Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome

Abstract

Orphan genes are genetic innovations that lack homologs in other lineages. Orphan genes can rapidly originate and become substantially functional, yet the mechanisms underlying their origins are still largely unknown in plants. Here, we investigated the origin of orphan genes in the Oryza sativa ssp. japonica “Nipponbare” genome using genome‐wide comparisons with 10 closely related Oryza species. We identified a total of 37 orphan genes in the Nipponbare genome that show short sequence lengths, elevated GC content, and absence of introns. Interestingly, half of the identified orphan genes originated by way of a distinctive mechanism that involved the generation of new coding sequences through independent and rapid divergence within the inserted transposable element. Our results provide valuable insight into genetic innovations in the model rice genome that formed on a very short timescale.

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest

“…incognita , almost 23% of the genes have been described as specific to plant–parasite species, without any recognizable homology in other species (Grynberg et al, 2020 ). Interestingly, TE movements can be involved in the emergence of species or genus‐specific “orphan” genes (Jin et al, 2019 ; Ruiz‐Orera et al, 2015 ; Wu & Knudson, 2018 ). Because some of the M .…”

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

“…Because some of the impacted genes are specific to plant-parasitic species and yet conserved in several of these phyto-parasites, a role in plant parasitism is possible. Interestingly, TE movements can be involved in the emergence of species or genusspecific 'orphan' genes (Ruiz-Orera et al 2015;Wu and Knudson 2018;Jin et al 2019). However, in the absence of known protein domains or functional characterization of these genes, the exact biochemical activity or biological processes in which they might be involved remains elusive.…”

New Genomic Signals Underlying the Emergence of Human Proto-Genes

“…It has already been shown that orphan genes can emerge via the exaptation of transposable elements [6]. In 2021, Jin et al (2021) [70] discovered that 37 orphan genes in the genome of Oryza sativa had emerged via recruitment of transposable elements. The presence of introns in "intergenic" proto-genes could also be an interesting indicator that proto-genes and/or their introns emerged via the movement of a transposable element.…”