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Correlation Between Subgenome-biased DNA Loss and DNA Transposon Activation Following Hybridization in the Allotetraploid Xenopus Frogs.
Suda, Kosuke; Suzuki, Takahiro; Hayashi, Shun; Okuyama, Honoka; Tsukamoto, Daisuke; Matsuo, Takuya; Tamura, Kei; Ito, Michihiko.
Afiliación
  • Suda K; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
  • Suzuki T; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
  • Hayashi S; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
  • Okuyama H; Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
  • Tsukamoto D; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
  • Matsuo T; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
  • Tamura K; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
  • Ito M; Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
Genome Biol Evol ; 16(9)2024 Sep 03.
Article en En | MEDLINE | ID: mdl-39304189
ABSTRACT
In certain tetraploid species resulting from interspecific hybridization, one parent's subgenome is known to selectively undergo DNA loss. The molecular mechanisms behind this remain unclear. In our study, we compared the genomes of a standard diploid species with two allotetraploid species from the Xenopus genus, both possessing L (longer) and S (shorter) homoeologous subgenomes. We observed substantial gene losses and intergenic DNA deletions in both the S and L subgenomes of the tetraploid species. Gene losses were around 1,000 to 3,000 for L and 4,000 to 6,000 for S, with especially prominent losses in the S subgenome. Many of these losses likely occurred shortly after interspecific hybridization in both L/S subgenomes. We also deduced frequent large inversions in the S subgenome. Upon reassessing transposon dynamics using updated genome databases, we reaffirmed heightened DNA transposon activity during the hybridization, as previously reported. We next investigated whether S subgenome-biased DNA loss could be correlated with the activation of DNA transposons following hybridization. Notably, distinct patterns were observed in the dynamics of DNA transposons between the L and S subgenomes. Several DNA transposon subfamilies correlated positively with DNA deletions in the S subgenome and negatively in the L subgenome. Based on these results, we propose a model that, upon and after hybridization between two related diploid Xenopus species, the mixture of their genomes resulted in the derepression of DNA transposons, especially in the S subgenome, leading to selective DNA loss in the S subgenome.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Xenopus / Elementos Transponibles de ADN / Genoma / Tetraploidía / Hibridación Genética Límite: Animals Idioma: En Revista: Genome Biol Evol Asunto de la revista: BIOLOGIA / BIOLOGIA MOLECULAR Año: 2024 Tipo del documento: Article País de afiliación: Japón Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Xenopus / Elementos Transponibles de ADN / Genoma / Tetraploidía / Hibridación Genética Límite: Animals Idioma: En Revista: Genome Biol Evol Asunto de la revista: BIOLOGIA / BIOLOGIA MOLECULAR Año: 2024 Tipo del documento: Article País de afiliación: Japón Pais de publicación: Reino Unido