Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome

Abstract

Caudata is an order of amphibians with great variation in genome size, which can reach enormous dimensions in salamanders. In this work, we analysed the activity of transposable elements (TEs) in the transcriptomes obtained from female and male gonads of the Chinese fire-bellied newt, Cynops orientalis, a species with a genome about 12-fold larger than the human genome. We also compared these data with genomes of two basal sarcopterygians, coelacanth and lungfish. In the newt our findings highlighted a major impact of non-LTR retroelements and a greater total TE activity compared to the lungfish Protopterus annectens, an organism also characterized by a giant genome. This difference in TE activity might be due to the presence of young copies in newt in agreement also with the increase in the genome size, an event that occurred independently and later than lungfish. Moreover, the activity of 33 target genes encoding proteins involved in the TE host silencing mechanisms, such as Ago/Piwi and NuRD complex, was evaluated and compared between the three species analysed. These data revealed high transcriptional levels of the target genes in both newt and lungfish and confirmed the activity of NuRD complex genes in adults. Finally, phylogenetic analyses performed on PRDM9 and TRIM28 allowed increasing knowledge about the evolution of these two key genes of the NuRD complex silencing mechanism in vertebrates. Our results confirmed that the gigantism of the newt genomes may be attributed to the activity and accumulation of TEs.

Transposable element and host silencing activity in gigantic genomes

“…Transposable element expression is higher in R. sibiricus testes than ovaries, a pattern also reported in Drosophila (Wei et al, 2022) and the medaka fish O. latipes (Saint-Leandre et al, 2020;Dechaud et al, 2021), but opposite the pattern reported in the carrion crow Corvus corone (Warmuth et al, 2022) and different from the non-sex-biased TE expression in the newt C. orientalis (Carducci et al, 2021). In Drosophila, testes expression levels of TE-mapping piRNAs and piRNA pathway genes, as well as the ping-pong signature, are lower than ovary expression levels, suggesting that lower male piRNAmediated silencing contributes to higher male TE expression (Saint- Leandre et al, 2020;Chen et al, 2021).…”

“…Transcriptomic data reveal a similarly mixed picture: for some piRNA pathway genes, germline expression is higher in salamanders (represented by the fire-bellied newt Cynops orientalis, ~44 Gb) than in the African lungfish, whereas for other genes, the pattern is reversed; comparisons with genomes of more typical size (coelacanth Latimeria menadoensis and zebrafish Danio rerio) show patterns of both higher and lower germline expression of TE silencing genes in the species with gigantic genomes (Biscotti et al, 2017;Carducci et al, 2021). Small RNA sequence data from the gonads of the northern dusky salamander Desmognathus fuscus (~15 Gb) reveal lower percentages of TE-mapping piRNAs than are found in smaller genomes, suggesting a less comprehensive TEtargeting piRNA pool in the gigantic genome (Madison-Villar et al, 2016).…”

Transposable element and host silencing activity in gigantic genomes

“…Transposable element expression is higher in R. sibiricus testes than ovaries, a pattern also reported in Drosophila (Wei et al, 2022) and Oryzias latipes (the medaka fish) (Saint-Leandre et al, 2020;Dechaud et al, 2021), but opposite the pattern reported in Corvus corone (carrion crow) (Warmuth et al, 2022) and different from the non-sex-biased TE expression in the fire-bellied newt Cynops orientalis (Carducci et al, 2021). In Drosophila, testes expression levels of TE-mapping piRNAs and piRNA pathway genes, as well as the pingpong signature, are lower than ovary expression levels, suggesting that lower male piRNAmediated silencing contributes to higher male TE expression (Saint-Leandre et al, 2020;Chen et al, 2021).…”

“…On the other hand, in the African lungfish, Wang et al (2021) suggested that the KRAB-ZFP TE transcriptional silencing machinery has expanded in scope in response to the high genomic TE load. Similarly, in the fire-bellied newt Cynops orientalis , it was suggested that TE silencing is now enhanced in response to high TE load, which accumulated in the past during a period of increased TE mobilization (Carducci et al, 2021). In both of these examples, the TEs are suggested to be currently on the defensive.…”

“…Expression data reveal a similarly mixed picture: for some piRNA pathway genes, germline expression is higher in salamanders (represented by the fire-bellied newt Cynops orientalis , ∼43 Gb) than in the African lungfish, whereas for other genes, the pattern is reversed; comparisons with genomes of more typical size (coelacanth Latimeria menadoensis and zebrafish Danio rerio ) show patterns of both higher and lower germline expression of TE silencing genes in the species with gigantic genomes (Biscotti et al, 2017;Carducci et al, 2021). Small RNA sequence data from the gonads of the northern dusky salamander Desmognathus fuscus (∼15 Gb) reveal lower percentages of TE-mapping piRNAs than are found in smaller genomes, suggesting a less comprehensive TE-targeting piRNA pool in the gigantic genome (Madison-Villar et al, 2016).…”