Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka FishOryzias latipes

Abstract

While genes with similar expression patterns are sometimes found in the same genomic regions, almost nothing is known on the relative organization in genomes of genes and transposable elements, which might influence each other at the regulatory level. In this study, we used transcriptomic data from male and female gonads of the Japanese medaka Oryzias latipes to define sexually biased genes and transposable elements and analyze their relative genomic localization. We identified 20,588 genes expressed in the adult gonads of O. latipes. Around 39% of these genes are differentially expressed between male and female gonads. We further analyzed the expression of transposable elements using the program SQuIRE and showed that more TE copies are over-expressed in testis than in ovaries (36% vs. 10%, respectively). We then developed a method to detect genomic regions enriched in testis or ovary-biased genes. This revealed that sex-biased genes and TEs are not randomly distributed in the genome and a part of them form clusters with the same expression bias. We also found a correlation of expression between TE copies and their closest genes, which increases with decreasing intervening distance. Such a genomic organization suggests either that TEs hijack the regulatory sequences of neighboring sexual genes, allowing their expression in germ line cells and consequently new insertions to be transmitted to the next generation, or that TEs are involved in the regulation of sexual genes, and might therefore through their mobility participate in the rewiring of sex regulatory networks.

Cross‐species conservation of a transposase‐linked element enables genetic sexing of commercial populations of Russian sturgeon (Acipenser gueldenstaedtii)

“…Thus, a possible function of AllWSEX2 and the transposase-like sequence located to the 3′ of AllWSEX2 should be further studied, including the possibility of their involvement in female transposon silencing. However, repression of transposable elements has been shown to participate in sex determination only in invertebrates (Yang et al, 2021); and transposable elements are over-expressed in testes of fish with no obvious association to sex determination (Dechaud et al, 2021).…”

Species-Specific Proteins in the Oviducts of Snail Sibling Species: Proteotranscriptomic Study of Littorina fabalis and L. obtusata

“…in [ 60 ]). Moreover, non-random distribution of sex-biased genes and TEs was demonstrated in the genome of the medaka fish: these elements form clusters with the same expression bias, and the regulatory links between sexual genes and TEs were inferred [ 61 ]. The TEs identified in the Littorina oviducts might be expected to be expressed via “hijack” on the transcription of neighboring female-biased genes and to accelerate their evolution.…”

Diversity of Harbinger-like Transposons in Teleost Fish Genomes

“…TE expression quantification was performed on RNAseq data from both male and female gonads of the medaka fish O. latipes , as previously published [ 39 ]. In brief, SquIRE [ 40 ] was used to estimate TE expression at the copy level using a custom TE library on the O. latipes genome ( , accessed on 15 September 2021).…”