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However, it remains unclear whether <jats:italic>RAFS<\/jats:italic> contributes to resistance to abiotic stress in plants, specifically in the <jats:italic>Gossypium<\/jats:italic> species.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this study, we identified 74 <jats:italic>RAFS<\/jats:italic> genes from <jats:italic>G. hirsutum<\/jats:italic>, <jats:italic>G. barbadense<\/jats:italic>, <jats:italic>G. arboreum<\/jats:italic> and <jats:italic>G. raimondii<\/jats:italic> by using a series of bioinformatic methods. Phylogenetic analysis showed that the <jats:italic>RAFS<\/jats:italic> gene family in the four <jats:italic>Gossypium<\/jats:italic> species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the <jats:italic>RAFS<\/jats:italic> gene structure was relatively conservative. Promoter analysis for <jats:italic>cis<\/jats:italic>-regulatory elements showed that some <jats:italic>RAFS<\/jats:italic> genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of <jats:italic>RAFS<\/jats:italic> under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of <jats:italic>RAFS<\/jats:italic> genes in <jats:italic>Gossypium<\/jats:italic> species. Transcriptome analysis suggested that <jats:italic>RAFS<\/jats:italic> genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that <jats:italic>GhRFS2A-GhRFS6A<\/jats:italic>, <jats:italic>GhRFS6D<\/jats:italic>, <jats:italic>GhRFS7D<\/jats:italic> and <jats:italic>GhRFS8A-GhRFS11A<\/jats:italic> were key genes, with high expression levels under salt, drought, cold and heat stress.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The findings may provide insights into the evolutionary relationships and expression patterns of <jats:italic>RAFS<\/jats:italic> genes in <jats:italic>Gossypium<\/jats:italic> species and a theoretical basis for the identification of stress resistance materials in cotton.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04276-4","type":"journal-article","created":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T19:02:36Z","timestamp":1624993356000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genome-wide identification and expression analysis of Raffinose synthetase family in cotton"],"prefix":"10.1186","volume":"22","author":[{"given":"Ruifeng","family":"Cui","sequence":"first","affiliation":[]},{"given":"Xiaoge","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Waqar Afzal","family":"Malik","sequence":"additional","affiliation":[]},{"given":"Xuke","family":"Lu","sequence":"additional","affiliation":[]},{"given":"Xiugui","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Delong","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Junjuan","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Shuai","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Chao","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Lixue","family":"Guo","sequence":"additional","affiliation":[]},{"given":"Quanjia","family":"Chen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0579-4909","authenticated-orcid":false,"given":"Wuwei","family":"Ye","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,6,29]]},"reference":[{"issue":"3","key":"4276_CR1","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1104\/pp.016386","volume":"131","author":"B Downie","year":"2003","unstructured":"Downie B, Gurusinghe S, Dahal P, Thacker RR, Snyder JC, Nonogaki H, Yim K, Fukanaga K, Alvarado V, Bradford KJ. 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