StORF-Reporter: finding genes between genes

Nicholas J. Dimonaco; Amanda Clare; Kim Kenobi; Wayne Aubrey; Christopher J. Creevey

doi:10.1093/nar/gkad814

StORF-Reporter: finding genes between genes

Nicholas J. Dimonaco^*
, Amanda Clare
, Kim Kenobi
, Wayne Aubrey
, Christopher J. Creevey

^*Corresponding author for this work

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

84 Downloads (Pure)

Abstract

Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.

Original language	English
Pages (from-to)	11504-11517
Number of pages	14
Journal	Nucleic Acids Research
Volume	51
Issue number	21
Early online date	28 Oct 2023
DOIs	https://doi.org/10.1093/nar/gkad814
Publication status	Published - 27 Nov 2023

Bibliographical note

Funding Information:
N.J.D. was funded by an IBERS Aberystwyth University PhD fellowship and was supported by Farncombe Digestive Health Disease Institute (McMaster University); Weston Family Microbiome Initiative; C.J.C. wishes to acknowledge funding from the BBSRC [BB/E/W/10964A01, BBS/OS/GC/000011B]; DAFM Ireland/DAERA Northern Ireland [Meth-Abate, R3192GFS]; EU via Horizon 2020 [818368, MASTER and 101000213, Holoruminant]. Funding for open access charge: Read and Publish agreement.

Funding Information:
Funding N.J.D. was funded by an IBERS Aberystwyth University PhD fellowship and was supported by Farncombe Diges- tive Health Disease Institute (McMaster University); We- ston Family Microbiome Initiative; C.J.C. wishes to ac- knowledge funding from the BBSRC [BB / E / W / 10964A01, BBS / OS / GC / 000011B]; D AFM Ireland / D AERA Northern Ireland [Meth-Abate, R3192GFS]; EU via Horizon 2020 [818368, MASTER and 101000213, Holoruminant]. Fund- ing for open access charge: Read and Publish agreement.

Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

Keywords

Genetics

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkad814Licence: CC BY

StORF-Reporter: finding genes between genes
© 2023 The Authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Final published version, 1.37 MBLicence: CC BY

Cite this

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abstract = "Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.",

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note = "Funding Information: N.J.D. was funded by an IBERS Aberystwyth University PhD fellowship and was supported by Farncombe Digestive Health Disease Institute (McMaster University); Weston Family Microbiome Initiative; C.J.C. wishes to acknowledge funding from the BBSRC [BB/E/W/10964A01, BBS/OS/GC/000011B]; DAFM Ireland/DAERA Northern Ireland [Meth-Abate, R3192GFS]; EU via Horizon 2020 [818368, MASTER and 101000213, Holoruminant]. Funding for open access charge: Read and Publish agreement. Funding Information: Funding N.J.D. was funded by an IBERS Aberystwyth University PhD fellowship and was supported by Farncombe Diges- tive Health Disease Institute (McMaster University); We- ston Family Microbiome Initiative; C.J.C. wishes to ac- knowledge funding from the BBSRC [BB / E / W / 10964A01, BBS / OS / GC / 000011B]; D AFM Ireland / D AERA Northern Ireland [Meth-Abate, R3192GFS]; EU via Horizon 2020 [818368, MASTER and 101000213, Holoruminant]. Fund- ing for open access charge: Read and Publish agreement. Publisher Copyright: {\textcopyright} 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

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N2 - Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.

AB - Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 21

ER -

StORF-Reporter: finding genes between genes

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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