Abstract
Rapeseed-mustard, the oleiferous Brassica species are important oilseed crops cultivated all over the globe. Mustard aphid Lipaphis erysimi (L.) Kaltenbach is a major threat to the cultivation of rapeseed-mustard. Wild mustard Rorippa indica (L.) Hiern shows tolerance to mustard aphids as a nonhost and hence is an important source for the bioprospecting of potential resistance genes and defense measures to manage mustard aphids sustainably. We performed mRNA sequencing of the R. indica plant uninfested and infested by the mustard aphids, harvested at 24 hours post-infestation. Following quality control, the high-quality reads were subjected to de novo assembly of the transcriptome. As there is no genomic information available for this potential wild plant, the raw reads will be useful for further bioinformatics analysis and the sequence information of the assembled transcripts will be helpful to design primers for the characterization of specific gene sequences. In this study, we also used the generated resource to comprehensively analyse the global profile of differential gene expression in R. indica in response to infestation by mustard aphids. The functional enrichment analysis of the differentially expressed genes reveals a significant immune response and suggests the possibility of chitin-induced defense signaling.
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Data availability
The raw FASTQ Illumina sequence data that support the findings of this study have been deposited in the NCBI Sequence Read Archive (SRR17327159, SRR17327158, SRR17346649, SRR17346648) under Bioproject PRJNA792073.
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23 March 2024
A Correction to this paper has been published: https://doi.org/10.1007/s10142-024-01335-w
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Acknowledgements
The work is funded by a project [Project No. SR/WOS-A/LS-45/2018 (G)] granted to Dr. Lekha Bandopadhyay from the Department of Science & Technology, Ministry of Science and Technology, India under the Women Scientist Scheme-A. The authors are thankful to Bose Institute, India for providing the necessary facilities. The authors acknowledge Sandor Lifesciences, India for their support in RNA-Seq data generation, processing and analyses. The authors are thankful to Prof. Zhumur Ghosh, Bose Institute, and Ms. Troyee Das, Bose Institute for their help in understanding the RNA Seq data. The authors are also thankful to Prof. Shubho Chaudhuri, Bose Institute for his administrative support throughout the course of this study. Lastly, the authors heartily thank two anonymous reviewers for their thoughtful suggestions to improve this report.
Funding
The work is funded by a project [Project No. SR/WOS-A/LS-45/2018 (G)] granted to Dr. Lekha Bandopadhyay from the Department of Science & Technology, Ministry of Science and Technology, India under the Women Scientist Scheme-A.
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Lekha Bandopadhyay, Debabrata Basu, and Samir Ranjan Sikdar contributed to the concept and design of this work. Lekha Bandopadhyay prepared the experimental materials and contributed to the analyses and interpretation of the data. Lekha Bandopadhyay wrote the manuscript. All authors read and approved the final version of the manuscript.
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Bandopadhyay, L., Basu, D. & Ranjan Sikdar, S. De novo transcriptome assembly and global analysis of differential gene expression of aphid tolerant wild mustard Rorippa indica (L.) Hiern infested by mustard aphid Lipaphis Erysimi (L.) Kaltenbach. Funct Integr Genomics 24, 43 (2024). https://doi.org/10.1007/s10142-024-01323-0
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DOI: https://doi.org/10.1007/s10142-024-01323-0