Z-Calling: a tool for A/Z (2,6-diaminopurine) base calling and dZ-DNA detection using PacBio HiFi reads

Pacbio CCS BAMs (containing kinetics signals) sequenced by our lab have been deposited in Genome Sequence Archive of China National Center for Bioinformation in project ID PRJCA031439 under GSA accessions CRA020168, CRA019888, and CRA020191. Human Sequel Ⅱ(HG002) and Revio (HG00106) datasets were acquired from the study of Baid et al.⁴² and Human Pangenome Reference Consortium³⁴, which are available at https://console.cloud.google.com/storage/browser/details/brain-genomics-public/research/deepconsensus/publication/sequencing/hg00215kb/m64008201124002822.subreads.bam?pageState=(%22StorageObjectListData%22:(%22f%22:%22%255B%255D%22))&walkthrough%20id=panels–storage–bucket and https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC/HG00106/raw_data/PacBio_HiFi/m84081_231112_034048_s4.hifi_reads.bc2070.bam. The plasmids pRS426-ApPurZ-ApdATPase and pRS425-ApDUF550 generated during the current study are available from the corresponding author on reasonable request under a standard Material Transfer Agreement. Source data for the graphs and charts in this study are available in the Figshare repository (https://doi.org/10.6084/m9.figshare.31281748)⁴³.

All codes written and used by this study have been deposited in our github repository (https://github.com/xiaochuanle/Z-Calling) and in Zenodo (https://doi.org/10.5281/zenodo.17840213)⁴¹. Partial command lines used in data analysis are described in Supplementary Notes.

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Author notes

1. These authors contributed equally: Bo Wu, Ying Chen, Yan Zhou, Longjian Niu, He-Xu Chen.

Authors and Affiliations

1. Shenzhen Eye Hospital, Shenzhen Eye Medical Center, Southern Medical University, 18 Zetian Road, Futian District, Shenzhen, China

   Bo Wu, Ying Chen, Longjian Niu, Jia-Yong Zhong & Wei Chi

2. State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China

   Bo Wu & Chuan-Le Xiao

3. Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China

   Yan Zhou & Yating Li

4. School of Artificial Intelligence, Sun Yat-Sen University, Zhuhai, China

   He-Xu Chen

5. iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai, China

   Suwen Zhao

6. Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai, China

   Suwen Zhao

7. Shanghai Clinical Research and Trial Center, Shanghai, China

   Suwen Zhao

8. Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China

   Yan Zhang

9. New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China

   Yan Zhang

10. Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China

    Yan Zhang

11. State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Yan Zhang

Contributions

C.-L.X., Y.Zhang, W.C., and S.Z. conceived the study. B.W., Y.C., C.-L.X., and H.-X.C. implemented the algorithms of Z-Calling. H.-X.C., Y.C., and B.W. wrote the codes of Z-Calling. L.N., Y.Zhou, and Y.L. carried out experiments. B.W., Y.Zhou, and J.-Y.Z. carried out data analysis. B.W., Y.Zhang, Y.C., Y.Zhou, L.N., and H.-X.C. wrote the manuscript. S.Z., W.C, C.-L.X., J.-Y.Z., and Y.L. modified and improved the manuscript. All authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Suwen Zhao, Wei Chi, Yan Zhang or Chuan-Le Xiao.

Competing interests

The authors declare no competing interests.

Peer review information

Communications Biology thanks Shanmuga Sozhamannan who co-reviewed with Rachael Sparklin; Osman Doluca and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editors: Rosie Bunton-Stasyshyn. A peer review file is available.

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