Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots
Pectobacterium atrosepticum (Pba) is a gram-negative bacterium that causes blackleg and tuber soft rot of potato but can also asymptomatically colonise other (non-host) plant species. The aim of this study was to investigate the molecular processes and responses involved in Pba-host (potato) and Pba...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-06-01
|
| Series: | Data in Brief |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S235234092400341X |
| _version_ | 1797214902458253312 |
|---|---|
| author | Ashleigh Holmes Sonia Humphris Susan Jones |
| author_facet | Ashleigh Holmes Sonia Humphris Susan Jones |
| author_sort | Ashleigh Holmes |
| collection | DOAJ |
| description | Pectobacterium atrosepticum (Pba) is a gram-negative bacterium that causes blackleg and tuber soft rot of potato but can also asymptomatically colonise other (non-host) plant species. The aim of this study was to investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions. To achieve this, we used total mRNA-sequencing to measure the gene expression patterns from all three species: Pba, potato and radish. We employed an end-point dual transcriptome approach. We used hydroponically grown potato (Solanum tuberosum var. Estima) and oil radish (Raphanus sativa var. Bento) roots inoculated with Pba SCRI1039 for 14 days compared to un-inoculated control plants or cultured bacteria. Total RNA was extracted from replicates of the two plant species and the bacterium using a Macherey-Nagel Nucleospin Plant RNA kit. The RNA from the 17 samples was then subjected to total mRNA-sequencing (paired-end) on an Illumina NovaSeq 6000™ sequencing platform. This gave between 39.2-58.1M reads per sample. The high-quality reads obtained were mapped to the corresponding reference genomes using Bowtie2 and the percentages of bacterium and plant transcripts calculated. This dataset constitutes the raw read fastq files and can be used to inform on genes active in plant rhizosphere-microbe interactions. |
| first_indexed | 2024-04-24T11:21:33Z |
| format | Article |
| id | doaj.art-87cf71ea6dc74eb381f90aac70dd1d40 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-04-24T11:21:33Z |
| publishDate | 2024-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-87cf71ea6dc74eb381f90aac70dd1d402024-04-11T04:41:22ZengElsevierData in Brief2352-34092024-06-0154110372Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish rootsAshleigh Holmes0Sonia Humphris1Susan Jones2Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, United Kingdom; Corresponding author.Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, United KingdomInformation and Computer Sciences, The James Hutton Institute, Dundee, DD2 5DA, United KingdomPectobacterium atrosepticum (Pba) is a gram-negative bacterium that causes blackleg and tuber soft rot of potato but can also asymptomatically colonise other (non-host) plant species. The aim of this study was to investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions. To achieve this, we used total mRNA-sequencing to measure the gene expression patterns from all three species: Pba, potato and radish. We employed an end-point dual transcriptome approach. We used hydroponically grown potato (Solanum tuberosum var. Estima) and oil radish (Raphanus sativa var. Bento) roots inoculated with Pba SCRI1039 for 14 days compared to un-inoculated control plants or cultured bacteria. Total RNA was extracted from replicates of the two plant species and the bacterium using a Macherey-Nagel Nucleospin Plant RNA kit. The RNA from the 17 samples was then subjected to total mRNA-sequencing (paired-end) on an Illumina NovaSeq 6000™ sequencing platform. This gave between 39.2-58.1M reads per sample. The high-quality reads obtained were mapped to the corresponding reference genomes using Bowtie2 and the percentages of bacterium and plant transcripts calculated. This dataset constitutes the raw read fastq files and can be used to inform on genes active in plant rhizosphere-microbe interactions.http://www.sciencedirect.com/science/article/pii/S235234092400341XRhizosphereMicrobe-plant interactionsTranscriptomicsDual-RNA-seqPectobacteriumPlant defence |
| spellingShingle | Ashleigh Holmes Sonia Humphris Susan Jones Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots Data in Brief Rhizosphere Microbe-plant interactions Transcriptomics Dual-RNA-seq Pectobacterium Plant defence |
| title | Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots |
| title_full | Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots |
| title_fullStr | Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots |
| title_full_unstemmed | Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots |
| title_short | Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots |
| title_sort | total mrna sequence dataset from pectobacterium atrosepticum colonising potato or radish roots |
| topic | Rhizosphere Microbe-plant interactions Transcriptomics Dual-RNA-seq Pectobacterium Plant defence |
| url | http://www.sciencedirect.com/science/article/pii/S235234092400341X |
| work_keys_str_mv | AT ashleighholmes totalmrnasequencedatasetfrompectobacteriumatrosepticumcolonisingpotatoorradishroots AT soniahumphris totalmrnasequencedatasetfrompectobacteriumatrosepticumcolonisingpotatoorradishroots AT susanjones totalmrnasequencedatasetfrompectobacteriumatrosepticumcolonisingpotatoorradishroots |