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Chicago and Dovetail Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome

Andrew B. Nuss, Arvind Sharma, View ORCID ProfileMonika Gulia-Nuss
doi: https://doi.org/10.1101/392126
Andrew B. Nuss
1Department of Biochemistry and Molecular Biology, University of Nevada, Reno, USA
2Department of Agriculture, Nutrition, and Veterinary Sciences, University of Nevada, Reno, USA
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Arvind Sharma
1Department of Biochemistry and Molecular Biology, University of Nevada, Reno, USA
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Monika Gulia-Nuss
1Department of Biochemistry and Molecular Biology, University of Nevada, Reno, USA
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  • ORCID record for Monika Gulia-Nuss
  • For correspondence: mgulianuss@unr.edu
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Abstract

A high-quality genome sequence is essential for understanding an organism on molecular level. However, the larger genomes with substantial repetitive sequences are challenging to assemble with the sequencing technologies. Hi-C technique is changing the genome architecture landscape by providing links across a variety of length scales, spanning even whole chromosomes. Ixodes scapularis haploid genome is 2.1 gbp and the current assembly consists of 369,495 scaffolds representing 57% of the genome. The fragmented genome poses challenges with functional gene analysis and an improved assembly is needed. We therefore used the Hi C technique to achieve chromosomal level assembly of tick genome. With Chicago and Dovetail Hi C assemblies, we were able to achieve 28 >10Mb sequences that correspond to 28 chromosomes in I. scapularis.

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Posted August 15, 2018.
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Chicago and Dovetail Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome
Andrew B. Nuss, Arvind Sharma, Monika Gulia-Nuss
bioRxiv 392126; doi: https://doi.org/10.1101/392126
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Chicago and Dovetail Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome
Andrew B. Nuss, Arvind Sharma, Monika Gulia-Nuss
bioRxiv 392126; doi: https://doi.org/10.1101/392126

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