A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes

Heiner Kuhl, Wen Hui Tan, Christophe Klopp, Wibke Kleiner, Baturalp Koyun, Mitica Ciorpac, Romain Feron, Martin Knytl, Werner Kloas, Manfred Schartl, Christoph Winkler () and Matthias Stöck ()
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Heiner Kuhl: Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Wen Hui Tan: National University of Singapore
Christophe Klopp: INRAe
Wibke Kleiner: Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Baturalp Koyun: Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Mitica Ciorpac: Danube Delta National Institute for Research and Development
Romain Feron: University of Lausanne
Martin Knytl: Charles University
Werner Kloas: Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Manfred Schartl: University of Wuerzburg, Am Hubland
Christoph Winkler: National University of Singapore
Matthias Stöck: Leibniz-Institute of Freshwater Ecology and Inland Fisheries

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5′-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.

Date: 2024
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DOI: 10.1038/s41467-024-49025-2

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