The chromosome‐scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolysable tannins

Lignans, phenolic plant secondary metabolites, are derived from the phenylpropanoid biosynthetic pathway. Although, being investigated for their health benefits in terms of antioxidant, antitumor, anti-inflammatory and antiviral properties, the role of these molecules in plants remains incompletely elucidated; a potential role in stress response mechanisms has been, however, proposed. In this study, a non-targeted metabolomic analysis of the roots, stems, and leaves of wild-type and PLR1-RNAi transgenic flax, devoid of (+) secoisolariciresinol diglucoside ((+) SDG)—the main flaxseed lignan, was performed using 1H-NMR and LC-MS, in order to obtain further insight into the involvement of lignan in the response of plant to osmotic stress. Results showed that wild-type and lignan-deficient flax plants have different metabolic responses after being exposed to osmotic stress conditions, but they both showed the capacity to induce an adaptive response to osmotic stress. These findings suggest the indirect involvement of lignans in osmotic stress response.

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Corrigendum to

Scientia Horticulturae ◽

10.1016/j.scienta.2021.110324 ◽

2021 ◽

pp. 110324

Author(s):

Zhen Chen ◽

Jingyong Jiang ◽

Xiaobai Li ◽

Yiwen Xie ◽

Zexin Jin ◽

...

Keyword(s):

Bioactive Compounds ◽

Fruit Quality ◽

Rubus Chingii ◽

Rubus Chingii Hu

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Highly Oxygenated Triterpenoids and Diterpenoids from Fructus Rubi (Rubus Chingii Hu) and Their NF-kappa B Inhibitory Effects

Molecules ◽

10.3390/molecules26071911 ◽

2021 ◽

Vol 26 (7) ◽

pp. 1911

Author(s):

Jiang Wan ◽

Xiao-Juan Wang ◽

Nan Guo ◽

Xi-Ying Wu ◽

Juan Xiong ◽

...

Keyword(s):

Inhibitory Effects ◽

Nf Kappa B ◽

Pentacyclic Triterpenoids ◽

Chemical Structures ◽

Phytochemical Investigation ◽

Ic50 Values ◽

Rubus Chingii ◽

Rubus Chingii Hu ◽

Type 3

During a phytochemical investigation of the unripe fruits of Rubus chingii Hu (i.e., Fructus Rubi, a traditional Chinese medicine named “Fu-Pen-Zi”), a number of highly oxygenated terpenoids were isolated and characterized. These included nine ursane-type (1, 2, and 4–10), five oleanane-type (3, 11–14), and six cucurbitane-type (15–20) triterpenoids, together with five ent-kaurane-type diterpenoids (21–25). Among them, (4R,5R,8R,9R,10R,14S,17S,18S,19R,20R)-2,19α,23-trihydroxy-3-oxo-urs-1,12-dien-28-oic acid (rubusacid A, 1), (2R*,4S*,5R*,8R*,9R*,10R*,14S*,17S*, 18S*,19R*,20R*)-2α,19α,24-trihydroxy-3-oxo-urs-12-en-28-oic acid (rubusacid B, 2), (5R,8R,9R,10R, 14S,17R,18S,19S)-2,19α-dihydroxy-olean-1,12-dien-28-oic acid (rubusacid C, 3), and (3S,5S,8S,9R, 10S,13R,16R)-3α,16α,17-trihydroxy-ent-kaur-2-one (rubusone, 21) were previously undescribed. Their chemical structures and absolute configurations were elucidated on the basis of spectroscopic data and electronic circular dichroism (ECD) analyses. Compounds 1 and 3 are rare naturally occurring pentacyclic triterpenoids featuring a special α,β-unsaturated keto-enol (diosphenol) unit in ring A. Cucurbitacin B (15), cucurbitacin D (16), and 3α,16α,20(R),25-tetrahydroxy-cucurbita-5,23- dien-2,11,22-trione (17) were found to have remarkable inhibitory effects against NF-κB, with IC50 values of 0.08, 0.61, and 1.60 μM, respectively.

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Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway

Horticulture Research ◽

10.1038/s41438-021-00627-7 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Hong-Lei Li ◽

Lin Wu ◽

Zhaoming Dong ◽

Yusong Jiang ◽

Sanjie Jiang ◽

...

