Chromosome-scale genome assembly of an important medicinal plant honeysuckle

Yu, Hang; Guo, Kun; Lai, Kunlong; Shah, Muhammad Ali; Xu, Zijian; Cui, Na; Wang, Haifeng

doi:10.1038/s41597-022-01385-4

Cited by 7 publications

(3 citation statements)

References 62 publications

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“…Although this short-read study was unable to uniquely identify the chromosomes of the L. maackii EPSP synthase genes, the significant sequence differences suggest that these are indeed remnants of an ancestral duplication. It would also be interesting to see if the duplication is observed in the L. japonica sequencing by Yu et al [ 28 ] which was published subsequent to our analysis. Studies of the transcriptional activity of both genes, in both Lonicera species, would be important to assess the potential for duplications of these genes to instill resistance.…”

Section: Discussionmentioning

confidence: 91%

Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle)

Kesel

Hudson

Osier

2022

Plants

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The invasive species Lonicera maackii (Amur Honeysuckle) is an increasing problem sweeping from the eastern United States toward the west, impacting normal forest development and animal survival across multiple taxa. Little is known about the genomics of this species, although a related invasive, Lonicera japonica, has been sequenced. Understanding the genomic foundation of the Lonicera maackii species could help us understand the biochemistry and life history that are the underpinnings of invasive success, as well as potential vulnerabilities and strengths which could guide research and development to control its spread. Here we present a draft, but high-quality, short-read whole-genome sequence, assembly, and annotation of Lonicera maackii, demonstrating that inexpensive and rapid short-read technologies can be successfully used in invasive species research. Despite being a short-read assembly, the genome length (7.93 × 108) and completeness (estimated as 90.2–92.1% by BUSCO and Merqury) are close to the previously published chromosome-level sequencing of L. japonica. No bias, by means of a Gene Ontology analysis, was identified among missing BUSCOs. A duplication of the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase gene in both Lonicera species is identified, and the potential impact on controlling these invasive species is discussed. Future prospects for a diversity analysis of invasive species is also discussed.

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Section: Discussionmentioning

confidence: 91%

Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle)

Kesel

Hudson

Osier

2022

Plants

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“…Over the past few decades, the comparative analyses of genetic linkage maps and genomic approaches have revealed that inversions are ubiquitous across plant and animal kingdoms ( Wellenreuther and Bernatchez, 2018 ). Chromosomal inversions have been known to segregate in natural populations of various plant species including Arabidopsis ( Zapata et al., 2016 ), sorghum ( Deschamps et al., 2018 ), barley ( Himmelbach et al., 2018 ) and honeysuckle ( Yu et al., 2022 ). They are believed to play a crucial role in facilitating local adaptations by reducing recombination between favorable combinations of alleles ( Thorstensen et al., 2022 ).…”

Section: Resultsmentioning

confidence: 99%

A de novo chromosome-scale assembly of the Lablab purpureus genome

Pootakham,

Somta,

Kongkachana

et al. 2024

Front. Plant Sci.

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IntroductionLablab (Lablab purpureus (L.) Sweet), an underutilized tropical legume crop, plays a crucial role in global food and nutritional security. To enhance our understanding of its genetic makeup towards developing elite cultivars, we sequenced and assembled a draft genome of L. purpureus accession PK2022T020 using a single tube long fragment read (stLFR) technique.Results and discussionThe preliminary assembly encompassed 367 Mb with a scaffold N50 of 4.3 Mb. To improve the contiguity of our draft genome, we employed a chromatin contact mapping (Hi-C) approach to obtain a pseudochromosome-level assembly containing 366 Mb with an N50 length of 31.1 Mb. A total of 327.4 Mb had successfully been anchored into 11 pseudomolecules, corresponding to the haploid chromosome number in lablab. Our gene prediction recovered 98.4% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses utilizing sequence information from single-copy orthologous genes demonstrated that L. purpureus diverged from the last common ancestor of the Phaseolus/Vigna species approximately 27.7 million years ago. A gene family expansion analysis revealed a significant expansion of genes involved in responses to biotic and abiotic stresses. Our high-quality chromosome-scale reference assembly provides an invaluable genomic resource for lablab genetic improvement and future comparative genomics studies among legume species.

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“…It is widely used to treat upper respiratory inflammation symptoms, such as cough and sore throat ( Guo et al, 2021 ). One of its extracts, Chlorogenic acid, has anti-inflammatory, antibacterial, antioxidant, and other pharmacological effects ( Yu et al, 2022 ). Platycodon grandiflorus (Jacq.)…”

Section: Introductionmentioning

confidence: 99%

Efficacy of botanical lozenges in the treatment of chronic pharyngitis: a randomized controlled trial

Wu,

Zhang,

Kuang

et al. 2024

Front. Pharmacol.

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Background: In clinical practice, antibiotics and/or inhaled or oral hormone preparations are the first line of treatment for chronic pharyngitis. However, this therapeutic regimen is not satisfactory enough. At present, medicinal plants as dietary supplements or functional foods are widely recognized for the treatment and prevention of different diseases.Purpose: This study aimed to evaluate the efficacy of the botanical lozenge made from several medicinal plant extracts in the treatment of chronic pharyngitis and its effects on patients’ illness perception and adherence to treatment.Methods: Patients with chronic pharyngitis were randomly assigned to the experimental group (n = 52) or the control group (n = 51). Patients were given botanical lozenges prepared from the extracts of medicinal plants such as Siraitia grosvenorii (Swingle) C. Jeffrey ex A.M.Lu and Zhi Y. Zhang [Cucurbitaceae; Siraitiae fructus], Lonicera japonica Thunb [Caprifoliaceae; Lonicerae japonicae flos], Platycodon grandiflorus (Jacq.) A. DC [Campanulaceae; Platycodon radix], and Glycyrrhiza uralensis Fisch. ex DC [Fabaceae; Glycyrrhizae radix et rhizoma] or placebos made of starch for 15 days. The improvement of pharyngeal symptoms and signs, illness perception, and adherence to treatment were evaluated at the end of the intervention.Results: The total score of pharyngeal symptoms of patients in the experimental group (3.33 ± 2.33) was significantly lower than that in the control group (5.20 ± 2.93) (p < 0.01). In comparison to the control group (3.43 ± 1.43), the total pharyngeal signs score of patients in the experimental group (2.69 ± 1.59) was considerably lower (p < 0.01). The improvement rates of pharyngeal itching, dry throat, pharyngeal foreign body sensation, aggravation due to excessive speaking, and congestion of pharyngeal mucosa in the experimental group were 73.81%, 67.50%, 67.57%, 65.22% and 44%, respectively, which were significantly higher than those in the control group (p < 0.05). In addition, patients taking botanical lozenges had better illness perception and adherence to treatment than those taking placebos (p < 0.05). Patients with low adherence to treatment showed less personal control, concerns, and understanding of chronic pharyngitis (p < 0.05).Conclusion: Botanical lozenges not only aided patients in recovering from chronic pharyngitis but also improved their positive perceptions of the disease, which helped them adhere to their treatment regimen.Clinical Trial Registration: [https://www.chictr.org.cn/], identifier [ChiCTR2200062139].

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Chromosome-scale genome assembly of an important medicinal plant honeysuckle

Cited by 7 publications

References 62 publications

Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle)

Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle)

A de novo chromosome-scale assembly of the Lablab purpureus genome

Efficacy of botanical lozenges in the treatment of chronic pharyngitis: a randomized controlled trial

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