De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology

Ma, Ligang; Dong, Chengming; Song, Chi; Wang, Xiaolan; Zheng, Xiaoke; Niu, Yan D.; Chen, Shilin; Feng, Weisheng

doi:10.1016/j.csbj.2021.07.006

Cited by 32 publications

(36 citation statements)

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“…These transcripts in plants may contain protein coding sequences, isoforms, and non-coding RNAs [ 21 , 22 , 24 ]. A reference genome for R. glutinosa has recently been reported and is predicted to contain 48,475 protein-coding genes [ 25 ]. The number of predicted genes differs from the 58,949 predicted CDS in our study ( Table 1 ), possibly because our transcriptome data also contain the isoforms of genes generated by alternative splicing [ 13 ].…”

Section: Discussionmentioning

confidence: 99%

Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in Rehmannia glutinosa

Kang

Han²,

Yang

et al. 2022

Genes

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Terpenoids are naturally occurring compounds involved in respiration, photosynthesis, membrane fluidity, and pathogen interactions and are classified according to the structure of their carbon skeleton. Although most terpenoids possess pharmacological activity, knowledge about terpenoid metabolism in medicinal plants is insufficient. Rehmannia glutinosa (R. glutinosa) is a traditional herb that is widely used in East Asia and has been reported to contain various terpenoids. In this study, we performed a comprehensive transcriptome analysis of terpenoid metabolism in R. glutinosa using two RNA sequencing platforms: Illumina and PacBio. The results show that the sterol, saponin, iridoid, and carotenoid pathways are active in R. glutinosa. Sterol and saponin biosynthesis were mevalonate pathway dependent, whereas iridoid and carotenoid biosynthesis were methylerythritol 4-phosphate pathway dependent. In addition, we found that the homologous genes of key enzymes involved in terpenoid metabolism were expressed differentially and that the differential expression of these genes was associated with specific terpenoid biosynthesis. The different expression of homologous genes encoding acetyl-CoA acetyltransferase, 3-hydroxy-3-methylglutaryl-CoA reductase, mevalonate kinase, mevalonate diphosphate decarboxylase, farnesyl pyrophosphate synthase, squalene synthase, and squalene epoxidase was associated with sterol and saponin biosynthesis. Homologous genes encoding 1-deoxy-D-xylulose 5-phosphate synthase were also differentially expressed and were associated with carotenoid and iridoid biosynthesis. These results suggest that the biosynthesis of specific terpenoids can be regulated by the homologous of key enzymes involved in plant terpenoid metabolism.

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Section: Discussionmentioning

confidence: 99%

Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in Rehmannia glutinosa

Kang

Han²,

Yang

et al. 2022

Genes

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“…Thus far, four orobanchaceous species’ genomes have been released, the autotrophic Rehmannia glutinosa (19) and the obligate hemiparasite Striga asiatica (15) and facultative hemiparasite Phtheirospermum japonicum (20) and Pedicularis cranolopha (21), but the genomes of orobanchaceous holoparasites are still lacking. In this study, we sequenced and assembled high-quality genomes of the autotroph Lindenbergia luchunensis and the holoparasites Orobanche cumana and Phelipanche aegyptiaca , among which the latter two are notorious parasitic pests in agriculture.…”

Section: Introductionmentioning

confidence: 99%

“…The degree of gene loss is generally considered to be positively associated with the degree of parasitism (16), as a greater degree of parasitism requires higher dependency on the host and fewer physiological processes are needed by the parasite itself, and gene loss may enable the parasite to synchronize its own physiology with that of the host, probably resulting in better fitness (18). Thus far, four orobanchaceous species' genomes have been released, the autotrophic Rehmannia glutinosa (19) and the obligate hemiparasite Striga asiatica (15) and facultative hemiparasite Phtheirospermum japonicum (20) and Pedicularis cranolopha (21), but the genomes of orobanchaceous holoparasites are still lacking. In this study, we sequenced and assembled high-quality genomes of the autotroph Lindenbergia luchunensis and the holoparasites Orobanche cumana and Phelipanche aegyptiaca, among which the latter two are notorious parasitic pests in agriculture.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism

