Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

Abstract

Elms, especially Ulmus minor and U. 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 single nucleotide polymorphisms (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.

Transcriptomic basis for reinforcement of elm antiherbivore defence mediated by insect egg deposition

“…This set of transcripts was used as the basis for our GO term enrichment and pathway analyses. Further annotations listed in the Supporting Information Tables are derived from Prunus persica and Malus domestica (both from Phytozome ) and U. minor (from Büchel et al., ; elm2015 from Perdiguero, Venturas, Cervera, Gil, & Collada, ) based on blast queries ( Blast N, threshold E < 10 −6 ).…”

Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms

“…Similar to C. parasitica, resistance to Ophiostoma spp. was linked to the increased expression of cell wall strengthening enzymes (Liao et al, 2014;Perdiguero et al, 2015) and a panel of phytohormones that differ from those induced in biotrophic interactions (i.e. brassinosteroid and auxin; Perdiguero et al, 2015).…”

Field Guide to Plant Model Systems

“…The genome sequences of the fast-growing hardwood trees, Eucalyptus grandis (640 Mb) and E. globulus (530 Mb), offer the opportunity for comparative angiosperm tree genomics as well as investigation of specialized metabolites, such as terpenes and oils (Myburg et al, 2014). While not a model for trees per se, transcriptome sequencing of Ulmus minor (elm) genotypes has shed insight on the impact that Dutch elm disease has had on Ulmus species and may illuminate possible avenues for conservation of Ulmus species (Perdoguero et al, 2015). …”