The complete chloroplast genome of <i>Damnacanthus indicus</i> C.F.Gaertn. (Rubiaceae)

Lou, Shu-Mao; Li, Hong; Qin, Xin‐Mei; Huang, Zhang-Ping; Shuiyuan, Jiang; Huang, Xueliang

doi:10.1080/23802359.2021.1903365

Cited by 2 publications

(2 citation statements)

References 5 publications

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“…We largely followed the method for mitogenome assembly described in Choi et al (2019) [20]. Plastome-filtered reads were generated for each individual by read mapping to the recently published plastome sequence of D. indicus (MW548283.1) [70] in Geneious Prime 2021.0.3 (https://www.geneious.com/; accessed on 30 April 2021). De novo genome assemblies were conducted for each individual based on plastome-filtered reads.…”

Section: Mitogenome Assembly and Annotationmentioning

confidence: 99%

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Han

Cho

Tamaki

et al. 2021

IJMS

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The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes of six Damnacanthus indicus (Rubiaceae, Rubioideae) representing two varieties (var. indicus and var. microphyllus). The gene and intron content of D. indicus was compared with mitogenomes from representative angiosperm species and mitochondrial contigs from the other Rubiaceae species. Mitogenome structural rearrangement and sequence divergence in D. indicus were analyzed in six individuals. The size of the mitogenome in D. indicus varied from 417,661 to 419,435 bp. Comparing the number of intact mitochondrial protein-coding genes in other Gentianales taxa (38), D. indicus included 32 genes representing several losses. The intron analysis revealed a shift from cis to trans splicing of a nad1 intron (nad1i728) in D. indicus and it is a shared character with the other four Rubioideae taxa. Two distinct mitogenome structures (type A and B) were identified. Two-step direct repeat-mediated recombination was proposed to explain structural changes between type A and B mitogenomes. The five individuals from two varieties in D. indicus diverged well in the whole mitogenome-level comparison with one exception. Collectively, our study elucidated the mitogenome evolution in Rubiaceae along with D. indicus and showed the reliable phylogenetic utility of the whole mitogenome data at a species-level evolution.

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Section: Mitogenome Assembly and Annotationmentioning

confidence: 99%

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Han

Cho

Tamaki

et al. 2021

IJMS

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“…Damnacanthus major, an evergreen shrub of the Rubiaceae family, is approximately 30-70 cm tall, and grows naturally in warm regions, such as Korea (southern), China (southern), Japan (southern), Thailand, and India [1,2]. Recently, the genetics [3,4], medicinal material quality control [5], and synthesis of new metabolites and drug prototypes [6] have been studied in the Rubiaceae family owing to the diversity of chemical constituents. Among various secondary metabolites produced by the Rubiaceae family, anthraquinones are biologically active with anti-inflammatory, antioxidant, anticancer, hemostatic, and antibacterial activities [7].…”

Section: Introductionmentioning

confidence: 99%

Metabolomics Reveals Rubiadin Accumulation and the Effects of Methyl Jasmonate Elicitation in Damnacanthus major Calli

Hyeon,

Jang,

Kim

et al. 2024

Plants

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Callus suspension techniques have been considered attractive for improving bioactive metabolite productivity; methyl jasmonate (MeJA) is a widely used elicitor for stimulating synthetic pathways. In this study, a multivariate analysis-based metabolomics approach was employed to investigate the primary and specialized metabolites in the leaves, unelicited calli, and 100 or 200 μM MeJA elicited calli of Damnacanthus major. Rubiadin, a powerful anthraquinone with various therapeutic properties, was only identified in D. major calli, accumulating in a MeJA elicitation concentration-dependent manner. Callus cultures also contained high levels of amino acids, sugars, and phenolic compounds, indicating energy metabolism and metabolic adaptation responses for proliferation and stabilization. Regarding MeJA application, elicited calli contained higher amounts of quinic acid, kaempferol, and glucose with lower amounts of sucrose and raffinose than those in the unelicited control, which were closely related to protective mechanisms against MeJA. Moreover, excessive elicitation increased the asparagine, fructose, and raffinose levels and decreased the glucose and sucrose levels, which was ascribed to increased activation of the aminoacyl-tRNA biosynthesis pathway and wider utilization of glucose than of fructose after sucrose degradation. These results will be useful for optimizing plant cell culture techniques to achieve high production rates for valuable specialized metabolites.

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The complete chloroplast genome of Damnacanthus indicus C.F.Gaertn. (Rubiaceae)

Cited by 2 publications

References 5 publications

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Metabolomics Reveals Rubiadin Accumulation and the Effects of Methyl Jasmonate Elicitation in Damnacanthus major Calli

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