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

Haiying Ren,Hongkun Zheng,Pu Yao,Haiyan Yu,Shujian Zhang,Shuwen Zhang,Xingjiang Qi,Xiliang Zheng,Senmiao Liang

doi:10.1186/s12864-019-5818-7

Abstract

BackgroundChinese 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.ResultsA 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.ConclusionsThis 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.

Highlights

Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds
An ancestral genome region in the basal eudicot V. vinifera was aligned to a genome region of M. rubra indicating paleohexaploidization, which is common in eudicots, but no recent whole-genome duplication event was detected in M. rubra (Figure 1a and b)
We suggest that K005888 (MRNA-011576-1), which encodes Caffeoyl-CoA O-methyltransferase (CCoAOMT) is the most important enzyme related to flavonoid biosynthesis, while K12930 (BZ1, MRNA_008272_1) is the key enzyme related to anthocyanin biosynthesis during fruit development

Summary

Introduction

Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds. The extract was found to increase the expression of cleaved caspases 3 and -7 and to induce apoptosis via an extracellular signalregulated kinase-dependent caspase-9 activation intrinsic apoptotic pathway by upregulating the pro-apoptotic proteins (BAD and BAX) and downregulating the antiapoptotic proteins (BCL-XL and BCL-2) [12]. It inhibits angiogenesis and induces G1 cell cycle arrest, further reducing the levels of reactive oxygen species and targeting the AKT/mTOR/P70S6K/4E-BP-1 pathway to reduce the expression of hypoxia-inducible factor 1-alpha and vascular endothelial growth factor, inhibiting angiogenesis [12, 13]. Treatment of human gastric cancer cells SGC-7901 with cyanidin-3-glucoside markedly increased KLF6 expression (an important tumor suppressor gene inactivated in many human cancers) and P21 protein levels, and inhibited cyclin-dependent kinase 4 and cyclin D1 expression [7]

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