Xu¹,

Zhang²,

et al. 2022

Preprint

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Orobanchaceae is the largest family of plant parasites comprising autotrophic and parasitic plants with all degrees of parasitism, making it by far the best family for studying the origin and evolution of plant parasitism. Here we provide three high-quality genomes of orobanchaceous plants, the autotrophic Lindenbergia luchunensis and holoparasitic Phelipanche aegyptiaca and Orobanche cumana. Phylogenomic analysis on these three genomes and the previously published genomes and transcriptomes of other orobanchaceous species created a robust phylogenetic framework of Orobanchaceae. An ancient whole-genome duplication (WGD; about 79.29 Mya) was detected in the common ancestor of Orobanchaceae and Mimulus guttatus, and this event might have contributed to the origin of parasitism; however, except for Striga, no WGD events occurred in any lineages of orobanchaceous parasites after divergence from their autotrophic common ancestor, and the expansion of the genomes of orobanchaceous parasitic plants was mainly due to retrotransposons. We detected evident convergent gene loss in all parasites within Orobanchaceae and between Orobanchaceae and dodder Cuscuta australis. The gene families in the orobanchaceous parasites showed a clear pattern of recent gains and expansions, and the expanded gene families are enriched in functions related to development of haustorium. Thus, recent gene family expansions may have facilitated the adaptation of orobanchaceous parasites to different hosts. These data well support the previously proposed model of parasitic plant genome evolution. This work illustrates the trajectory of the evolution of orobanchaceous parasites, and will facilitate future studies on parasitism and the control of parasitic plants in agriculture.

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“…The previous study confirmed that most prenyltransferases involved in terpenoid backbone biosynthesis were the member of FPP/GGPP synthase families, and all prenyltransferases were interacted with biotin carboxylase CAC2 (Chen et al, 2021 ). A reference genome of R. glutinosa was reported using Nanopore technology, Illumina, and Hi-C sequencing, in which the expansion of the UDP-dependent glycosyltransferases and the terpene synthase gene families was demonstrated (Ma et al, 2021 ). Nevertheless, the regulation of genes involved in iridoid glycoside biosynthesis was rarely reported in R. glutinosa .…”

Section: Discussionmentioning

confidence: 99%

Effects of 5-azaC on Iridoid Glycoside Accumulation and DNA Methylation in Rehmannia glutinosa

Dong

Song²,

Wang³

et al. 2022

Front. Plant Sci.

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Iridoid glycoside is the important secondary metabolite and the main active component in Rehmannia glutinosa. However, the mechanisms that underlie the regulation of iridoid glycoside biosynthesis remain poorly understood in R. glutinosa. Herein, the analysis of RNA-seq data revealed that 3,394 unigenes related to the biosynthesis of secondary metabolites were identified in R. glutinosa. A total of 357 unigenes were involved in iridoid glycoside synthesis, in which the highly conservative genes, such as DXS, DXR, GPPS, G10H, and 10HGO, in organisms were overexpressed. The analysis of the above genes confirmed that the co-occurrence ratio of DXS, DXR, and GPPS was high in plants. Further, our results showed that under normal and 5-azacytidine (5-azaC) treatment, the expression levels of DXS, DXR, GPPS, G10H, and 10HGO were consistent with the iridoid glycoside accumulation in R. glutinosa, in which the application of the different concentrations of 5-azaC, especially 50 μM 5-azaC, could significantly upregulate the expression of five genes above and iridoid glycoside content. In addition, the changes in the spatiotemporal specificity of degree and levels of DNA methylation were observed in R. glutinosa, in which the hemi-methylation was the main reason for the change in DNA methylation levels. Similar to the changes in 5-methyl cytosine (5mC) content, the DNA demethylation could be induced by 5-azaC and responded in a dose-dependent manner to 15, 50, and 100 μM 5-azaC. Taken together, the expression of iridoid glycoside synthesis gene was upregulated by the demethylation in R. glutinosa, followed by triggering the iridoid glycoside accumulation. These findings not only identify the key genes of iridoid glycoside synthesis from R. glutinosa, but also expand our current knowledge of the function of methylation in iridoid glycoside accumulation.

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De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology

Abstract: Graphical abstract

Cited by 32 publications

References 100 publications

Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in Rehmannia glutinosa

Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in Rehmannia glutinosa

Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism

Effects of 5-azaC on Iridoid Glycoside Accumulation and DNA Methylation in Rehmannia glutinosa

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