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PreprintCited by 5Chromosomal and Genetic VariationsAnimal Behavior and ReproductionEvolution and Genetic Dynamics

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Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

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Almeida, Miguel Vasconcelos, Blumer, Moritz, Yuan, Chengwei Ulrika, Sierra, Pío, Price, Jonathan L., Quah, Fu Xiang, Friman, Aleksandr, Dallaire, Alexandra, Vernaz, Grégoire, Putman, Audrey L. K., Smith, Alan M., Joyce, Domino A., Butter, Falk, Haase, Astrid D., Durbin, Richard, Santos, M. Emília, Miska, Eric A.·2024·bioRxiv (Cold Spring Harbor Laboratory)
DOI 10.1101/2024.04.01.587621PMC PMC11014572

Preprint — published as 10.1186/s13059-025-03475-z

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Abstract

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

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Metadata

Authors
Almeida, M. V., Blumer, M., Yuan, C. U., Sierra, P., Price, J. L., Quah, F. X., Friman, A., Dallaire, A., Vernaz, G., Putman, A. L. K., Smith, A. M., Joyce, D. A., Butter, F., Haase, A. D., Durbin, R., Santos, M. E., & Miska, E. A.
Affiliations
  • University of Cambridge (GB)
  • National Institutes of Health (US)
  • University of Basel (CH)
  • University of Hull (GB)
  • Friedrich-Loeffler-Institut (DE)
Corresponding author
Almeida, Miguel Vasconcelos
ORCID
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2024-04-01
DOI
10.1101/2024.04.01.587621
PMC
PMC11014572
OpenAlex
W4393444553
Cited by
5
References
3
Citations by year
2026: 1 · 2025: 2 · 2024: 2
Type
posted content
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
Funders
  • Wellcome Trust (207492, 219475/Z/19/Z, 092096/Z/10/Z, Z/17/Z, C6946/A24843, 203144, 108864/B/15/Z, 092096, 203144/Z/16/Z)
  • Cancer Research UK (C6946/A24843, 092096, C6946, A24843, C13474/A27826)
  • University of Cambridge
  • European Commission (101027241, 219475, HORIZON2020, 956229)
  • University of Stirling
  • Cambridge Trust
  • Medical Research Council
  • Natural Environment Research Council (NE/R01504X/1, IRF NE/R01504X/1)
  • National Institute of Diabetes and Digestive and Kidney Diseases (DK075111, ZIADK075111)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Animal Behavior and Reproduction
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
transposable elements, piRNA pathway, piggyBac transposon, transposon silencing, epigenetic silencing, African cichlid fishes, Lake Malawi cichlids, gonad development, early development, gene family expansion, positive selection, coevolution, genomic diversity

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