The genome-wide meiotic recombination landscape in ciliates and its implications for crossover regulation and genome evolution

Lu Fu; Chen Gu; Kazufumi Mochizuki; Jie Xiong; Wei Miao; Guangying Wang

doi:10.1016/j.jgg.2023.09.013

Volume 51 Issue 3

Mar. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(3): 302-312

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The genome-wide meiotic recombination landscape in ciliates and its implications for crossover regulation and genome evolution

doi: 10.1016/j.jgg.2023.09.013

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:

We would like to thank Xiaocui Chai at The Analysis and Testing Center of Institute of Hydrobiology, Chinese Academy of Sciences for her help with genome sequencing experiments. We also thank the members of Protist 10,000 Genomes Project (P10K) consortium for their helpful suggestions. The bioinformatics analysis was supported by the Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China. The culture and storage of cell strains was supported by the National Aquatic Biological Resource Center (NABRC). This work was supported by the Bureau of Frontier Sciences and Education, Chinese Academy of Sciences (ZDBS-LY-SM026), the National Natural Science Foundation of China (32370457, 32122015, 32130011, 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).

Received Date: 2023-08-12
Accepted Date: 2023-09-27
Rev Recd Date: 2023-09-26
Publish Date: 2023-10-04

Abstract

Abstract

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 towards 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.
- Meiotic recombination,
- Hotspot,
- Crossover interference,
- Adaptive evolution

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References(75)

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