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

Abstract

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.

Response of Resistant and Susceptible Bayberry Cultivars to Infection of Twig Blight Pathogen by Histological Observation and Gibberellin Related Genes Expression

“…The bayberry-resistant cultivar Zaojia and susceptible cultivar Dongkui were used in this study, which was collected from Lanxi County, Zhejiang Province, China. The two bayberry cultivars were currently widely planted in Zhejiang province, China, while Zaojia was bred by the Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, China [ 18 ].…”

“…cDNA was synthesized by using the PrimeScript™ RT reagent Kit with gRNA Eraser (Perfect Real Time, TaKaRa Company, Dalian, China). The quantitative real-time PCR reaction was carried out as described in our previous study [ 18 ] in LightCycler ® (Roche Diagnostics) amplification instrument using SYBR ® Premix DimerEraser™ (Perfect Real Time, TaKaRa Company). The relative expression of each gene was analyzed using the 2 −ΔΔCt method with MrUBQ1 as the internal standard.…”

“…At present, compared with the highly susceptible cultivar Dongkui, Zaojia is the main variety of bayberry with high resistance to twig blight in the market. This resistance may be mainly due to its characteristics of dwarf trees and short fruit maturity [ 18 ]. However, up to now, there is no systematic study on the difference in the infection process between resistant and susceptible varieties of bayberry [ 6 ].…”

Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

“…), also known as Chinese bayberry, is an economically important fruit crop that has been cultivated in China for more than two thousand years. Its fruit is not only very tasty but also rich in anthocyanins, vitamin C, and other antioxidant compounds (Ren et al, 2019). Red bayberry has a small genome size of~323 Mbp, and three draft genomes of the species have been published recently (Jia et al, 2019;Ren et al, 2019).…”

“…Its fruit is not only very tasty but also rich in anthocyanins, vitamin C, and other antioxidant compounds (Ren et al, 2019). Red bayberry has a small genome size of~323 Mbp, and three draft genomes of the species have been published recently (Jia et al, 2019;Ren et al, 2019). Red bayberry has separate male and female trees, which are diploid and propagate sexually under natural conditions.…”