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Mustard aphid, a specialist aphid species on rapeseed-mustard crops, rapidly multiplies and colonizes the plants leading to successful infestation. In contrary, legume specific cowpea aphid,<jats:italic>A. craccivora<\/jats:italic>when released on<jats:italic>B. juncea<\/jats:italic>plants fails to build up population and thus remains unsuccessful in infestation. In the present study, differential host response of<jats:italic>B. juncea<\/jats:italic>to the two aphid species, one being successful insect-pest and the other being unsuccessful on it has been studied based on transcriptome analysis. Differential feeding efficiency of the two aphid species on mustard plants was evident from the amount of secreted honeydews. Leaf-transcriptomes of healthy and infested plants, treated with the two aphid species, were generated by RNA sequencing on Illumina platform and<jats:italic>de novo<\/jats:italic>assembly of the quality reads. A comparative assessment of the differentially expressed genes due to treatments revealed a large extent of overlaps as well as distinctness with respect to the set of genes and their direction of regulation. With respect to host-genes related to transcription factors, oxidative homeostasis, defense hormones and secondary metabolites,<jats:italic>L. erysimi<\/jats:italic>led to either suppression or limited activation of the transcript levels compared to<jats:italic>A<\/jats:italic>.<jats:italic>craccivora<\/jats:italic>. Further, a comprehensive view of the DEGs suggested more potential of successful insect-pests towards transcriptional reprogramming of the host. qRT-PCR based validation of randomly selected up- and down-regulated transcripts authenticated the transcriptome data.<\/jats:p>","DOI":"10.1038\/s41598-020-66217-0","type":"journal-article","created":{"date-parts":[[2020,6,29]],"date-time":"2020-06-29T10:03:01Z","timestamp":1593424981000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Comparative transcriptomics revealed differential regulation of defense related genes in Brassica juncea leading to successful and unsuccessful infestation by aphid species"],"prefix":"10.1038","volume":"10","author":[{"given":"Lianthanzauva","family":"Duhlian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Murali Krishna","family":"Koramutla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Subramanian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohit","family":"Chamola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramcharan","family":"Bhattacharya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,29]]},"reference":[{"key":"66217_CR1","first-page":"1","volume":"31","author":"G Dhaliwal","year":"2004","unstructured":"Dhaliwal, G., Arora, R. & Dhawan, A. 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