Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat

Abstract

Wheat leaf rust, caused by the basidiomycete Puccinia triticina, can cause yield losses of up to 20% in wheat producing regions. During infection, the fungus forms haustoria that secrete proteins into the plant cell and effect changes in plant transcription, metabolism, and defense. It is hypothesized that new races emerge as a result of overcoming plant resistance via changes in the secreted effector proteins. To understand gene expression during infection and find genetic differences associated with races, RNA from wheat leaves infected with six different rust races, at 6 days post inoculation, was sequenced using Illumina. As P. triticina is an obligate biotroph, RNA from both the host and fungi were present and separated by alignment to the P. triticina genome and a wheat EST reference. A total of 222,571 rust contigs were assembled from 165 million reads. An examination of the resulting contigs revealed 532 predicted secreted proteins among the transcripts. Of these, 456 were found in all races. Fifteen genes were found with amino acid changes, corresponding to putative avirulence effectors potentially recognized by 11 different leaf rust resistance (Lr) genes. Twelve of the potential avirulence effectors have no homology to known genes. One gene had significant similarity to cerato-platanin, a known fungal elicitor, and another showed similarity to fungal tyrosinase, an enzyme involved in melanin synthesis. Temporal expression profiles were developed for these genes by qRT-PCR and show that the genes expression patterns were consistent between races from infection initiation to just prior to spore eruption.

Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions

“…Some studies have studied wheat–rust interactions to identify/locate the key genes involved in resistance mechanism such as those using the Affymetrix® GeneChip® Wheat Genome Array (Hulbert et al, 2007; Coram et al, 2009), EST sequencing (Manickavelu et al, 2010), cDNA-AFLP analysis (Bruce et al, 2014), SAGE (Chandra et al, 2016), and RNAseq (Zhang et al, 2014; Dobon et al, 2016). …”

Expression of apoplast-targeted plant defensin MtDef4.2 confers resistance to leaf rust pathogen Puccinia triticina but does not affect mycorrhizal symbiosis in transgenic wheat

“…Plants were grown in a growth chamber with a photoperiod of 16 h light/8 h dark, 23/16 °C day/night temperature, 50 % relative humidity (RH) and light intensity of 500 μmol m −2  s −1 . For growth, development and seed production comparison T 6 generation of transgenic and non-transgenic wheat lines were grown in the greenhouse at 20–22 °C during the day and 19–21 °C at night, 40–75 % RH and supplemental light when light intensity went below 300 μmol m −2  s −1 during 600–2200 h. Transgenic and non-transgenic wheat plants for Pt inoculation were grown at the USDA-ARS Hard Winter Wheat Genetics Research Unit, Department of Plant Pathology, Kansas State University, KS (Bruce et al 2014). …”

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).…”