Universität zu Köln

Gao, Shan ORCID: 0000-0002-7392-711X (2025). The genomic implications of sex and its absence in old taxa. PhD thesis, Universität zu Köln.

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Abstract

Reproduction is a fundamental characteristic of organisms, and sexual reproduction is nearly universal in eukaryotes. The last eukaryotic common ancestor (LECA) is thought to have been capable of sexual reproduction, as this mode of reproduction is common across many different groups of eukaryotes. Sexual reproduction has three critical processes: meiosis, recombination and cell fusion, all of which are considered ancient aspects of sexual reproduction. Protists are considered the closest eukaryotes to the LECA and have evolved into many clades. Their abundance and primitive characteristics are crucial for elucidating the origins and evolution of sexual reproduction. However, most of the protists were considered to be asexual or facultative sex because of less sexual behavior or gender observed. This may be due to the protists being too diminutive to directly observe and trace in nature, and examining their entire lifespan when culturing most unicellular protists in laboratory presents a challenge. Detecting potential sexual processes by identifying meiosis-related genes and their expression dynamics may serve as a valuable approach during cell fusion. Fisculla terrestris (Thecofilosea, Rhizaria, SAR Supergroup) is a unicellular, shell-bearing amoeba living in soils that can be reared in the lab. Starvation triggers cell fusion and cell disintegration when food re-supplied are observed in F. terrestris. To check the presence of meiosis-associated genes and the dynamics of their expression during cell separation and aggregation, we sequenced the transcriptomes of the two treatments of starvation and food supply. We found that genes related to recombination are upregulated in the starving treatment compared to the food supply treatment. This might imply the exchange of genetic material and cryptic sex. Contrasting unicellular protists, most metazoans are known to reproduce sexually. However, there are a few metazoans that have stopped reproducing sexually and reproduce obligately asexually. Although asexuality was regarded as a dead end in evolution due to harmful mutation accumulation, some organisms still survived and evolved in the long-term without sex: "ancient asexual scandals," such as oribatid mites, bdelloid rotifers, and darwinulid ostracods. Studying how these organisms escape extinction and adapt to the environment can help us to understand why sexual reproduction is important and how these species evolved. To elucidate the enigma of asexual evolution following a prolonged absence of sex, we used genome and haplotypic assemblies of P. peltifer to detect genomic features as a consequence of asexuality over time. We detected the “Meselson effect” in the P. peltifer genome, which indicated long-term asexual reproduction. The haplotypes independently evolved, leading to one allele relaxed and the other allele conserved, which was also reflected on the patterns of differently expressed alleles (DEAs) and horizontal gene transfer (HGT). About 2% of genes showed a HGT origin, and they might provide new traits like cell wall degradation and pesticide resistance, strengthening the mites as decomposers in soil. Selection analysis showed that most of the alleles are under purifying selection, potentially alleviating deleterious mutation accumulation, while certain genes under positive selection may facilitate adaptation. Our results provide insight into long-term asexual genomic features and the potential mechanism for ancient asexual persistence and evolution. Exploring the sexual reproduction of basal eukaryotic protists and studying the genomic features of obligately ancient asexual mites can help understand the prevalence of sexual reproduction. Additionally, the putative sexual reproduction in protists and genomic evolution after loss of sex in mites can provide a new insight into the implication of sexual reproduction.

Item Type:	Thesis (PhD thesis)
Translated title:	Title Language The genomic implications of sex and its absence in old taxa English
Creators:	Creators Email ORCID ORCID Put Code Gao, Shan gaoshan12138@gmail.com orcid.org/0000-0002-7392-711X UNSPECIFIED
URN:	urn:nbn:de:hbz:38-787715
Date:	2025
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Zoologisches Institut
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language sex evolution English meiosis English asexual reproduction English
Date of oral exam:	22 July 2025
Referee:	Name Academic Title Wiehe, Thomas Prof. Dr. Thomma, Bart Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/78771