Title |
Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
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Published in |
Genome Biology, September 2015
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DOI | 10.1186/s13059-015-0746-6 |
Pubmed ID | |
Authors |
Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia Rogers, Brian Williams, Igor Antoshechkin, Ming-Min Lee, Zane Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, Ali Mortazavi |
Abstract |
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). 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. 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. |
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Geographical breakdown
Country | Count | As % |
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United States | 5 | 26% |
United Kingdom | 5 | 26% |
Netherlands | 1 | 5% |
Canada | 1 | 5% |
Unknown | 7 | 37% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 13 | 68% |
Scientists | 5 | 26% |
Science communicators (journalists, bloggers, editors) | 1 | 5% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Mexico | 2 | 2% |
Canada | 1 | <1% |
Finland | 1 | <1% |
Taiwan | 1 | <1% |
Poland | 1 | <1% |
Unknown | 107 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 27 | 24% |
Researcher | 18 | 16% |
Student > Master | 12 | 11% |
Professor > Associate Professor | 7 | 6% |
Student > Bachelor | 6 | 5% |
Other | 20 | 18% |
Unknown | 23 | 20% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 51 | 45% |
Biochemistry, Genetics and Molecular Biology | 27 | 24% |
Computer Science | 2 | 2% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | <1% |
Nursing and Health Professions | 1 | <1% |
Other | 6 | 5% |
Unknown | 25 | 22% |