Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C

Yu-Xi Lu , Jin-Bao Yang , Chen-Ying Li , Yun-Han Tian , Rong-Rong Chang , Da-Shuai Kong , Shu-Lin Yang , Yan-Fang Wang , Yu-Bo Zhang , Xiu-Sheng Zhu , Wei-Hua Pan , Si-Yuan Kong

iMeta ›› 2024, Vol. 3 ›› Issue (5) : e227

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iMeta ›› 2024, Vol. 3 ›› Issue (5) :e227 DOI: 10.1002/imt2.227
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Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C
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Yu-Xi Lu, Jin-Bao Yang, Chen-Ying Li, Yun-Han Tian, Rong-Rong Chang, Da-Shuai Kong, Shu-Lin Yang, Yan-Fang Wang, Yu-Bo Zhang, Xiu-Sheng Zhu, Wei-Hua Pan, Si-Yuan Kong. Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C. iMeta, 2024, 3(5): e227 DOI:10.1002/imt2.227

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References

[1]

Almeida, Alexandre, Alex L. Mitchell, Miguel Boland, Samuel C. Forster, Gregory B. Gloor, Aleksandra Tarkowska, Trevor D. Lawley, and Robert D. Finn. 2019. “A New Genomic Blueprint of the Human Gut Microbiota.” Nature 568: 499-504. https://doi.org/10.1038/s41586-019-0965-1

[2]

Parks, Donovan H., Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J. Woodcroft, Paul N. Evans, Philip Hugenholtz, and Gene W. Tyson. 2017. “Recovery of Nearly 8,000 Metagenome-Assembled Genomes Substantially Expands the Tree of Life.” Nature Microbiology 2: 1533-1542. https://doi.org/10.1038/s41564-017-0012-7

[3]

Quince, Christopher, Alan W. Walker, Jared T. Simpson, Nicholas J. Loman, and Nicola Segata. 2017. “Shotgun Metagenomics, from Sampling to Analysis.” Nature Biotechnology 35: 833-844. https://doi.org/10.1038/nbt.3935

[4]

Putnam, Nicholas H., Brendan L. O'Connell, Jonathan C. Stites, Brandon J. Rice, Marco Blanchette, Robert Calef, Christopher J. Troll, et al. 2016. “Chromosome-Scale Shotgun Assembly Using an in Vitro Method for Long-Range Linkage.” Genome Research 26: 342-350. https://doi.org/10.1101/gr.193474.115

[5]

Bickhart, Derek M., Mikhail Kolmogorov, Elizabeth Tseng, Daniel M. Portik, Anton Korobeynikov, Ivan Tolstoganov, Gherman Uritskiy, et al. 2022. “Generating Lineage-Resolved, Complete Metagenome-Assembled Genomes from Complex Microbial Communities.” Nature Biotechnology 40: 711-719. https://doi.org/10.1038/s41587-021-01130-z

[6]

Yaffe, Eitan, and Amos Tanay. 2011. “Probabilistic Modeling of Hi-C Contact Maps Eliminates Systematic Biases to Characterize Global Chromosomal Architecture.” Nature Genetics 43: 1059-1065. https://doi.org/10.1038/ng.947

[7]

Kong, Siyuan, and Yubo Zhang. 2019. “Deciphering Hi-C: from 3D Genome to Function.” Cell Biology and Toxicology 35: 15-32. https://doi.org/10.1007/s10565-018-09456-2

[8]

Gounot, Jean-Sebastien, Minghao Chia, Denis Bertrand, Woei-Yuh Saw, Aarthi Ravikrishnan, Adrian Low, Yichen Ding, et al. 2022. “Genome-Centric Analysis of Short and Long Read Metagenomes Reveals Uncharacterized Microbiome Diversity in Southeast Asians.” Nature Communications 13: 6044-6054. https://doi.org/10.1038/s41467-022-33782-z

[9]

Stewart, Robert D., Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximilian O. Press, Kyle W. Langford, Ivan Liachko, et al. 2018. “Assembly of 913 Microbial Genomes from Metagenomic Sequencing of the Cow Rumen.” Nature Communications 9: 870-880. https://doi.org/10.1038/s41467-018-03317-6

[10]

Bickhart, Derek M., Mick Watson, Sergey Koren, Kevin Panke-Buisse, Laura M. Cersosimo, Maximilian O. Press, Curtis P. Van Tassell, et al. 2019. “Assignment of Virus and Antimicrobial Resistance Genes to Microbial Hosts in a Complex Microbial Community By Combined Long-Read Assembly and Proximity Ligation.” Genome Biology 20: 153-170. https://doi.org/10.1186/s13059-019-1760-x

[11]

Stalder, Thibault, Maximilian O. Press, Shawn Sullivan, Ivan Liachko, and Eva M. Top. 2019. “Linking the Resistome and Plasmidome to the Microbiome.” The ISME Journal 13: 2437-2446. https://doi.org/10.1038/s41396-019-0446-4

[12]

Dixon, Jesse R., Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S. Liu, and Bing Ren. 2012. “Topological Domains in Mammalian Genomes Identified By Analysis of Chromatin Interactions.” Nature 485: 376-380. https://doi.org/10.1038/nature11082

[13]

Rao, Suhas S. P., Miriam H. Huntley, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, et al. 2014. “A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.” Cell 159: 1665-1680. https://doi.org/10.1016/j.cell.2014.11.021

[14]

Burton, Joshua N., Andrew Adey, Rupali P. Patwardhan, Ruolan Qiu, Jacob O. Kitzman, and Jay Shendure. 2013. “Chromosome-Scale Scaffolding of De Novo Genome Assemblies Based on Chromatin Interactions.” Nature Biotechnology 31: 1119-1125. https://doi.org/10.1038/nbt.2727

[15]

Marbouty, Martial, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, and Romain Koszul. 2014. “Metagenomic Chromosome Conformation Capture (meta3C) Unveils the Diversity of Chromosome Organization in Microorganisms.” eLife 3: e03318. https://doi.org/10.7554/eLife.03318

[16]

Zhang, Yan, Fan Jiang, Boyuan Yang, Sen Wang, Hengchao Wang, Anqi Wang, Dong Xu, and Wei Fan. 2022. “Improved Microbial Genomes and Gene Catalog of the Chicken Gut from Metagenomic Sequencing of High-Fidelity Long Reads.” GigaScience 11: giac116. https://doi.org/10.1093/gigascience/giac116

[17]

DeMaere, Matthew Z., and Aaron E. Darling. 2019. “bin3C: Exploiting Hi-C Sequencing Data to Accurately Resolve Metagenome-Assembled Genomes.” Genome Biology 20: 46-61. https://doi.org/10.1186/s13059-019-1643-1

[18]

Lieberman-Aiden, Erez, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, et al. 2009. “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.” Science 326: 289-293. https://doi.org/10.1126/science.1181369

[19]

Meslier, Victoria, Benoit Quinquis, Kévin Da Silva, Florian Plaza Oñate, Nicolas Pons, Hugo Roume, Mircea Podar, and Mathieu Almeida. 2022. “Benchmarking Second and Third-Generation Sequencing Platforms for Microbial Metagenomics.” Scientific Data 9: 694-702. https://doi.org/10.1038/s41597-022-01762-z

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2024 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.

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