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dc.contributor.authorvan Steenbrugge, Joris J.M.
dc.contributor.authorvan den Elsen, Sven
dc.contributor.authorHolterman, Martijn
dc.contributor.authorSterken, Mark G.
dc.contributor.authorThorpe, Peter
dc.contributor.authorGoverse, Aska
dc.contributor.authorSmant, Geert
dc.contributor.authorHelder, Johannes
dc.date.accessioned2021-08-12T10:30:08Z
dc.date.available2021-08-12T10:30:08Z
dc.date.issued2021-08-11
dc.identifier.citationvan Steenbrugge , J J M , van den Elsen , S , Holterman , M , Sterken , M G , Thorpe , P , Goverse , A , Smant , G & Helder , J 2021 , ' Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns ' , BMC Genomics , vol. 22 , 611 . https://doi.org/10.1186/s12864-021-07914-6en
dc.identifier.issn1471-2164
dc.identifier.otherPURE: 275433078
dc.identifier.otherPURE UUID: d8d050de-5aa2-4351-80eb-2835487ef543
dc.identifier.otherRIS: urn:4D8CFFD6D2E145DC01D720278EE94741
dc.identifier.otherRIS: van Steenbrugge2021
dc.identifier.otherWOS: 000684208100001
dc.identifier.otherScopus: 85112304764
dc.identifier.urihttp://hdl.handle.net/10023/23766
dc.descriptionThis work was funded as part of a grant by the Netherlands Organization for Scientific Research (NWO) as part of the Applied and Technical Science domain (TTW) under grant no. 14708. PT: bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF award 105621/Z/14/Z.en
dc.description.abstractBackground: Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is both fundamentally and practically of limited value. Hence, resistant potato varieties are used worldwide in a poorly informed manner. Results : We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 19 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family studied herein with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. Conclusions : Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a basis for an effectorome-based virulence scheme for this notorious pathogen.
dc.format.extent19
dc.language.isoeng
dc.relation.ispartofBMC Genomicsen
dc.rightsCopyright © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.en
dc.subjectHeterozygosityen
dc.subjectGland proteinsen
dc.subjectInnate immune systemen
dc.subjectSPRYSECen
dc.subjectCLEen
dc.subjectEffectoromicsen
dc.subjectQH426 Geneticsen
dc.subjectQR Microbiologyen
dc.subject3rd-DASen
dc.subject.lccQH426en
dc.subject.lccQRen
dc.titleComparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patternsen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.School of Medicineen
dc.identifier.doihttps://doi.org/10.1186/s12864-021-07914-6
dc.description.statusPeer revieweden


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