A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

Chen, Hongyu; Guo, Miaoxian; Dong, Shuting; Wu, Xinling; Zhang, Guobin; He, Liu; Jiao, Yuannian; Chen, Shilin; Li, Li; Luo, Hongmei

doi:10.1016/j.xplc.2023.100516

Cited by 22 publications

(15 citation statements)

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“…Based on biosequence analysis using profile hidden Markov models (HMMER) and Basic Local Alignment Search Tool for proteins (BLASTP) selection, and after determining the presence of the Aux/IAA (PF02309) domain using the Pfam, a total of 61 Aux/IAA members were identified in the genome data of A. argyi ( Table 1 ) [ 30 ]. Identified genes were named from AaIAA1 to AaIAA61 based on the AaIAA location on the chromosomes ( Figure 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…However, the identification and functional information of Aux/IAA genes in medicinal plants are also limited and uncharacterized, especially in the A. argyi genome. The recent publication of the whole genome data of A. argyi enabled a massive progression in the comprehension of genome organization, which allowed for the identification of Aux/IAA genes [ 30 ]. Examining the role of Aux/IAA genes in A. argyi could provide an improved understanding of the functional attributes of this gene family in A. argyi and stimulate further research in related medicinal plant organisms.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones

Lian,

Lan,

et al. 2024

Plants

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Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones

Lian,

Lan,

et al. 2024

Plants

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“…Relative expression values were determined by the 2 −ΔΔCt method 9 . Primer design and evaluation are described by Chen et al 43 . The primer sequences are listed in Table 1.…”

Section: Methodsmentioning

confidence: 99%

Artemisia argyi extract exerts antioxidant properties and extends the lifespan of Drosophila melanogaster

Yang,

Cao,

Zhang

et al. 2024

J Sci Food Agric

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BACKGROUNDChinese mugwort (Artemisia argyi) possesses extensive pharmacological activities associated with anti‐tumour, antioxidative and anti‐inflammatory effects. The present study aimed to investigate the antioxidant and anti‐ageing effects of A. argyi extract (AAE) on the fruit fly (Drosophila melanogaster) ageing model by detecting antioxidant enzyme activities and the mRNA level of antioxidant genes.RESULTSAAE could significantly lengthen the mean lifespan, 50% survival days, and maximum lifespan of D. melanogaster, especially when the amount of AAE added reached 6.68 mg mL−1, the mean lifespan of both female and male flies increased by 23.74% and 22.30%, respectively, indicating the effective life extension effect of AAE. At the same time, AAE could improve the climbing ability and tolerance to hydrogen peroxide in D. melanogaster. In addition, the addition of AAE effectively increased the activities of copper‐zinc‐containing superoxide dismutase, manganese‐containing superoxide dismutase and catalase in D. melanogaster and reduced the contents of malondialdehyde. Moreover, when reared with diets containing AAE, the expression of antioxidant‐related genes SOD1, SOD2 and CAT was up‐regulated in D. melanogaster and down‐regulated for MTH genes.CONCLUSIONThe study indicates that AAE effectively enhances the antioxidant capacity of D. melanogaster and has potential applications as an antioxidant and anti‐ageing agent in the nutraceutical industry. © 2024 Society of Chemical Industry.

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“…4 ). With the development of herbal genomics [ 20 ] and generation of more genome-wide fine maps [ [65] , [66] , [67] , [68] , [69] ], pangenome-based identification will greatly facilitate resource discovery, breeding and quality improvement of traditional Chinese medicinal materials.…”

Section: Super-barcode: Genome-based Identification For Closely Relat...mentioning

confidence: 99%

DNA barcoding in herbal medicine: Retrospective and prospective

Chen

Yin

Han

et al. 2023

Journal of Pharmaceutical Analysis

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A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

Cited by 22 publications

References 88 publications

Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones

Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones

Artemisia argyi extract exerts antioxidant properties and extends the lifespan of Drosophila melanogaster

DNA barcoding in herbal medicine: Retrospective and prospective

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