Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease
Elms, especially Ulmus minor and Ulmus americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and co...
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doaj-1adeb4aada344960b5a50652f82d62b82020-11-25T00:50:25ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-07-01610.3389/fpls.2015.00541137647Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm diseasePedro ePerdiguero0Pedro ePerdiguero1Martin eVenturas2Maria Teresa Cervera3Maria Teresa Cervera4Luis eGil5Luis eGil6Carmen eCollada7Carmen eCollada8Universidad Politénica de Madrid. Sistemas y recursos forestalesINIA/UPMUniversidad Politénica de Madrid. Sistemas y recursos forestalesInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)INIA/UPMUniversidad Politénica de Madrid. Sistemas y recursos forestalesINIA/UPMUniversidad Politénica de Madrid. Sistemas y recursos forestalesINIA/UPMElms, especially Ulmus minor and Ulmus americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to SNPs (27,359). In a subset randomly selected for validation, 87 % of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00541/fullTranscriptomeUlmusNext-generation sequencingsnpsDutch elm disease |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Pedro ePerdiguero Pedro ePerdiguero Martin eVenturas Maria Teresa Cervera Maria Teresa Cervera Luis eGil Luis eGil Carmen eCollada Carmen eCollada |
spellingShingle |
Pedro ePerdiguero Pedro ePerdiguero Martin eVenturas Maria Teresa Cervera Maria Teresa Cervera Luis eGil Luis eGil Carmen eCollada Carmen eCollada Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease Frontiers in Plant Science Transcriptome Ulmus Next-generation sequencing snps Dutch elm disease |
author_facet |
Pedro ePerdiguero Pedro ePerdiguero Martin eVenturas Maria Teresa Cervera Maria Teresa Cervera Luis eGil Luis eGil Carmen eCollada Carmen eCollada |
author_sort |
Pedro ePerdiguero |
title |
Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease |
title_short |
Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease |
title_full |
Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease |
title_fullStr |
Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease |
title_full_unstemmed |
Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease |
title_sort |
massive sequencing of ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of dutch elm disease |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2015-07-01 |
description |
Elms, especially Ulmus minor and Ulmus americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to SNPs (27,359). In a subset randomly selected for validation, 87 % of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations. |
topic |
Transcriptome Ulmus Next-generation sequencing snps Dutch elm disease |
url |
http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00541/full |
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