Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling

Abstract

Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the “symbiosis toolkits” and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.

Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus

“…Thus, in accordance with the EdgeR guidelines, a BCV (biological coefficient variation) of 0.1 was assigned [37]. This procedure has been successfully used previously in other studies, for which biological replicates were also not available [38]. After the identification of the differentially expressed (DE) genes, correction for multiple testing was performed by applying the Benjamini-Hochberg method [39] on the p-values, to control the false discovery rate (FDR).…”

“…The protein domains were also identified for the set of predicted genes using InterProScan, providing information about the functional classes of GO terms and KEGG pathways. Over the set of predicted genes, 77.7% (64,853) had at least one protein domain identified, 46.4% (38,762) were associated with at least one GO term (BP: 29.6%, CC: 11.3% and MF: 41.4%) and 5.9% (4904) were associated with at least one KEGG pathway. The total number of different GO terms and KEGG pathways identified over the whole gene set was 1810 and 111, respectively.…”

Mycorrhization of Fagaceae Forests Within Mediterranean Ecosystems

“…Within a national initiative, a Portuguese consortium was created to study cork oak ESTs and thus develop a new genomic resource for studying Q. suber (Pereira-Leal et al 2014). This achievement has been used to better understand processes related with plant development (Rocheta et al 2014;Teixeira et al 2014) and adaptation responses to both biotic (Sebastiana et al 2014) and abiotic factors (Magalhães et al 2016). The global overview of up-and downregulated genes in cork oak roots following inoculation with the P. tinctorius resulted in a better insight of those molecular events that control ECM symbiosis (Sebastiana et al 2014).…”

Characterization of Ectomycorrhizal species through molecular biology tools and morphotyping

“…Brundrett et al, 1996 corrhizal fungi (Gao et al, 2015). These tools, besides allowing the identification of ectomycorrhizae, can contribute to a better understanding of the mutualistic interaction between plant and fungus (Larsen et al, 2011;Sebastiana et al, 2014). The use of a technique varies depending on the purpose of the study.…”