eprintid: 10105473
rev_number: 14
eprint_status: archive
userid: 608
dir: disk0/10/10/54/73
datestamp: 2020-07-20 10:55:18
lastmod: 2021-09-21 22:09:06
status_changed: 2020-07-20 10:55:18
type: article
metadata_visibility: show
creators_name: Zile, K
creators_name: Dessimoz, C
creators_name: Wurm, Y
creators_name: Masel, J
title: Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence
ispublished: inpress
divisions: UCL
divisions: B02
divisions: C08
divisions: D09
divisions: F99
note: © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
abstract: Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously non-coding 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 (non-functional 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 non-coding 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 D. simulans and D. 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 pre-dates their ORF. 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.
date: 2020
date_type: published
official_url: https://doi.org/10.1093/gbe/evaa127
oa_status: green
full_text_type: other
language: eng
primo: open
primo_central: open_green
verified: verified_manual
elements_id: 1795692
doi: 10.1093/gbe/evaa127
pii: 5863250
lyricists_name: Dessimoz, Christophe
lyricists_id: CDESS31
actors_name: Flynn, Bernadette
actors_id: BFFLY94
actors_role: owner
full_text_status: public
publication: Genome Biology and Evolution
event_location: England
issn: 1759-6653
citation:        Zile, K;    Dessimoz, C;    Wurm, Y;    Masel, J;      (2020)    Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence.                   Genome Biology and Evolution        10.1093/gbe/evaa127 <https://doi.org/10.1093/gbe%2Fevaa127>.    (In press).    Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/10105473/1/evaa127.pdf