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Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies
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  • Kazuaki Yamaguchi,
  • Mitsutaka Kadota,
  • Osamu Nishimura,
  • Yuta Ohishi,
  • Yuki Naito,
  • Shigehiro Kuraku
Kazuaki Yamaguchi
RIKEN Center for Biosystems Dynamics Research

Corresponding Author:kazuaki.yamaguchi@riken.jp

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Mitsutaka Kadota
RIKEN Center for Biosystems Dynamics Research
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Osamu Nishimura
RIKEN Center for Biosystems Dynamics Research
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Yuta Ohishi
RIKEN Center for Biosystems Dynamics Research
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Yuki Naito
Database Center for Life Science
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Shigehiro Kuraku
RIKEN Center for Biosystems Dynamics Research
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Abstract

The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture that was originally developed for investigating the long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi-C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi-C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome-scale genome assemblies using single-copy reference orthologs, and report problems of the widely used program pipeline BUSCO.
10 May 2021Submitted to Molecular Ecology
24 May 2021Reviewer(s) Assigned
26 Jun 2021Review(s) Completed, Editorial Evaluation Pending
12 Jul 2021Editorial Decision: Revise Minor
28 Jul 2021Review(s) Completed, Editorial Evaluation Pending
28 Jul 20211st Revision Received
18 Aug 2021Editorial Decision: Accept
Dec 2021Published in Molecular Ecology volume 30 issue 23 on pages 5923-5934. 10.1111/mec.16146