Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei

Abstract

Natural rubber (Hevea brasiliensis) is a tropical tree used commercially for the production of latex, from which 40,000 products are generated. The fungus Microcyclus ulei infects this tree, causing South American leaf blight (SALB) disease. This disease causes developmental delays and significant crop losses, thereby decreasing the production of latex. Currently several groups are working on obtaining clones of rubber tree with durable resistance to SALB through the use of extensive molecular biology techniques. In this study, we used a secondary clone that was resistant to M. ulei isolate GCL012. This clone, FX 3864 was obtained by crossing between clones PB 86 and B 38 (H. brasiliensis x H. brasiliensis). RNA-Seq high-throughput sequencing technology was used to analyze the differential expression of the FX 3864 clone transcriptome at 0 and 48 h post infection (hpi) with the M. ulei isolate GCL012. A total of 158,134,220 reads were assembled using the de novo assembly strategy to generate 90,775 contigs with an N50 of 1672. Using a reference-based assembly, 76,278 contigs were generated with an N50 of 1324. We identified 86 differentially expressed genes associated with the defense response of FX 3864 to GCL012. Seven putative genes members of the AP2/ERF ethylene (ET)-dependent superfamily were found to be down-regulated. An increase in salicylic acid (SA) was associated with the up-regulation of three genes involved in cell wall synthesis and remodeling, as well as in the down-regulation of the putative gene CPR5. The defense response of FX 3864 against the GCL012 isolate was associated with the antagonistic SA, ET and jasmonic acid (JA) pathways. These responses are characteristic of plant resistance to biotrophic pathogens.

Transcriptome analysis of a powdery mildew pathogen (Podosphaera pannosa) infecting Eucalyptus urophylla: De novo assembly, expression profiling and secretome prediction

“…These reads can be aligned to a reference genome when available or assembled de novo without the genomic reference to produce a genome-scale transcription map comprising both the transcriptional profile and/or level of expression for each gene (Wang, Gerstein, & Snyder, 2009). Transcriptome sequencing by RNA-Seq provides fundamental information for gene discovery and quantification of gene expression (Huynh, Page, Richardson, & Udall, 2015;Kim et al, 2014), comparative genomic studies (Bindschedler, Panstruga, & Spanu, 2016;Páez, Romero, Restrepo, Gutiérrez, & Castaño, 2015;Wang, Shi, & Rinehart, 2015), secretome analysis and prediction of fungal candidate effectors (Bruce et al, 2014;Guyon, Balagué, Roby, & Raffaele, 2014;Liu et al, 2015;Meinhardt et al, 2014). Whole-genome sequencing and assembly for powdery mildew pathogens are hampered by the obligate nature of the pathogen and by large numbers of repetitive elements throughout the genomes (Spanu et al, 2010).…”

“…Whole-genome sequencing and assembly for powdery mildew pathogens are hampered by the obligate nature of the pathogen and by large numbers of repetitive elements throughout the genomes (Spanu et al, 2010). Transcriptome sequencing by RNA-Seq provides fundamental information for gene discovery and quantification of gene expression (Huynh, Page, Richardson, & Udall, 2015;Kim et al, 2014), comparative genomic studies (Bindschedler, Panstruga, & Spanu, 2016;Páez, Romero, Restrepo, Gutiérrez, & Castaño, 2015;Wang, Shi, & Rinehart, 2015), secretome analysis and prediction of fungal candidate effectors (Bruce et al, 2014;Guyon, Balagué, Roby, & Raffaele, 2014;Liu et al, 2015;Meinhardt et al, 2014). Thus, the aim of our study was to develop genomic resources, through transcriptome profiling of epiphytic hyphae/conidia and haustoria and identification of potential microsatellites for population genetic studies of P. pannosa, infecting an economically important tree crop Eucalyptus urophylla.…”

The rubber tree genome reveals new insights into rubber production and species adaptation

“…The first draft Hevea genome was released by a Malaysian team 7 that was participant to the recent boom in transcriptomic and proteomic studies of the species [8][9][10][11] . However, its low sequence coverage (∼13×) and a lack of large insert libraries (such as fosmid-or BAC-based clone libraries) have limited the success of genome assembly (a scaffold N50 size of 2,972 bp), precluding its application for furthering quality research in the field.…”

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

“…Different initiatives have associated GWAS results with RNA-Seq data (Yan et al, 2020), linking causal genes relevant to the observed phenotypic variation with cell transcription activity profiles (Schaefer et al, 2018; Nguyen et al, 2019). In Hevea, however, RNA-Seq-based studies have been mainly performed to investigate differentially expressed genes (DEGs) under different environmental or stress conditions and profiling rubber tree samples (Hurtado Páez et al, 2015; Sathik et al, 2018; Mantello et al, 2019; Ding et al, 2020; Ding et al, 2020). Although the integration of GWAS with RNA-Seq methodologies has proven to provide a deeper comprehension of the genetic relationships involved in trait definition, there is no study, to date, aggregating such data in Hevea.…”