The Library
Repertoire-wide gene structure analyses : a case study comparing automatically predicted and manually annotated gene models
Tools
Tools
Tools
Wilbrandt, Jeanne, Misof, Bernhard, Panfilio, Kristen A. and Niehuis, Oliver (2019) Repertoire-wide gene structure analyses : a case study comparing automatically predicted and manually annotated gene models. BMC Genomics, 20 (1). 753. doi:10.1186/s12864-019-6064-8 ISSN 1471-2164.
|
PDF
WRAP-repertoire-wide-gene-analyses-manually-models-Panfilio-2019.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (1846Kb) | Preview |
Official URL: http://dx.doi.org/10.1186/s12864-019-6064-8
Abstract
Background
The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative.
Results
Our results show that the subset of genes chosen for manual annotation by a research community (3.5–7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species’ gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities.
Conclusions
In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.
| Item Type: | Journal Article | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Subjects: | Q Science > QH Natural history > QH426 Genetics | |||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
| Library of Congress Subject Headings (LCSH): | Genomics -- Technique -- Computer programs, Bioinformatics -- Research, Gene expression -- Research, Gene mapping -- Data processing | |||||||||
| Journal or Publication Title: | BMC Genomics | |||||||||
| Publisher: | BioMed Central Ltd. | |||||||||
| ISSN: | 1471-2164 | |||||||||
| Official Date: | December 2019 | |||||||||
| Dates: |
|
|||||||||
| Volume: | 20 | |||||||||
| Number: | 1 | |||||||||
| Article Number: | 753 | |||||||||
| DOI: | 10.1186/s12864-019-6064-8 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 24 October 2019 | |||||||||
| Date of first compliant Open Access: | 24 October 2019 | |||||||||
| RIOXX Funder/Project Grant: |
|
Request changes or add full text files to a record
Repository staff actions (login required)
 |
View Item |
Downloads
Downloads per month over past year
