Genomic and transcriptomic data for the frog Platyplectrum ornatum

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 or rate of DNA gain and
loss, are well known, but the underlying molecular mechanisms that drive
or constrain 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 ~1.06 Gb, the P. ornatum genome is like that
of birds, revealing four major mechanisms underlying TE dynamics: reduced
abundance of all major classes of transposable elements (TEs); increased
net deletion bias in TEs; drastic reduction in the lengths of introns; and
expansion via gene duplication of the repertoire of TE-suppressing Piwi
genes, accompanied by increased expression of piRNA-based TE-silencing
pathway genes in germline cells. Transcriptome data 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 in vertebrates generally.