A comprehensive collection of transcriptome data to support life cycle analysis of the poplar rust fungus Melampsora larici-populina

Abstract

Melampsora larici-populina is an obligate biotrophic plant pathogen responsible for the poplar rust disease. This fungus belongs to the taxonomical order Pucciniales and exhibits a complex heteroecious and macrocyclic life cycle, i.e. it has the capacity to infect two unrelated host plants, larch and poplar, and to form five distinct spore types through the year. The M. larici-populina genome has been sequenced and annotated in 2011 and since, different transcriptomic analyses were conducted at different stages with oligoarrays and later on with RNA-Seq covering most of its life cycle. Here, we collected published transcriptome data for the poplar rust fungus, transposed them for the version 2 of the genome now available at the Joint Genome Institute Mycocosm website and performed normalization of different oligoarray datasets on one hand, and of RNA-Seq on the other hand. We report a comprehensive normalized dataset for this fungus, made available for the community, which allows life cycle transcriptomics analysis.

A remarkable expansion of oligopeptide transporter genes in rust fungi (Pucciniales) suggests a specialization in nutrients acquisition for obligate biotrophy

“…M. larici-populina is a model rust fungus with extensive transcriptome information acquired along its whole lifecycle allowing for the study of expression patterns in given cellular categories (Guerillot et al 2021; Louet et al 2021). We extracted normalized expression data for 684 transporter genes, out of 743 total transporters for this rust fungus (missing data are from early oligoarraybased transcriptome studies; Supplementary Table S3).…”

“…Briefly, gene expression data were retrieved for dormant and germinated urediniospores, time course infection of poplar leaves and telia by oligoarrays (Duplessis et al 2011b; Hacquard et al 2013) and for basidia, spermogonia and aecia on larch needles by RNAseq (Lorrain et al 2018a). For this study, we extracted expression profiling of M. larici-populina transporter genes from an open transcriptomic dataset (Guerillot et al 2021; Supplementary Table S3). The Morpheus tool from the Broad Institute website (https://software.broadinstitute.org/morpheus/) was used to present normalized transcript expression levels using the k -means partitioning method.…”

“…Supplementary Table S3. Expression values of transporter genes along the life cycle of the poplar rust fungus Melampsora larici-populina (extracted from Guerillot et al 2021). URE and UREg, dormant and germinating poplar rust urediniospores, respectively; T24 to T168, hours post-inoculation in a time course infection series on poplar leaves inoculated with urediniospores; TEL, telia; BSD, basidia; SPG and AEC, spermogonia and aecia formed on larch needles, respectively.…”

A Remarkable Expansion of Oligopeptide Transporter Genes in Rust Fungi (Pucciniales) Suggests a Specialization in Nutrient Acquisition for Obligate Biotrophy

“…Briefly, gene expression data were retrieved for dormant and germinated urediniospores, time course infection of poplar leaves and telia by oligoarrays (Duplessis et al 2011b;Hacquard et al 2013) and for basidia, spermogonia and aecia on larch needles by RNAseq (Lorrain et al 2018a). For this study, we extracted expression profiling of M. larici-populina transporter genes from an open transcriptomic dataset (Guerillot et al 2021; Supplementary Table S3). The Morpheus tool from the Broad Institute website (https://software.broadinstitute.org/morpheus/) was used to present normalized transcript expression levels using the k-means partitioning method.…”

“…Beyond genomes, complementary transcriptomic studies allow to pinpoint the transporter genes which are specifically expressed during colonization, biotrophic growth or sporulation (Duplessis et al 2014(Duplessis et al , 2021. The transcriptome of the model rust fungus Melampsora larici-populina has been studied extensively along its life cycle which allows for a comprehensive survey of specific gene categories through transcriptomics of the whole life cycle (Guerillot et al 2021).…”