A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum
- 8 March 2021
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 118 (11)
- https://doi.org/10.1073/pnas.2011649118
Abstract
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 ∼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 TE-silencing 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.This publication has 107 references indexed in Scilit:
- The Evolution of Intron Size in Amniotes: A Role for Powered Flight?Genome Biology and Evolution, 2012
- LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid SalamandersGenome Biology and Evolution, 2011
- The genome of the green anole lizard and a comparative analysis with birds and mammalsNature, 2011
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeNature Biotechnology, 2011
- High-quality draft assemblies of mammalian genomes from massively parallel sequence dataProceedings of the National Academy of Sciences of the United States of America, 2010
- Genome Size and Species DiversificationEvolutionary Biology, 2010
- TopHat: discovering splice junctions with RNA-SeqBioinformatics, 2009
- Deletional Bias across the Three Domains of LifeGenome Biology and Evolution, 2009
- Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamandersZoology, 2008
- RNA regulation: a new genetics?Nature Reviews Genetics, 2004