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Genome fractionation and loss of heterozygosity in hybrids and polyploids: mechanisms, consequences for selection, and link to gene function

View ORCID ProfileKarel Janko, Oldřich Bartoš, View ORCID ProfileJan Kočí, Jan Roslein, Edita Janková Drdová, Jan Kotusz, Jan Eisner, Eva Štefková-Kašparová
doi: https://doi.org/10.1101/2020.07.30.229369
Karel Janko
1Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic
2Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Oldřich Bartoš
1Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic
3Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
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Jan Kočí
1Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic
2Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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  • For correspondence: janxkoci@gmail.com
Jan Roslein
1Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic
2Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Edita Janková Drdová
4Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
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Jan Kotusz
5Uniwersytet Przyrodniczy we Wroclawiu, Museum of Natural History, Wroclaw, Poland
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Jan Eisner
6Department of Mathematics and Biomathematics, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
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Eva Štefková-Kašparová
1Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic
7Czech Life Science university, Prague, Czech Republic
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Abstract:

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. During their evolution, the subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that may enforce specific evolutionary pathways.

We studied the genome evolution in asexual diploid and polyploid hybrids between fish from the genus Cobitis. Comparing exome sequencing with published cytogenetic and RNAseq data revealed that clonal genomes remain static on chromosome-scale levels but undergo considerable small-scale restructurations owing to two major processes; hemizygous deletions and gene conversions. Interestingly, polyploids were much more tolerant to accumulating deletions than diploid asexuals where gene conversions prevailed. The genomic restructurations accumulated preferentially in genes characterized by high transcription levels, relatively strong purifying selection and some specific functions such as interacting with intracellular membranes. The likelihood of an ortholog’s retention or loss correlated with its parental-species ancestry, GC content, and expression. Furthermore, all hybrids showed a strong bias towards the retention of one parental subgenome. Contrary to expectations, however, the preferentially retained subgenome was not transcriptionally dominant as all hybrids were phenotypically more similar to the other parent.

The present study demonstrated that the fate of subgenomes in asexual hybrids and polyploids depends on the complex interplay of selection and several molecular mechanisms whose impact depends on ploidy, sequence composition, gene expression as well as parental ancestry.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Updated abstract, figures, and English edited in parts of the text.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 24, 2020.
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Genome fractionation and loss of heterozygosity in hybrids and polyploids: mechanisms, consequences for selection, and link to gene function
Karel Janko, Oldřich Bartoš, Jan Kočí, Jan Roslein, Edita Janková Drdová, Jan Kotusz, Jan Eisner, Eva Štefková-Kašparová
bioRxiv 2020.07.30.229369; doi: https://doi.org/10.1101/2020.07.30.229369
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Genome fractionation and loss of heterozygosity in hybrids and polyploids: mechanisms, consequences for selection, and link to gene function
Karel Janko, Oldřich Bartoš, Jan Kočí, Jan Roslein, Edita Janková Drdová, Jan Kotusz, Jan Eisner, Eva Štefková-Kašparová
bioRxiv 2020.07.30.229369; doi: https://doi.org/10.1101/2020.07.30.229369

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