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To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers. two examples including 3-79 and TM-1 10 DPA fibers

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