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Chromosome-scale assembly and annotation of Phytophthora capsici isolate BYA5
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  • Published: 05 January 2026

Chromosome-scale assembly and annotation of Phytophthora capsici isolate BYA5

  • Yiman Wan1,2 na1,
  • Fuqiang Zhu2,3 na1,
  • Meng Zhang2,
  • Xiaohui Li2,4,
  • Chunxue Xie2,5,
  • Shenglan Gao2,6,
  • Qunqing Wang  ORCID: orcid.org/0000-0002-3424-80181 &
  • …
  • Yuan Chen2,6 

Scientific Data , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Genome assembly algorithms
  • Pathogens

Abstract

Phytophthora capsici is a globally widespread oomycete pathogen that causes severe damage to diverse host plants, posing major agricultural challenges. Here, we present a high-quality, chromosome-level genome assembly of P. capsici isolate BYA5 using PacBio HiFi, ultralong Oxford Nanopore, and Hi-C sequencing data. The assembled genome spans 83.96 Mb and comprises 18 chromosomes, capturing all centromeres and most telomeres (32/36). The assembled genome exhibits a contiguous N50 of 3.84 Mb, representing the first chromosome-level genome sequence of a pathogenic P. capsici. A total of 15,688 protein-coding genes were annotated, including 337 RxLRs and 115 Crinkler (CRN) effectors. This high-quality reference genome provides a valuable resource for advancing our understanding of oomycete pathobiology and evolution, facilitating further research on virulence mechanisms and host-pathogen interactions.

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Data availability

The authors confirm that the data supporting the findings of this study are available in the National Genomics Data Center (NGDC), and National Center for Biotechnology Information (NCBI), and figshare, can be accessed via. https://ngdc.cncb.ac.cn/gwh/Assembly/92621/show (assembled genome in NGDC). https://ngdc.cncb.ac.cn/gsa/browse/CRA025046 (raw data in NGDC). https://identifiers.org/ncbi/insdc.gca:GCA_053541045.1 (assembled genome in NCBI). https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1248058 (raw data in NCBI). https://doi.org/10.6084/m9.figshare.28856261 (genome annotations archive in figshare).

Code availability

All commands and pipelines used in data processing were executed according to the manual and protocols of the corresponding bioinformatic software and described in the Methods section, along with the versions. No custom code was generated for these analyses.

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Acknowledgements

This work was supported by Taishan Scholar Foundation of Shandong Province (tsqn202103162, tsqn202211093), Key R&D Program of Shandong Province, China (2024CXPT03), Yunnan Department of Science and Technology-Development and adoption of innovative ‘green’ management tools against insect pest and disease on tomato and pepper in Yunnan (No. 202502AQ370001), the Natural Science Foundation of Shandong Province (SYS202206), National Natural Science Foundation of China (32172387). We thank Dr. Xili Liu of Northwest Agriculture and Forestry University for providing P. capsici isolate BYA5. We thank Dr. Daolong Dou of Nanjing Agricultural University for providing the genomic data and GFF annotation files of P. capsici isolate LT263. This work was supported by the bioinformatics services from Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China), particularly in data processing and genomic annotation.

Author information

Author notes

  1. These authors contributed equally: Yiman Wan, Fuqiang Zhu.

Authors and Affiliations

  1. College of Plant Protection, Shandong Agricultural University, Tai’an, 271018, Shandong, China

    Yiman Wan & Qunqing Wang

  2. State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China

    Yiman Wan, Fuqiang Zhu, Meng Zhang, Xiaohui Li, Chunxue Xie, Shenglan Gao & Yuan Chen

  3. State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, 271018, China

    Fuqiang Zhu

  4. College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China

    Xiaohui Li

  5. State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, 271018, China

    Chunxue Xie

  6. Southwest United Graduate School, Kunming, 650092, China

    Shenglan Gao & Yuan Chen

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Contributions

Y.C. and Q.W. conceived and supervised the project. Y.W., F.Z., C.X. and X.L. collected the samples and strain preservation; M.Z. and Y.W. performed the genomic data analysis; S.G. submitted the genome assembly data to the NCBI database. Y.W. and F.Z. drafted the initial version of the manuscript. Q.W. and Y.C. finalized the manuscript. All authors read and prove the final version of the manuscript.

Corresponding authors

Correspondence to Qunqing Wang or Yuan Chen.

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The authors declare no competing interests.

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Supplementary information

Distribution of RxLR and CRN effectors in the P. capsici isolate BYA5.

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Wan, Y., Zhu, F., Zhang, M. et al. Chromosome-scale assembly and annotation of Phytophthora capsici isolate BYA5. Sci Data (2026). https://doi.org/10.1038/s41597-025-06501-8

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  • Received: 28 April 2025

  • Accepted: 18 December 2025

  • Published: 05 January 2026

  • DOI: https://doi.org/10.1038/s41597-025-06501-8

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