title: The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle.
abstract: The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode's genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.|Laboratory of Agrogenomic Sciences, Universidad Nacional Autónoma de México (UNAM), ENES-León, 37684, León, Guanajuato, Mexico.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Rougon-Cardoso
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: Mitzi
authors.initials: M
authors.lastname: Flores-Ponce
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: Hilda Eréndira
authors.initials: HE
authors.lastname: Ramos-Aboites
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: Christian Eduardo
authors.initials: CE
authors.lastname: Martínez-Guerrero
authors.affiliation: College of Life Science, ChongQing Normal University, ChongQing 401331, China.
authors.forename: You-Jin
authors.initials: YJ
authors.lastname: Hao
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Park Place, Sir Martin Evans Building, Museum Avenue, Cardiff, Wales CF10 3US, UK.
authors.forename: Luis
authors.initials: L
authors.lastname: Cunha
authors.affiliation: Laboratory of Agrogenomic Sciences, Universidad Nacional Autónoma de México (UNAM), ENES-León, 37684, León, Guanajuato, Mexico.
authors.forename: Jonathan Alejandro
authors.initials: JA
authors.lastname: Rodríguez-Martínez
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: Cesaré
authors.initials: C
authors.lastname: Ovando-Vázquez
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: José Roberto
authors.initials: JR
authors.lastname: Bermúdez-Barrientos
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
authors.affiliation: Cuerpo Académico de Biotecnología Agroalimentaria. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo. Av. Universidad Km 1, Rancho Universitario, Tulancingo de Bravo, Hidalgo, C.P. 43600, Mexico.
authors.forename: Norberto
authors.initials: N
authors.lastname: Chavarría-Hernández
authors.affiliation: CIRN/Departamento de Biologia, Universidade dos Açores, Rua Mãe de Deus, 13. 9500-321 Ponta Delgada. S. Miguel-Açores, Portugal.
authors.forename: Nelson
authors.initials: N
authors.lastname: Simões
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, Mexico.
authors.forename: Rafael
authors.initials: R
authors.lastname: Montiel
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005075:Biological Evolution; D002875:Chromosomes / Q000235:genetics; D063990:Gene Ontology; D049751:Genome, Helminth; D015801:Helminth Proteins / Q000378:metabolism; D058977:Molecular Sequence Annotation; D010447:Peptide Hydrolases / Q000378:metabolism; D010802:Phylogeny; D020543:Proteome / Q000378:metabolism*; D017168:Rhabditida / Q000235:genetics* / Q000378:metabolism*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D015801:Helminth Proteins; D020543:Proteome; D010447:Peptide Hydrolases