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Background Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important fruit tree in China, and has high medicinal value. At present, the genome, transcriptome and germplasm resources of bayberry have been reported. In order to make more convenient use of these data, the Bayberry Database was established. Results The Bayberry Database is a comprehensive and intuitive data platform for examining the diverse annotated genome and germplasm resources of this species. This database contains nine central functional domains to interact with multiomic data: home, genome, germplasm, markers, tools, map, expression, reference, and contact. All domains provide pathways to a variety of data types composed of a reference genome sequence, transcriptomic data, gene patterns, phenotypic data, fruit images of Myrica rubra varieties, gSSR data, gene maps with annotation and evolutionary analyses. The tools module includes BLAST search, keyword search, sequence fetch and enrichment analysis functions. Conclusions The web address of the database is as follows http://www.bayberrybase.cn/. The Myrica rubra database is an intelligent, interactive, and user-friendly system that enables researchers, breeders and horticultural personnel to browse, search and retrieve relevant and useful information and thus facilitate genomic research and breeding efforts concerning Myrica rubra. This database will be of great help to bayberry research and breeding in the future.

Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.

Decline disease causes serious damage and rapid death in bayberry, an important fruit tree in south China, but the cause of this disease remains unclear. The aim of this study was to investigate soil quality, microbial community structure and metabolites of rhizosphere soil samples from healthy and diseased trees. The results revealed a significant difference between healthy and diseased bayberry in soil properties, microbial community structure and metabolites. Indeed, the decline disease caused a 78.24% and 78.98% increase in Rhizomicrobium and Cladophialophora, but a 28.60%, 57.18%, 38.84% and 68.25% reduction in Acidothermus, Mortierella, Trichoderma and Geminibasidium, respectively, compared with healthy trees, based on 16S and ITS amplicon sequencing of soil microflora. Furthermore, redundancy discriminant analysis of microbial communities and soil properties indicated that the main variables of bacterial and fungal communities included pH, organic matter, magnesium, available phosphorus, nitrogen and calcium, which exhibited a greater influence in bacterial communities than in fungal communities. In addition, there was a high correlation between the changes in microbial community structure and secondary metabolites. Indeed, GC–MS metabolomics analysis showed that the healthy and diseased samples differed over six metabolic pathways, including thiamine metabolism, phenylalanine–tyrosine–tryptophan biosynthesis, valine–leucine–isoleucine biosynthesis, phenylalanine metabolism, fatty acid biosynthesis and fatty acid metabolism, where the diseased samples showed a 234.67% and 1007.80% increase in palatinitol and cytidine, respectively, and a 17.37–8.74% reduction in the other 40 metabolites compared to the healthy samples. Overall, these results revealed significant changes caused by decline disease in the chemical properties, microbiota and secondary metabolites of the rhizosphere soils, which provide new insights for understanding the cause of this bayberry disease.

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.