Keyword(s):

Biosynthetic Pathway ◽

Southwest China ◽

Reference Genome ◽

Zingiber Officinale ◽

Gene Families ◽

Chromosome Conformation ◽

Long Reads ◽

Transcription Factor Networks ◽

Species Specific ◽

Haplotype 1

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

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Integrative Transcriptomic, and Proteomic Analysis of Flavonoid Biosynthesis During Fruit Maturation In Chinese Raspberry “Rubus Chingii Hu”

10.21203/rs.3.rs-284541/v1 ◽

2021 ◽

Author(s):

Xiaobai Li ◽

Jian Sun ◽

Jingyong Jiang ◽

Zhen Chen ◽

Aaron Jackson

Keyword(s):

Anthocyanin Biosynthesis ◽

Flavonoid Biosynthesis ◽

Fruit Maturation ◽

Genetic Base ◽

Kaempferol Glycosides ◽

Flavonoid Composition ◽

Rubus Chingii ◽

Rubus Chingii Hu ◽

Anthocyanin Production ◽

Low Expression

Abstract Rubus chingii, is a red-fruited species of Rubus native to China, which is a popular and nutritious fruit in China. However, change in flavonoid composition and content during fruit maturation is poorly understood. This study examined flavonoids and the genes/proteins during four fruit ripening phases using LC-MS/MS. As a result, six major kinds of anthocyanins were first identified in R. chingii, which primarily consisted of flavanol-anthocyanins, are new to Rubus. Apart from anthocyanins, concentrations of fruit flavonoids were much higher than most berries including raspberries, and it is this that contributes to their high phenolic concentrations and antioxidant capabilities. In contrast to other known raspberries, R. chingii had a decline in flavonoids during fruit maturation, which was due to down-regulation of genes/proteins involved in phenylpropanoid and flavonoid biosynthesis. Surprisingly, anthocyanin continuously decreased during fruit coloration. This suggests that anthocyanins are not responsible for the fruit’s reddish coloration. The biosynthesis of these flavanol-anthocyanins consumed two flavonoid units both produced through the same upstream pathway. Their presence indicates a reduction in the potential biosynthesis of anthocyanin production. Also, the constantly low expression of RcANS gene down-regulated overall anthocyanin biosynthesis. The lack of RcF3’5’H gene/protein hindered the production of delphinidin glycosides. Flavonoids primarily comprising of quercetin/kaempferol-glycosides were predominately located at fruit epidermal-hair and placentae. The profile and biosynthesis of R. chingii flavonoids are unique to Rubus. It could be used to broaden the genetic base of raspberry cultivars and to improve their fruit quality.

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Genome Assembly and Population Resequencing Reveal the Geographical Divergence of 'Shanmei'(Rubus corchorifolius)

10.1101/2021.11.22.469527 ◽

2021 ◽

Author(s):

Yinqing Yang ◽

Kang Zhang ◽

Ya Xiao ◽

Lingkui Zhang ◽

Yile Huang ◽

...

Keyword(s):

Genome Assembly ◽

Ancestral Population ◽

Effective Population ◽

High Quality ◽

Local Environments ◽

Rubus Species ◽

Rubus Chingii ◽

Rubus Chingii Hu ◽

Genomic Regions ◽

High Quality Genome

Rubus corchorifolius (Shanmei or mountain berry, 2n =14) is widely distributed in China, and its fruit has high nutritional and medicinal values. Here, we report a high-quality chromosome-scale genome assembly of Shanmei, with a size of 215.69 Mb and encompassing 26696 genes. Genome comparisons among Rosaceae species show that Shanmei and Fupenzi(Rubus chingii Hu) are most closely related, and then is blackberry (Rubus occidentalis). Further resequencing of 101 samples of Shanmei collected from four regions in provinces of Yunnan, Hunan, Jiangxi and Sichuan in South China reveals that the Hunan population of Shanmei possesses the highest diversity and may represent the relatively more ancestral population. Moreover, the Yunnan population undergoes strong selection based on nucleotide diversity, linkage disequilibrium and the historical effective population size analyses. Furthermore, genes from candidate genomic regions that show strong divergence are significantly enriched in flavonoid biosynthesis and plant hormone signal transduction, indicating the genetic basis of adaptation of Shanmei to the local environments. The high-quality genome sequences and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

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