Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus

Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development

Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lungfish in having the largest vertebrate genomes-3 to 40 times that of humans-as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.

Transposable element and host silencing activity in gigantic genomes

Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.

Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models

Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilianIchthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

Transposable elements, contributors in the evolution of organisms (from an arms race to a source of raw materials)

There is a concept proposing that the primitive lineages of prokaryotes, eukaryotes, and viruses emerged from the primordial pool of primitive genetic elements. In this genetic pool, transposable elements (TEs) became a source of raw material for primitive genomes, tools of genetic innovation, and ancestors of modern genes (e.g. ncRNAs, tRNAs, and rRNAs). TEs contributed directly to the genome evolution of three forms of life on the earth. TEs now appear as tools that were used to giving rise to sexual dimorphism and sex determination, lineage-specific expression of genes and tissue differentiation and finally genome stability and lifespan determination.

Molecular Evolution of Antigen-Processing Genes in Salamanders: Do They Coevolve with MHC Class I Genes?

Proteins encoded by antigen-processing genes (APGs) prepare antigens for presentation by the major histocompatibility complex class I (MHC I) molecules. Coevolution between APGs and MHC I genes has been proposed as the ancestral gnathostome condition. The hypothesis predicts a single highly expressed MHC I gene and tight linkage between APGs and MHC I. In addition, APGs should evolve under positive selection, a consequence of the adaptive evolution in MHC I. The presence of multiple highly expressed MHC I genes in some teleosts, birds, and urodeles appears incompatible with the coevolution hypothesis. Here, we use urodele amphibians to test two key expectations derived from the coevolution hypothesis: 1) the linkage between APGs and MHC I was studied in Lissotriton newts and 2) the evidence for adaptive evolution in APGs was assessed using 42 urodele species comprising 21 genera from seven families. We demonstrated that five APGs (PSMB8, PSMB9, TAP1, TAP2, and TAPBP) are tightly linked (<0.5 cM) to MHC I. Although all APGs showed some codons under episodic positive selection, we did not find a pervasive signal of positive selection expected under the coevolution hypothesis. Gene duplications, putative gene losses, and divergent allelic lineages detected in some APGs demonstrate considerable evolutionary dynamics of APGs in salamanders. Overall, our results indicate that if coevolution between APGs and MHC I occurred in urodeles, it would be more complex than envisaged in the original formulation of the hypothesis.

The emerging importance of noncoding RNAs in the insecticide tolerance, with special emphasis on Plutella xylostella (Lepidoptera: Plutellidae)

Recently generated high-throughput sequencing data sets have shed light on the important regulatory roles of noncoding RNA (ncRNA) molecules in the development of higher organisms. Nowadays it is well-known that regulatory ncRNAs can bind complementary RNA or DNA sequences and recruit chromatin remodelers to selectively modulate gene expression. Consequently, genome sequencing and transcriptomics technologies are now being used to reveal hidden associations among ncRNAs and distinct biological mechanisms. This is the case for the diamondback moth Plutella xylostella, a worldwide pest known to infest cruciferous crops and to display resistance to most insecticides, including Bacillus thuringiensis (Bt) based biopesticides. In P. xylostella, it is thought that ncRNAs could play important roles in both development and insecticide resistance. This review will highlight recent insights into the roles of ncRNAs in P. xylostella and related lepidopterans, and will outline genetic engineering technologies which might be used to design efficient ncRNA-based pest control strategies. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation

PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.

Is There an Upper Limit to Genome Size?

At 50-fold the size of the human genome (3 Gb), the staggeringly huge genome of 147.3 Gb recently discovered in the fern Tmesipteris obliqua is comparable in size to those of the other plant and animal record-holders (i.e., Paris japonica, a flowering plant with a genome size of 148.8 Gb, and Protopterus aethiopicus, a lungfish with a genome of 130 Gb). The synthesis of available information on giant genomes suggests that the biological limit to genome size expansion in eukaryotes may have been reached. We propose several explanations for why the genomes of ferns, flowering plants, and lungfish, all of which have independently undergone dramatic increases in genome size through a variety of mechanisms, do not exceed 150 Gb.