The chromosome-scale genome of Black Wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

Plant Diversity, Journal Year: 2025, Volume and Issue: 47(2), P. 201 - 213

Published: Jan. 6, 2025

The black wolfberry (L ycium ruthenicum; 2n = 2x 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, alkaloids, high nutritional However, the lack available genomic resources for this species has hindered research on its evolutionary mechanisms. In study, we developed telomere-to-telomere (T2T) nearly gapless genome L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, Hi-C technologies. assembled comprised 12 chromosomes 37,149 protein-coding genes functionally annotated. Approximately 80% repetitive sequences were identified, which long terminal repeats (LTRs) most abundant, accounting 73.01%. abundance LTRs might be main reason larger compared to that other Lycium species. species-specific related defense mechanisms, salt tolerance, drought resistance, oxidative stress, further demonstrating their superior adaptability arid environments. