Home About Browse Search
Svenska


De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)

Mahmood, Khalid and Orabi, Jihad and Kristensen, Peter Skov and Sarup, Pernille and Jorgensen, Lise Nistrup and Jahoor, Ahmed (2020). De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea). Scientific Reports. 10 , 13475 , 1-16
[Journal article]

[img] PDF
2MB

Abstract

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.

Authors/Creators:Mahmood, Khalid and Orabi, Jihad and Kristensen, Peter Skov and Sarup, Pernille and Jorgensen, Lise Nistrup and Jahoor, Ahmed
Title:De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)
Year of publishing :2020
Volume:10
Article number:13475
Number of Pages:16
Publisher:Springer Nature
ISSN:2045-2322
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Agricultural Science
URN:NBN:urn:nbn:se:slu:epsilon-p-107736
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-107736
Additional ID:
Type of IDID
DOI10.1038/s41598-020-70406-2
Web of Science (WoS)000561124300011
ID Code:17545
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:06 Oct 2020 07:31
Metadata Last Modified:06 Oct 2020 07:31

Repository Staff Only: item control page

Downloads

Downloads per year (since September 2012)

View more statistics

Downloads
Hits