Genome evolution and transposable element expansion reveal host-associated genomic features in Cladosporium cucumerinum

How pathogens adapt to specific hosts remains an open question. Here, we investigate Cladosporium cucumerinum, a pathogen largely associated with Cucurbitaceae. Comparative genomic analysis of five newly Cladosporium sequenced genomes together with 19 publicly available genomes indicates that the diversification of C. cucumerinum occurred after that of its cucumber host lineage. We observe gene family contraction alongside lineage-specific expansion of long terminal repeat retrotransposons, accompanied by variation in gene repertoires including carbohydrate-active enzymes and secondary metabolite gene clusters. A lineage-specific β-glucosidase, CcBGL258, is required for pathogenicity but is dispensable for vegetative growth under in vitro conditions. Transcriptomic analyses reveal dynamic changes in gene expression during infection in both the pathogen and the host. Together, these results provide a genomic framework for host-associated features in C. cucumerinum, although we highlight that several associations observed in the study remain correlative and require further functional validation.

The authors acknowledge support for this work from the Organism Interaction Program of Zhejiang Xianghu Laboratory, the Key R&D Program of Zhejiang Province (2024SSYS0104), the Lingyan Research and Development Project of Zhejiang Province (2022C02029), and the Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding (2021C02064).

State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Provincial Key Laboratory of Agricultural Microbiomics, Institute of Biotechnology, Zhejiang University, Hangzhou, China

Xuanjun Lu, Qianxi Li, Zhenfeng Bai, Mengrong Wang, Wenxiu Zheng, Hongkai Wang, Zhenzhu Su & Fucheng Lin

State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Provincial Key Laboratory of Agricultural Microbiomics, Key Laboratory of Agricultural Microbiome (MARA), Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China

College of Life Sciences, Nanjing Agricultural University, Nanjing, China

The authors declare no competing interests.

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Lu, X., Li, Q., Zeng, Y. et al. Genome evolution and transposable element expansion reveal host-associated genomic features in Cladosporium cucumerinum. Commun Biol (2026). https://doi.org/10.1038/s42003-026-10563-8

DOI: https://doi.org/10.1038/s42003-026-10563-8

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