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However, the regulatory mechanisms of bitter gourd in response to cold stress are still poorly elucidated. In this study, phytohormone determination and comparative transcriptome analyses in XY (cold-tolerant) and QF (cold-sensitive) after low temperature treatment were conducted. Under cold stress, the endogenous contents of abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) in XY were significantly increased at 24\u00a0h after treatment (HAT), indicating that ABA, JA and SA might function in regulating cold resistance. RNA-seq results revealed that more differentially expressed genes were identified at 6 HAT in QF and 24 HAT in XY, respectively. KEGG analysis suggested that the plant hormone signal transduction pathway was significantly enriched in both genotypes at all the time points. In addition, transcription factors showing different expression patterns between XY and QF were identified, including <jats:italic>CBF3<\/jats:italic>, <jats:italic>ERF2<\/jats:italic>, <jats:italic>NAC90<\/jats:italic>, <jats:italic>WRKY51<\/jats:italic> and <jats:italic>WRKY70<\/jats:italic>. Weighted gene co-expression network analysis suggested <jats:italic>MARK1<\/jats:italic>, <jats:italic>ERF17<\/jats:italic>, <jats:italic>UGT74E2<\/jats:italic>, <jats:italic>GH3.1<\/jats:italic> and <jats:italic>PPR<\/jats:italic> as hub genes. These results will deepen the understanding of molecular mechanism of bitter gourd in response to cold stress and the identified genes may help to facilitate the genetic improvement of cold-resistant cultivars.<\/jats:p>","DOI":"10.1038\/s41598-024-58754-9","type":"journal-article","created":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T19:02:14Z","timestamp":1721242934000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Comparative transcriptomics analysis of tolerant and sensitive genotypes reveals genes involved in the response to cold stress in bitter gourd (Momordica charantia L.)"],"prefix":"10.1038","volume":"14","author":[{"given":"Yu","family":"Ning","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renjie","family":"Qi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xihan","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longzheng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,17]]},"reference":[{"key":"58754_CR1","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1007\/s12374-013-0903-y","volume":"56","author":"J Jeon","year":"2013","unstructured":"Jeon, J. & Kim, J. 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