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Background  Longan ( Dimocarpus longan  Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting  D. longan  fruit yield, the difficulty and instability of blossoming is one of the most challenging issues. Perpetual flowering (PF) is a crucial trait for fruit trees and is directly linked to production potential. Therefore, studying the molecular regulatory mechanism of longan PF traits is crucial for understanding and solving problems related to flowering. In this study, comparative transcriptome analysis was performed using two longan cultivars that display opposite flowering phenotypes during floral induction.    Results  We obtained 853.72 M clean reads comprising 125.08 Gb. After comparing these data with the longan genome, 27,266 known genes and 1913 new genes were detected. Significant differences in gene expression were observed between the two genotypes, with 6150 and 6202 differentially expressed genes (DEGs) for ‘SJ’ and ‘SX’, respectively. The transcriptional landscape of floral transition at the early stage was very different in these two longan genotypes with respect to key hormones, circadian rhythm, sugar metabolism, and transcription factors. Almost all flowering-related DEGs identified are involved in photoperiod and circadian clock pathways, such as CONSTANS-like ( COL ), two-component response regulator-like ( APRRs ), gigantea ( GI ), and early flowering ( EFL ). In addition, the leafy ( LFY ) gene, which is the central floral meristem identity gene, may inhibit PF formation in ‘SJ’.    Conclusion  This study provides a platform for understanding the molecular mechanisms responsible for changes between PF and seasonal flowering (SF) longan genotypes and may benefit studies on PF trait mechanisms of evergreen fruit trees.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5461-3) contains supplementary material, which is available to authorized users.

Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition