a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
b University of Chinese Academy of Sciences, Beijing 100049, China
c Institute of Human Genetics (IGH), CNRS, University of Montpellier, 34396 Montpellier, France
d Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
e Key laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
Funds:
This work was supported by the Bureau of Frontier Sciences and Education, Chinese Academy of Sciences (Grant No. ZDBS- LY-SM026), the National Natural Science Foundation of China (32122015, 31900316 and 31900339), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB0480000), PJA3 grant of ARC Foundation (ARCPJA2021060003830) and Equipes 2022 grant of Foundation Recherche Médicale (EQU202203014651).
Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa. However, genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates: the synaptonemal complex (SC)-independent meiosis and the nuclear dimorphism. Here we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny. We detect 1021 crossover (CO) events (35.8 per meiosis), corresponding to an overall CO rate of 9.9 cM/Mb. However, gene conversion by non-crossover is rare (1.03 per meiosis) and not biased toward G or C alleles. Consistent with the reported roles of SC in CO interference, we find no obvious sign of CO interference. CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions. Gene Ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes. We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.