Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq
- 3 April 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Protocols
- Vol. 15 (5), 1673-1689
- https://doi.org/10.1038/s41596-020-0301-0
Abstract
Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long.Keywords
Funding Information
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Grant 181602)
- Fonds De La Recherche Scientifique - FNRS (1.B456.20, M.i.S. F.4515.17)
This publication has 26 references indexed in Scilit:
- A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the fieldNucleic Acids Research, 2018
- Circular DNA elements of chromosomal origin are common in healthy human somatic tissueNature Communications, 2018
- Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeriProceedings of the National Academy of Sciences of the United States of America, 2018
- Cassava Mosaic and Brown Streak Diseases: Current Perspectives and BeyondAnnual Review of Virology, 2017
- Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the CirculationMolecular Cancer Research, 2017
- New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and MetagenomicsPLOS ONE, 2015
- Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern BrazilPLOS ONE, 2015
- Global Genomic Diversity of Human Papillomavirus 6 Based on 724 Isolates and 190 Complete Genome SequencesJournal of Virology, 2014
- Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal TissuesScience, 2012
- Sequencing genomes from single cells by polymerase cloningNature Biotechnology, 2006