Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 118, Issue 11, Pages -Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.2011649118
Keywords
Anura; frog; intron; Piwi genes; transposable elements
Categories
Funding
- Harvard Research Computing
- Institute for Applied Ecology, University of Canberra
- Wenner Gren Postdoctoral Fellowship
- National Science Foundation
- Harvard University
- Wetmore Colles Fund of the Museum of Comparative Zoology
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The study of the genome of the ornate burrowing frog from Australia reveals four major mechanisms driving reduction in genome size, including decreased abundance of transposable elements, increased net deletion bias in TEs, drastic reduction in intron lengths, and expansion of TE-suppressing Piwi genes. Transcriptomes from multiple tissues confirm these results and provide insights into sex-differentiation pathways in Platyplectrum. The genome offers a model for future comparative studies on genome size reduction mechanisms in amphibians and vertebrates.
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At similar to 1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TEsilencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum. Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.
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