The draft genome and multi-omics analyses reveal new insights into geo-herbalism properties of Citrus grandis ‘Tomentosa’

Xian, Lin; Sahu, Sunil Kumar; Huang, Liying; Fan, Yannan; Lin, Jianhua; Su, Jianmu; Bai, Mei; Chen, Yewen; Wang, Shujie; Peng, Ye; Wang, Fang; Luo, Qun; Bai, Haiyi; Lin, Xiaojing; Cao, Yuan; Geng, Xiaodie; Liu, Huan; Wu, Hong

doi:10.1016/j.plantsci.2022.111489

Cited by 12 publications

(4 citation statements)

References 95 publications

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“…But the expression of all the aforementioned genes did not show any evident difference between the A and B regions, except valencene synthase, which belongs to the TPS family and showed considerable expansion in A. oxyphylla . This coincides with reports on other plant species, such as O. sanctum ( Kumar et al., 2018 ), W. villosa ( Yang et al., 2022 ), Z. officinale ( Cheng et al., 2021b ), and Citrus grandis ‘Tomentosa’ ( Xian et al., 2022 ). Previous studies have suggested that the expansion of the TPS-a and TPS-b subfamilies contributes to the diversity and content enrichment of sesquiterpenoids and monoterpenoids, respectively ( Chaw et al., 2019 ; Yang et al., 2022 ).…”

Section: Discussionsupporting

confidence: 90%

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

et al. 2023

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IntroductionAlpinia oxyphylla Miquel (A. oxyphylla), one of the “Four Famous South Medicines” in China, is an essential understory cash crop that is planted widely in the Hainan, Guangdong, Guangxi, and Fujian provinces. Particularly, A. oxyphylla from Hainan province is highly valued as the best national product for geo-herbalism and is an important indicator of traditional Chinese medicine efficacy. However, the molecular mechanism underlying the formation of its quality remains unspecified.MethodsTo this end, we employed a multi-omics approach to investigate the authentic quality formation of A. oxyphylla.ResultsIn this study, we present a high-quality chromosome-level genome assembly of A. oxyphylla, with contig N50 of 76.96 Mb and a size of approximately 2.08Gb. A total of 38,178 genes were annotated, and the long terminal repeats were found to have a high frequency of 61.70%. Phylogenetic analysis demonstrated a recent whole-genome duplication event (WGD), which occurred before A. oxyphylla’s divergence from W. villosa (~14 Mya) and is shared by other species from the Zingiberaceae family (Ks, ~0.3; 4DTv, ~0.125). Further, 17 regions from four provinces were comprehensively assessed for their metabolite content, and the quality of these four regions varied significantly. Finally, genomic, metabolic, and transcriptomic analyses undertaken on these regions revealed that the content of nootkatone in Hainan was significantly different from that in other provinces.DiscussionOverall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant A. oxyphylla.

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Section: Discussionsupporting

confidence: 90%

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

et al. 2023

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“…But the expression of all the aforementioned genes did not show any evident difference between the A and B regions, except valencene synthase, which belongs to the TPS family and showed considerable expansion in A. oxyphylla. This coincides with reports on other plant species, such as O. sanctum (Kumar et al, 2018), W. villosa , Z. officinale (Cheng et al, 2021b), and Citrus grandis 'Tomentosa' (Xian et al, 2022). Previous studies have suggested that the expansion of the TPS-a and TPS-b subfamilies contributes to the diversity and content enrichment of sesquiterpenoids and monoterpenoids, respectively (Chaw et al, 2019;.…”

Section: Discussionsupporting

confidence: 86%

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

2024

Frontiers Research Topics

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Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

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“…HZYs were the most wide source of Huajuhong medicines. We assembled the HZY‐T genome with chromosome levels and high completeness (99.1%), which is better than the previous genome with contig levels and low completeness (94.1%) (Xian et al ., 2022 ). Gene family analysis found that the expanded gene families in pummelo were enriched in the flavonoid biosynthetic process, phenylpropanoid biosynthetic process, response to oxidative stress and response to water deprivation.…”

Section: Discussionmentioning

confidence: 99%

Evolution‐guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo

Zheng

Zhang

Liu

et al. 2023

Plant Biotechnology Journal

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Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.

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The draft genome and multi-omics analyses reveal new insights into geo-herbalism properties of Citrus grandis ‘Tomentosa’

Cited by 12 publications

References 95 publications

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

Evolution‐guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo

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