De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea).
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
10 08 2020
10 08 2020
Historique:
received:
16
03
2020
accepted:
24
07
2020
entrez:
12
8
2020
pubmed:
12
8
2020
medline:
18
12
2020
Statut:
epublish
Résumé
Rye is used as food, feed, and for bioenergy production and remain an essential grain crop for cool temperate zones in marginal soils. Ergot is known to cause severe problems in cross-pollinated rye by contamination of harvested grains. The molecular response of the underlying mechanisms of this disease is still poorly understood due to the complex infection pattern. RNA sequencing can provide astonishing details about the transcriptional landscape, hence we employed a transcriptomic approach to identify genes in the underlying mechanism of ergot infection in rye. In this study, we generated de novo assemblies from twelve biological samples of two rye hybrids with identified contrasting phenotypic responses to ergot infection. The final transcriptome of ergot susceptible (DH372) and moderately ergot resistant (Helltop) hybrids contain 208,690 and 192,116 contigs, respectively. By applying the BUSCO pipeline, we confirmed that these transcriptome assemblies contain more than 90% of gene representation of the available orthologue groups at Virdiplantae odb10. We employed a de novo assembled and the draft reference genome of rye to count the differentially expressed genes (DEGs) between the two hybrids with and without inoculation. The gene expression comparisons revealed that 228 genes were linked to ergot infection in both hybrids. The genome ontology enrichment analysis of DEGs associated them with metabolic processes, hydrolase activity, pectinesterase activity, cell wall modification, pollen development and pollen wall assembly. In addition, gene set enrichment analysis of DEGs linked them to cell wall modification and pectinesterase activity. These results suggest that a combination of different pathways, particularly cell wall modification and pectinesterase activity contribute to the underlying mechanism that might lead to resistance against ergot in rye. Our results may pave the way to select genetic material to improve resistance against ergot through better understanding of the mechanism of ergot infection at molecular level. Furthermore, the sequence data and de novo assemblies are valuable as scientific resources for future studies in rye.
Identifiants
pubmed: 32778722
doi: 10.1038/s41598-020-70406-2
pii: 10.1038/s41598-020-70406-2
pmc: PMC7417550
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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