, please refer to: Zhang et al. (2020).

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902544PMC
http://dx.doi.org/10.1016/j.xpro.2021.100343DOI Listing

Publication Analysis

Top Keywords

ultra-long read
12
ultra-long dna
8
read genome
8
genome sequencing
8
high molecular
8
molecular weight
8
weight dna
8
ultra-long
5
dna
5
dna molecule
4

Similar Publications

Single-molecule toxicogenomics: Optical genome mapping of DNA-damage in nanochannel arrays.

DNA Repair (Amst)

January 2025

School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel; Department of Biomedical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel. Electronic address:

Quantitative genomic mapping of DNA damage may provide insights into the underlying mechanisms of damage and repair. Sequencing based approaches are bound to the limitations of PCR amplification bias and read length which hamper both the accurate quantitation of damage events and the ability to map them to structurally complex genomic regions. Optical Genome mapping in arrays of parallel nanochannels allows physical extension and genetic profiling of millions of long genomic DNA fragments, and has matured to clinical utility for characterization of complex structural aberrations in cancer genomes.

View Article and Find Full Text PDF

DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (cancer and repetitive sequences-associated diseases) are regulated. Nanopore sequencing has emerged as a novel technique that can analyze long strands of DNA (long-read sequencing) without chemically treating the DNA. Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties.

View Article and Find Full Text PDF
Article Synopsis
  • Long-read technologies from PacBio and ONT have revolutionized genomics research, but there are ongoing challenges in representing genetic diversity and assembling comprehensive pangenomes.
  • The study investigates the necessary data types and volumes for effective de novo genome assembly in pangenome projects, comparing the performance of ONT's Duplex and PacBio HiFi datasets.
  • Results indicate that achieving high-quality phased genomes requires significant amounts of long reads and various supplemental data, with PacBio HiFi showing better phasing accuracy and ONT Duplex producing more complete contigs.
View Article and Find Full Text PDF

DeepCorr: a novel error correction method for 3GS long reads based on deep learning.

PeerJ Comput Sci

July 2024

Department of Electronic Engineering, Information School, Yunnan University, Kunming, Yunnan, China.

Long reads generated by third-generation sequencing (3GS) technologies are involved in many biological analyses and play a vital role due to their ultra-long read length. However, the high error rate affects the downstream process. DeepCorr, a novel error correction algorithm for data from both PacBio and ONT platforms based on deep learning is proposed.

View Article and Find Full Text PDF
Article Synopsis
  • - The study focuses on Facioscapulohumeral dystrophy type 1 (FSHD1), a serious muscle disorder, and emphasizes the need for a comprehensive approach to understand its genetics.
  • - Researchers conducted genome sequencing and linkage analysis in a family suspected of having FSHD1, identifying a specific disease locus on chromosome 4q35.2.
  • - By using advanced ultra-long-read genome sequencing, they successfully genotyped a pathogenic allele associated with FSHD1, highlighting the effectiveness of these genomic tools in disease mapping and characterization.
View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!