DOI: 10.5061/dryad.73n5tb2w9
title: Genomic and transcriptomic data for the frog Platyplectrum ornatum

description: 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.
description: Genomic sequence data of an ornate burrowing frog
 <i>(Platyplectrum ornatum) </i>was generated from DNA isolated
 from the muscle of an adult female. Based on the expected genome size of
 0.96 Gb, the <i>P. ornatum </i>genome was sequenced to ~140X
 coverage (Supplementary Table 2), on Illumina HiSeq 2500 platform using
 two different sequence libraries, (a) fragment library with average insert
 size of 220 bp (b) jumping library with average insert size of 6 kb,
 generating ~ 1.2 billion paired end reads with read length of 125 bp each.
 We also collected brain, heart, muscle and gonad tissues from one male and
 one adult female <i>P. ornatum</i> individuals and generated ~
 540 million transcriptome reads to use the data for genome annotations. We
 first generated a female transcriptome assembly combining RNAseq data from
 brain, gonad, heart and muscle using Trinity. In addition, we mapped
 RNAseq data from the male individual to the reference <i>P.
 ornatum</i> genome assembly using TopHat and extracted exon/intron
 junction information for downstream usage for genome
 annotations.
description: We provide detailed results of our RepeatMasker analysis, which
 can be parsed and used in meta-analsyes of repeat landscapes in
 vertebrates. We also provide files and results for the Orthofinder
 analysis, which is based on a rooted species tree, and yields counts of
 orthologs in each species, which are provided in a table
 ("Gene_count_per_orthogroup.txt"). The gene trees for each
 ortholog group are also provided. Finally, we provide fasta files and the
 gene tree in newick format used in the analysis of Piwi genes. The full
 results of the aBSREL analysis are also provided.