Universität zu Köln

Kuan, Chen-Yu ORCID: 0000-0002-1176-4802 (2026). Genome evolution in the plant-pathogenic fungus Verticillium dahliae in the absence of apparent sexual reproduction. PhD thesis, Universität zu Köln.

PDF PhD_thesis_Chen-Yu Kuan_wio_Declaration_CV_Signatures.pdf - Accepted Version Download (7MB)

Abstract

Sexual reproduction is a hallmark of eukaryotes and occurs across nearly all branches of the eukaryotic tree of life. By promoting genetic variation through meiotic recombination, it has played a fundamental role in the evolution of life. However, many eukaryotes present an evolutionary paradox because they do not exhibit apparent sexual reproduction, despite having the conserved genetic machinery required for this process. A classic example is the broad host-range vascular wilt pathogen Verticillium dahliae, which is considered strictly asexual because no sexual stage has been observed. Nevertheless, its genome contains genes typically involved in sexual reproduction, including mating-type (MAT) and meiotic genes. This raises the intriguing question whether these genes remain functional in V. dahliae. If so, they may support cryptic sexual reproduction, meaning rare and hidden sexual reproduction, or, alternatively, have been repurposed for biological processes beyond sexual reproduction. Moreover, the genome of V. dahliae is characterized by extensive large-scale chromosomal rearrangements, which are thought to be incompatible with proper chromosome pairing during meiosis and may therefore promote the persistence of asexuality in V. dahliae. These rearrangements contribute to the generation of highly dynamic adaptive genomic regions (AGRs) that facilitate host adaptation and are therefore considered important drivers of V. dahliae adaptation. Yet, it remains unclear whether such rearrangements represent ancient events inherited from ancestral V. dahliae lineages or continue to arise during ongoing genome evolution. During my doctoral research, I investigated how V. dahliae evolves in the absence of apparent sexual reproduction, with a particular focus on the occurrence of chromosomal rearrangements and the functional roles of MAT genes. To investigate the adaptability of V. dahliae, I first established a collection of V. dahliae lineages generated under diverse conditions, including abiotic stress and repeated passage through the host plant Arabidopsis thaliana. Among these lineages, I identified a de novo inter-chromosomal rearrangement that emerged after passage through A. thaliana, and demonstrated that this rearrangement confers a competitive advantage to V. dahliae during host colonization. These results show that large-scale chromosomal rearrangements can contribute to ongoing genome evolution and host adaptation in V. dahliae. Expanding beyond non-sexual mechanisms of genome evolution, we used transcriptomic analyses to show that the sexual machinery of V. dahliae is transcriptionally active, including MAT genes and 85 sex-related genes. These findings suggest that V. dahliae may have the potential for cryptic sexuality. Moreover, I showed that MAT genes influence transcription beyond the 85 identified sex-related genes, indicating noncanonical regulatory roles. These findings may help explain the paradox of MAT gene presence in V. dahliae, as MAT genes may contribute not only to sexual reproduction but also to broader biological processes.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Kuan, Chen-Yu kuancherry84@gmail.com https://orcid.org/0000-0002-1176-4802 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-810108
Date:	2026
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Botanical Institute
Subjects:	Natural sciences and mathematics Life sciences Agriculture
Uncontrolled Keywords:	Keywords Language Genome evolution English Fungal reproduction English Chromosomal rearrangement English
Date of oral exam:	16 July 2026
Referee:	Name Academic Title Thomma, Bart Prof. Dr. Cook, David Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/81010