Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.

Details

Serval ID
serval:BIB_FE830F452AA4
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.
Journal
Genome biology and evolution
Author(s)
Zile K., Dessimoz C., Wurm Y., Masel J.
ISSN
1759-6653 (Electronic)
ISSN-L
1759-6653
Publication state
Published
Issued date
01/08/2020
Peer-reviewed
Oui
Editor
Alba Mar
Volume
12
Number
8
Pages
1355-1366
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.
Keywords
Genetics, Ecology, Evolution, Behavior and Systematics, Drosophila, de novo gene birth, de novo genes, genome evolution, new genes, taxonomically restricted genes
Pubmed
Web of science
Open Access
Yes
Funding(s)
Swiss National Science Foundation
Create date
03/07/2020 18:06
Last modification date
19/01/2021 7:26
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