Chinese raspberry (Rubus chingii Hu) is a fruit valued for it's health benefits, which is indigenous to China. It is a great source of antioxidants. However, the fruit phytochemicals are poorly understood. Phenolics and carotenoids attract much attention for their antioxidant capability, and they dramatically change during fruit ripening, leading to the difference in color, flavor and medicinal components. In this study, we investigated the change of carotenoids, phenolics and antioxidant activity using spectrophotometry during four different ripening phases i.e. mature green (MG), green yellow (GY), yellow orange (YO) and red (RE). The major components of carotenoids, anthocyanins, ellagitannins and flavonols were identified and quantified by LC-MS/MS. As a result, five carotenoids (mainly β-Citraurin and its esters), six anthocyanins (mainly anthocyanins covalently linked to another flavonoid unit), methyl (S)-flavogallonate and rourinoside were first identified in Rubus. In contrast to other known raspberries, R. chingii had a continuous decrease in total phenolics during fruit ripening, which was due to a continuous decrease in flavonoids (including anthocyanin). Total anthocyanin and flavonoid respectively declined from 19.5 to 6.9 mg/100 g FW, and 646.2 to 128.5 mg/100 g FW during fruit maturation and coloration. Accordingly, the components of anthocyanins, ellagitannins and flavonols also declined, thus resulting in a decrease in antioxidant activity (from 41.2 to 10.1 TEAC/100 g FW in ABTS and from 35.3 to 7.7 mmol TEAC/100 g FW in FRAP). In contrast, total carotenoid increased from 184.2 to 305.4 mg/100 g FW. Accordingly, the components of carotenoids also increased, with the exception of lutein. Additionally, kaempferol and quercetin were the main flavonoid aglycones, which were linked to a variety of glycosides. These kaempferol- and quercetin-glycosides mainly accumulated in epidermal hair and placentae. Notably, carotenoids (i.e. β-citraurin esters), instead of anthocyanins, gradually accumulated during fruit ripening, imparting the reddish color to ripe fruit.

Lindera aggregata is a species of the Lauraceae family, which has important medicinal, economic and ornamental values. In this study, we sequenced, assembled and annotated the chloroplast genome of L. aggregata and reannotated and corrected eight unverified annotations in the same genus. The chloroplast genomes taxa from Lindera and from different genera of Lauraceae were compared and analyzed, and their phylogenetic relationship and divergence time were speculated. All the 36 chloroplast genomes had typical quadripartite structures that ranged from 150,749 to 154,736 bp in total length. These genomes encoded 111–112 unique genes, including 78–79 protein-coding genes, 29–30 tRNA and 4 rRNA. Furthermore, there were 78–97 SSRs loci in these genomes, in which mononucleotide repeats were the most abundant; there were 24–49 interspersed repeats, and forward repeat types were the most frequent. The codon bias patterns of all species tended to use codons ending with A or U. Five and six highly variable regions were identified within genus and between genera, respectively, and three common regions (ycf1, ndhF-rpl32 and rpl32-trnL) were identified, which can be used as important DNA markers for phylogeny and species identification. According to the evaluation of the Ka/Ks ratio, most of the genes were under purifying selection, and only 10 genes were under positive selection. Finally, through the construction of the evolutionary tree of 39 chloroplast genomes, the phylogenetic relationship of Lauraceae was clarified and the evolutionary relationship of Lindera was revealed. The species of genus Lindera experienced rapid adaptive radiation from Miocene to Pleistocene. The results provided valuable insights for the study of chloroplast genomes in the Lauraceae family, especially in the genus Lindera.

Improving fruit size or weight, firmness, and shelf life is a major target for horticultural crop breeding. It is associated with the depolymerization and rearrangement of cell components, including pectin, hemicellulose, cellulose, and other structural (glyco)proteins. Expansins are structural proteins to loosen plant cell wall polysaccharides in a pH-dependent manner and play pivotal roles in the process of fruit development, ripening, and softening. Rubus chingii Hu, a unique Chinese red raspberry, is a prestigious pharmaceutical and nutraceutical dual-function food with great economic value. Thirty-three RchEXPs were predicted by genome-wide identification in this study, containing twenty-seven α-expansins (EXPAs), three β-expansins (EXPBs), one expansin-like A (EXPLA), and two expansin-like B (EXPLBs). Subsequently, molecular characteristics, gene structure and motif compositions, phylogenetic relationships, chromosomal location, collinearity, and regulatory elements were further profiled. Furthermore, transcriptome sequencing (RNA-seq) and real-time quantitative PCR assays of fruits from different developmental stages and lineages showed that the group of RchEXPA5, RchEXPA7, and RchEXPA15 were synergistically involved in fruit expanding and ripening, while another group of RchEXPA6 and RchEXPA26 might be essential for fruit ripening and softening. They were regulated by both abscisic acid and ethylene and were collinear with phylogenetic relationships in the same group. Our new findings laid the molecular foundation for improving the fruit texture and shelf life of R. chingii medicinal and edible fruit.