Improving the annotation of the Heterorhabditis bacteriophora genome
Abstract
Background: Genome assembly and annotation remain exacting tasks. As the tools available for these tasks improve, it is useful to return to data produced with earlier techniques to assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes. Findings: We revisited the H. bacteriophora genome assembly and gene predictions to determine whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant. Conclusions: Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species' genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published genome assemblies.
Additional Information
© 2018 The Authors. Published by Oxford University Press. 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. Received: 05 November 2017; Revision Received: 05 March 2018; Accepted: 23 March 2018; Published: 02 April 2018. The authors declare that they have no competing interests. This project was supported by FMs Wellcome Trust-funded graduate programme [204052/Z/16/Z]. Author's contributions: Conceptualization, MB; Methodology, FM, DB, and MB; Formal analysis, FM, DRL and MB; Supervision, MB; Writing- original draft, FM and DRL; Writing- review and editing, FM, MB, DRL, DB, HTS; Resources, HTS. Sujai Kumar, Lewis Stevens, Carlos Caurcel and Elisabeth Sjokvist offered expert technical support and advice. Igor Antoshechkin of the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech assisted with Illumina sequencing. Adler Dillman provided the parental strain for the inbred H. bacteriophora strain G2a1223.Attached Files
Published - giy034.pdf
Submitted - 225904.full.pdf
Supplemental Material - giy034_giga-d-17-00297_original_submission.pdf
Supplemental Material - giy034_giga-d-17-00297_revision_1.pdf
Supplemental Material - giy034_response_to_reviewer_comments_original_submission.pdf
Supplemental Material - giy034_reviewer_1_report__original_submission_.pdf
Supplemental Material - giy034_reviewer_2_report__original_submission_.pdf
Supplemental Material - giy034_reviewer_3_report__original_submission_.pdf
Supplemental Material - giy034_supp.zip
Files
Name | Size | Download all |
---|---|---|
md5:9aa3c7769d176591198f23249f2ae3e6
|
681.0 kB | Preview Download |
md5:e67d9a9cacca88cd0770a4addf1407ab
|
121.5 kB | Preview Download |
md5:832121e5a0f8147c60af21ec938ca9f3
|
4.7 MB | Preview Download |
md5:ebed8b64ec0832cf697c447b57e051c4
|
31.2 kB | Preview Download |
md5:5c6335f6a270543772bf5cd67d89a076
|
343.8 kB | Preview Download |
md5:0e2b14c96f239063975f92b12c553fda
|
35.3 kB | Preview Download |
md5:d478c1db6f5fb6b7c1f4f67792a3fa06
|
30.0 kB | Preview Download |
md5:b34e1937745f6933476516dc8a12cdca
|
26.1 kB | Preview Download |
md5:78e5fdb2348ae87cfe421b6d0819e65c
|
5.1 MB | Preview Download |
Additional details
- PMCID
- PMC5906903
- Eprint ID
- 85718
- Resolver ID
- CaltechAUTHORS:20180410-090306072
- 204052/Z/16/Z
- Wellcome Trust
- Created
-
2018-04-10Created from EPrint's datestamp field
- Updated
-
2023-06-01Created from EPrint's last_modified field