[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Mehta, Devang
Cornet, Luc ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
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Bibliography
De Sales Lima, F. E. et al. Genomic characterization of novel circular ssDNA viruses from insectivorous bats in Southern Brazil. PLoS One 10, 1–11 (2015).
Hansen, T. A. et al. New type of papillomavirus and novel circular single stranded DNA virus discovered in urban Rattus norvegicus using circular DNA enrichment and metagenomics. PLoS One 10, 1–11 (2015).
Jelen, M. M. et al. Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences. J. Virol. 88, 7307–7316 (2014).
Mehta, D. et al. 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 field. Nucleic Acids Res. 47, e9 (2019).
Rey, C. & Vanderschuren, H. V. Cassava mosaic and brown streak diseases: current perspectives and beyond. Annu. Rev. Virol. 4, 429–452 (2017).
Shibata, Y. et al. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 336, 82–86 (2012).
Møller, H. D. et al. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nat. Commun. 9, 1–12 (2018).
Kumar, P. et al. Normal and cancerous tissues release extrachromosomal circular DNA (eccDNA) into the circulation. Mol. Cancer Res. 15, 1–8 (2017).
Koo, D.-H. et al. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc. Natl Acad. Sci. USA 115, 3332–3337 (2018).
Zhang, K. et al. Sequencing genomes from single cells by polymerase cloning. Nat. Biotechnol. 24, 680–686 (2006).
Whon, T. W. et al. Metagenomic characterization of airborne viral DNA diversity in the near-surface atmosphere. J. Virol. 86, 8221–8231 (2012).
Rosario, K., Morrison, C. M., Mettel, K. A. & Betancourt, W. Q. Novel circular Rep-encoding single-stranded DNA viruses detected in treated wastewater. Microbiol. Resour. Announc. 8, 9–10 (2019).
Møller, H. D., Parsons, L., Jørgensen, T. S., Botstein, D. & Regenberg, B. Extrachromosomal circular DNA is common in yeast. Proc. Natl Acad. Sci. USA 112, E3114–E3122 (2015).
Shoura, M. J. et al. Intricate and cell type-specific populations of endogenous circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. G3 (Bethesda) 7, 3295–3303 (2017).
Lanciano, S. et al. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet. 13, e1006630 (2017).
Møller, H. D. et al. Formation of extrachromosomal circular DNA from long terminal repeats of retrotransposons in Saccharomyces cerevisiae. G3 (Bethesda) 6, 453–462 (2016).
Volden, R. et al. Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc. Natl Acad. Sci. USA 115, 9726–9731 (2018).
Roux, S. et al. Minimum information about an uncultivated virus genome (MIUVIG). Nat. Biotechnol. 37, 29–37 (2019).
Nooij, S., Schmitz, D., Vennema, H., Kroneman, A. & Koopmans, M. P. G. Overview of virus metagenomic classification methods and their biological applications. Front. Microbiol. 9, 749 (2018).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Li, W. & Godzik, A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Chang, S., Puryear, J. & Cairney, J. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Report. 11, 113–116 (1993).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–1797 (2004).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009).
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