Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Abstract
Background: Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri). Results: We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis. Conclusions: We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein–DNA relationships shared between these two genera.
Additional Information
© 2015 Dillman et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Received: 1 June 2015 Accepted: 10 August. Published online: 21 September 2015. This research was supported by grants from the US National Institutes of Health (NIH) and the Howard Hughes Medical Institute, for which PWS is an investigator. ARD was supported by NIH training grants (5T32GM007616 and 5T32HG000044). AM and MM were supported by an NIH New Innovator Award to AM (DP2 GM111100). XL was supported by the UW-Madison Graduate School research funds. Authors' contributions: ARD, MM, PWS, and AM conceived the project. ARD and MM carried out all experiments. IA, BW and MM built as well as sequenced all libraries. MM and AM did the primary genome assemblies and gene annotations. ARD and BJA did the phylogenetic analysis. ARD and MM did all comparative analyses. ARD, MM, PWS, and AM wrote the manuscript. All authors read and approved the final manuscript.Attached Files
Published - s13059-015-0746-6.pdf
Supplemental Material - s13059-015-0746-6-s1.pdf
Supplemental Material - s13059-015-0746-6-s10.txt
Supplemental Material - s13059-015-0746-6-s11.txt
Supplemental Material - s13059-015-0746-6-s12.txt
Supplemental Material - s13059-015-0746-6-s13.txt
Supplemental Material - s13059-015-0746-6-s2.pdf
Supplemental Material - s13059-015-0746-6-s3.txt
Supplemental Material - s13059-015-0746-6-s4.txt
Supplemental Material - s13059-015-0746-6-s5.txt
Supplemental Material - s13059-015-0746-6-s6.txt
Supplemental Material - s13059-015-0746-6-s7.htm
Supplemental Material - s13059-015-0746-6-s8.txt
Supplemental Material - s13059-015-0746-6-s9.png
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Additional details
- PMCID
- PMC4578762
- Eprint ID
- 60578
- Resolver ID
- CaltechAUTHORS:20150928-125105151
- Howard Hughes Medical Institute (HHMI)
- NIH Predoctoral Fellowship
- 5T32GM007616-37
- NIH Predoctoral Fellowship
- 5T32HG000044
- NIH
- DP2 GM111100
- University of Wisconsin
- Created
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2015-09-29Created from EPrint's datestamp field
- Updated
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2022-05-23Created from EPrint's last_modified field