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Background  Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree ( Hevea brasiliensis  Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood.    Results  In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors ( AUX-like1 ,  GH3.1 ,  SAUR32-like ,  IAA9-like ,  IAA14-like ,  IAA27-like ,  IAA28-like  and  ARF5-like ). The transcription factors including  WRKY40 ,  WRKY70 ,  MYBS3-like ,  MYB1R1 - like ,  AIL6  and  bHLH93-like  were characterized as molecular markers for rubber tree late SE.  CML13 ,  CML36 ,  CAM-7 ,  SERK1  and  LEAD-29-like  were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE.    Conclusions  This study provides important information to elucidate the molecular regulation during rubber tree late SE.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07501-9.

Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis