Yelena Chernyavskaya1,2, Xiaofei Zhang2,3, Jinze Liu4, Jessica Blackburn5,6. 1. Department of Cellular & Molecular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA. 2. Markey Cancer Center at the University of Kentucky, Lexington, KY, 40536, USA. 3. Department of Computer Science, University of Kentucky, Lexington, KY, 40536, USA. 4. Department of Biostatistics, Virginia Commonwealth University, Richmond, USA. Jinze.Liu@vcuhealth.org. 5. Department of Cellular & Molecular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA. jsblackburn@uky.edu. 6. Markey Cancer Center at the University of Kentucky, Lexington, KY, 40536, USA. jsblackburn@uky.edu.
Abstract
BACKGROUND: Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers. RESULTS: We used long-read nanopore sequencing to generate a de novo assembly of the zebrafish genome and compared our assembly to the current reference genome, GRCz11. The new assembly identified 1697 novel insertions and deletions over one kilobase in length and placed 106 previously unlocalized scaffolds. We also discovered additional sites of retrotransposon integration previously unreported in GRCz11 and observed the expression of these transposable elements in adult zebrafish under physiologic conditions, implying they have active mobility in the zebrafish genome and contribute to the ever-changing genomic landscape. CONCLUSIONS: We used nanopore sequencing to improve upon and resolve the issues plaguing the current zebrafish reference assembly, GRCz11. Zebrafish is a prominent model of human disease, and our corrected assembly will be useful for studies relying on interspecies comparisons and precise linkage of genetic events to disease phenotypes.
BACKGROUND: Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers. RESULTS: We used long-read nanopore sequencing to generate a de novo assembly of the zebrafish genome and compared our assembly to the current reference genome, GRCz11. The new assembly identified 1697 novel insertions and deletions over one kilobase in length and placed 106 previously unlocalized scaffolds. We also discovered additional sites of retrotransposon integration previously unreported in GRCz11 and observed the expression of these transposable elements in adult zebrafish under physiologic conditions, implying they have active mobility in the zebrafish genome and contribute to the ever-changing genomic landscape. CONCLUSIONS: We used nanopore sequencing to improve upon and resolve the issues plaguing the current zebrafish reference assembly, GRCz11. Zebrafish is a prominent model of human disease, and our corrected assembly will be useful for studies relying on interspecies comparisons and precise linkage of genetic events to disease phenotypes.
Authors: I G Woods; P D Kelly; F Chu; P Ngo-Hazelett; Y L Yan; H Huang; J H Postlethwait; W S Talbot Journal: Genome Res Date: 2000-12 Impact factor: 9.043
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