Cargando…
De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)
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 dis...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7417550/ https://www.ncbi.nlm.nih.gov/pubmed/32778722 http://dx.doi.org/10.1038/s41598-020-70406-2 |
_version_ | 1783569518534066176 |
---|---|
author | Mahmood, Khalid Orabi, Jihad Kristensen, Peter Skov Sarup, Pernille Jørgensen, Lise Nistrup Jahoor, Ahmed |
author_facet | Mahmood, Khalid Orabi, Jihad Kristensen, Peter Skov Sarup, Pernille Jørgensen, Lise Nistrup Jahoor, Ahmed |
author_sort | Mahmood, Khalid |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7417550 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-74175502020-08-11 De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) Mahmood, Khalid Orabi, Jihad Kristensen, Peter Skov Sarup, Pernille Jørgensen, Lise Nistrup Jahoor, Ahmed Sci Rep Article 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. Nature Publishing Group UK 2020-08-10 /pmc/articles/PMC7417550/ /pubmed/32778722 http://dx.doi.org/10.1038/s41598-020-70406-2 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Mahmood, Khalid Orabi, Jihad Kristensen, Peter Skov Sarup, Pernille Jørgensen, Lise Nistrup Jahoor, Ahmed De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) |
title | De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) |
title_full | De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) |
title_fullStr | De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) |
title_full_unstemmed | De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) |
title_short | De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea) |
title_sort | de novo transcriptome assembly, functional annotation, and expression profiling of rye (secale cereale l.) hybrids inoculated with ergot (claviceps purpurea) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7417550/ https://www.ncbi.nlm.nih.gov/pubmed/32778722 http://dx.doi.org/10.1038/s41598-020-70406-2 |
work_keys_str_mv | AT mahmoodkhalid denovotranscriptomeassemblyfunctionalannotationandexpressionprofilingofryesecalecerealelhybridsinoculatedwithergotclavicepspurpurea AT orabijihad denovotranscriptomeassemblyfunctionalannotationandexpressionprofilingofryesecalecerealelhybridsinoculatedwithergotclavicepspurpurea AT kristensenpeterskov denovotranscriptomeassemblyfunctionalannotationandexpressionprofilingofryesecalecerealelhybridsinoculatedwithergotclavicepspurpurea AT saruppernille denovotranscriptomeassemblyfunctionalannotationandexpressionprofilingofryesecalecerealelhybridsinoculatedwithergotclavicepspurpurea AT jørgensenlisenistrup denovotranscriptomeassemblyfunctionalannotationandexpressionprofilingofryesecalecerealelhybridsinoculatedwithergotclavicepspurpurea AT jahoorahmed denovotranscriptomeassemblyfunctionalannotationandexpressionprofilingofryesecalecerealelhybridsinoculatedwithergotclavicepspurpurea |