{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T01:49:19Z","timestamp":1792288159729,"version":"4.4.0"},"reference-count":86,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T00:00:00Z","timestamp":1621296000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/R011311\/1"],"award-info":[{"award-number":["BB\/R011311\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/N021908\/1"],"award-info":[{"award-number":["BB\/N021908\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/S006397\/1"],"award-info":[{"award-number":["BB\/S006397\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010665","name":"H2020 Marie Sk\u0142odowska-Curie Actions","doi-asserted-by":"publisher","award":["XXX"],"award-info":[{"award-number":["XXX"]}],"id":[{"id":"10.13039\/100010665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.<\/jats:p>","DOI":"10.3390\/genes12050771","type":"journal-article","created":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T23:34:46Z","timestamp":1621380886000},"page":"771","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":46,"title":["Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes"],"prefix":"10.3390","volume":"12","author":[{"given":"Martine","family":"Da Rocha","sequence":"first","affiliation":[{"name":"INRAE, Institut Sophia Agrobiotech, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, 06903 Sophia Antipolis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2980-1691","authenticated-orcid":false,"given":"Caroline","family":"Bournaud","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0038-3705","authenticated-orcid":false,"given":"Julie","family":"Dazeni\u00e8re","sequence":"additional","affiliation":[{"name":"INRAE, Institut Sophia Agrobiotech, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, 06903 Sophia Antipolis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Thorpe","sequence":"additional","affiliation":[{"name":"School of Medicine, Medical &amp; Biological Sciences, University of St. Andrews, St Andrews KY16 9AJ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Bailly-Bechet","sequence":"additional","affiliation":[{"name":"INRAE, Institut Sophia Agrobiotech, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, 06903 Sophia Antipolis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cl\u00e9ment","family":"Pellegrin","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2070-641X","authenticated-orcid":false,"given":"Arthur","family":"P\u00e9r\u00e9","sequence":"additional","affiliation":[{"name":"INRAE, Institut Sophia Agrobiotech, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, 06903 Sophia Antipolis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4009-9538","authenticated-orcid":false,"given":"Priscila","family":"Grynberg","sequence":"additional","affiliation":[{"name":"Embrapa Genetic Resources and Biotechnology, Bras\u00edlia 70770-917, DF, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laetitia","family":"Perfus-Barbeoch","sequence":"additional","affiliation":[{"name":"INRAE, Institut Sophia Agrobiotech, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, 06903 Sophia Antipolis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8833-9679","authenticated-orcid":false,"given":"Sebastian","family":"Eves-van den Akker","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4146-5608","authenticated-orcid":false,"given":"Etienne G. J.","family":"Danchin","sequence":"additional","affiliation":[{"name":"INRAE, Institut Sophia Agrobiotech, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, 06903 Sophia Antipolis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,5,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Perry, R.N., and Moens, M. (2013). Structure and classification. Plant Nematology, CABI.","DOI":"10.1079\/9781780641515.0000"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1111\/mpp.12057","article-title":"Top 10 plant-parasitic nematodes in molecular plant pathology","volume":"14","author":"Jones","year":"2013","journal-title":"Mol. Plant. 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