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Background  Chinese bayberry ( Myrica rubra  Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds. Elucidating the genetic basis of the biosynthesis of active antioxidant compounds in bayberry is fundamental for genetic improvement of bayberry and industrial applications of the fruit’s antioxidant components. Here, we report the genome sequence of a multiple disease-resistant bayberry variety, ‘Zaojia’, in China, and the transcriptome dynamics in the course of fruit development.    Results  A 289.92 Mb draft genome was assembled, and 26,325 protein-encoding genes were predicted. Most of the  M. rubra  genes in the antioxidant signaling pathways had multiple copies, likely originating from tandem duplication events. Further, many of the genes found here present structural variations or amino acid changes in the conserved functional residues across species. The expression levels of antioxidant genes were generally higher in the early stages of fruit development, and were correlated with the higher levels of total flavonoids and antioxidant capacity, in comparison with the mature fruit stages. Based on both gene expression and biochemical analyses, five genes, namely, caffeoyl-CoA O-methyltransferase, anthocyanidin 3-O-glucosyltransferase, (+)-neomenthol dehydrogenase, gibberellin 2-oxidase, and squalene monooxygenase, were suggested to regulate the flavonoid, anthocyanin, monoterpenoid, diterpenoid, and sesquiterpenoid/triterpenoid levels, respectively, during fruit development.    Conclusions  This study describes both the complete genome and transcriptome of  M. rubra . The results provide an important basis for future research on the genetic improvement of  M. rubra  and contribute to the understanding of its genetic evolution. The genome sequences corresponding to representative antioxidant signaling pathways can help revealing useful traits and functional genes.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5818-7) contains supplementary material, which is available to authorized users.

Genome sequencing provides insights into the evolution and antioxidant activity of Chinese bayberry