Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
Biomarker Technologies Corporation, Beijing, China.
BMC Genomics. 2019 Jun 6;20(1):458. doi: 10.1186/s12864-019-5818-7.
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.
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.
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.
杨梅（Myrica rubra Sieb. & Zucc.）是一种经济价值很高的果树，其果实多汁，富含抗氧化化合物。阐明杨梅中活性抗氧化化合物生物合成的遗传基础，对于杨梅的遗传改良和果实抗氧化成分的工业应用具有重要意义。本研究报道了中国多抗杨梅品种‘早佳’的基因组序列和果实发育过程中的转录组动态。
组装得到一个 289.92 Mb 的基因组草图，预测到 26325 个蛋白编码基因。抗氧化信号通路中的大多数杨梅基因都有多个拷贝，可能起源于串联重复事件。此外，这里发现的许多基因在跨物种的保守功能残基中存在结构变异或氨基酸变化。与成熟果实阶段相比，抗氧化基因在果实发育早期的表达水平普遍较高，且与总类黄酮和抗氧化能力的高水平呈正相关。基于基因表达和生化分析，推测五个基因，即咖啡酰辅酶 A O-甲基转移酶、花青素 3-O-葡萄糖基转移酶、（+）-新薄荷醇脱氢酶、赤霉素 2-氧化酶和角鲨烯单加氧酶，分别调节类黄酮、花青素、单萜、二萜和倍半萜/三萜水平在果实发育过程中。
本研究描述了杨梅的全基因组和转录组。研究结果为杨梅的遗传改良研究提供了重要基础，并有助于了解其遗传进化。代表性抗氧化信号通路的基因组序列有助于揭示有用的性状和功能基因。
