Neofunctionalization of a Noncoding Portion of a DNA Transposon in the Coding Region of the Chimerical Sex-Determining Gene dm-W in Xenopus Frogs

Abstract

Most vertebrate sex-determining genes (SDGs) emerge as neofunctionalized genes through duplication and/or mutation of ancestral genes that are involved with sexual differentiation. We previously demonstrated dm-W to be the SDG in the African clawed frog Xenopus laevis and found that a portion of this gene emerged from the masculinization gene dmrt1 after allotetraploidization by interspecific hybridization between two ancestral species around 17-18 million years ago. dm-W has four exons consisting of a noncoding exon 1, dmrt1-derived exons 2 and 3, and an orphan exon 4 (Ex4) of unknown origin that includes coding sequence. In this study, we searched for the origin of Ex4 and investigated the function of the coding sequence of this exon. We found that the Ex4-coding sequence (CDS) is derived from a non-coding portion of the hAT-10 family of DNA transposon. Evolutionary analysis of transposons and determination of the Ex4 sequences from three other species indicated that Ex4 was generated before the diversification of most or all extant allotetraploid species in subgenus Xenopus, during which time we hypothesize that transposase activity of this hAT superfamily was active. Using DNA-protein binding and transfection assays, we further demonstrate that the Ex4-encoded amino acid sequence increases the DNA-binding ability and transcriptional activity of DM-W. These findings suggest that the conversion of the noncoding transposon sequence to the CDS of dm-W contributed to neofunctionalization of a new chimeric SDG in the ancestor of the allotetraploid Xenopus species, offering new insights into de novo origin and functional evolution of chimerical genes.

Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus)

“…In mammalian genomes, TEs are an important source of various cis-regulatory sequences; 20% of the cis-regulatory elements (CREs) in the human genome may have been taken from TEs ( Sundaram and Wysocka, 2020 ), and TEs often contribute to zebrafish cis-regulatory elements, tissue-specific expression and alternative promoters ( Lee et al, 2022 ). Researchers have found that the fourth exon (Ex4) of the sex-determining gene dm-W in the African clawed frog ( Xenopus laevis ) originated from a non-coding fragment of the hAT-10 family of DNA transposons ( Hayashi et al, 2022 ). An experimental evidence from sablefish ( Anoplopoma fimbria ) demonstrated that a TE insertion in the promoter region of gsdfY produced allelic diversification by bringing a cis-regulatory module, leading to transcriptional reprofiling and generating a new sex-determined gene for this species ( Herpin et al, 2021 ).…”

A New Hope: A Hermaphroditic Nematode Enables Analysis of a Recent Whole Genome Duplication Event

“…DNA/hAT is active and recently expanded in the bat genus Myotis, which has high plasticity and diversification ( Ray et al 2006 ). Additionally, a DNA/hAT element is involved in neofunctionalization in X. laevis ( Hayashi et al 2022 ). In A. sudhausi , we determined the DNA/hAT-Ac family expanded very recently based on pairwise analysis ( fig.…”

Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis

“…laevis genome assembly. Combined with the differing genomic locations of paralogous genes [ 28 ], the overlapping transcribed regions of dm-w and scan-w is consistent with a chimerical origin of dm-w wherein exons 2 and 3 originated via separate duplication/translocation events from exon 1 and exon 4 [ 29 , 36 , 41 ].…”

“…clivii are denoted “L” and “S” [ 40 ] and homeologous genes in each subgenome generally include these letters as a suffix (e.g., dmrt1L and dmrt1S are homeologs that by definition are duplicated genes that arose from genome duplication). Strikingly, dm-w appears to be a chimerical gene, whose components are derived from as many as three different sources including: (i) the second and third exons and flanking regions, which formed from gene duplication of dmrt1S [ 28 , 35 , 36 ], (ii) the fourth exon and flanking regions, which arose from a noncoding DNA transposon called hAT-10 [ 36 ], and (iii) the first exon and flanking regions, which does not have discernible homology to dmrt1S , is rich in transposable elements, and has unclear origins [ 41 ]. A recent genome assembly for X .…”