May 31, 2022

Public workspaceHi-C library construction from young Maize leaves

DOI
dx.doi.org/10.17504/protocols.io.bp2l61mkzvqe/v1
  • Yikun Zhao1,
  • Yuancong Wang1,
  • De Ma2,
  • Guang Feng3,
  • Yongxue Huo1,
  • Zhihao Liu1,
  • Ling Zhou4,
  • Yunlong Zhang1,
  • Liwen Xu1,
  • Liang Wang3,
  • Han Zhao4,
  • Jiuran Zhao1,
  • Fengge Wang1
  • 1Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding;
  • 2Novogene Bioinformatics Institute;
  • 3Dandong Academy of Agricultural Sciences;
  • 4Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences
wjcjxqw.jpg
Icon indicating open access to content
QR code linking to this content
DOI: dx.doi.org/10.17504/protocols.io.bp2l61mkzvqe/v1
External link: https://doi.org/https://doi.org/10.1101/2021.04.26.441299
Protocol Citation: Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang 2022. Hi-C library construction from young Maize leaves. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l61mkzvqe/v1
Manuscript citation:
Zhao Y, Wang Y, Ma D, Feng G, Huo Y, Liu Z, Zhou L, Zhang Y, Xu L, Wang L, Zhao H, Zhao J, Wang F, A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340. GigaByte doi: https://doi.org/10.1101/2021.04.26.441299
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: May 18, 2022
Last Modified: May 31, 2022
Protocol Integer ID: 62800
Abstract
In a recent study we constructed a high-quality chromosome-level reference genome for the maize cultivar Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads.

A Hi-C library was constructed using young leaves following previously published procedures with slight modifications. See the source paper and the following protocol.

CITATION
Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J (2012). Hi-C: a comprehensive technique to capture the conformation of genomes.. Methods (San Diego, Calif.).
LINK
https://doi.org/10.1016/j.ymeth.2012.05.001

ApproximatelyAmount5 g leaf samples from seedling were cut into minute pieces and cross-linked by 4% formaldehyde solution at room temperature in a vacuum forDuration00:30:00 .

30m
Each sample was mixed with an excess of Concentration2.5 Molarity (M) glycine to quench the crosslinking reaction for Duration00:05:00 and then placed on ice forDuration00:15:00 .

20m
The cross-linked DNA was extracted and then digested for Duration12:00:00 with 20 units of DpnII restriction enzyme (NEB) at Temperature37 °C , and the resuspended mixture was incubated atTemperature65 °C forDuration00:20:00 to inactivate the restriction enzyme.

12h 20m
The sticky ends of the digested fragments were biotinylated and proximity ligated to form enriched ligation junctions and then ultrasonically sheared to a size of 300 - 600 bp.
The biotin-labelled DNA fragments were pulled down and ligated with Illumina paired-end adapters, and then amplified by PCR to produce the Hi-C sequencing library.
The library was sequenced using an Illumina HiSeq X Ten platform with 2 × 150 bp paired-end reads (Illumina, San Diego, CA, USA).
After removing low-quality sequences and trimming adapter sequences, we had 304.37 Gb (approximately 130×) of clean data generated. This is then used for genome assembly.
Citations
Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes.
https://doi.org/10.1016/j.ymeth.2012.05.001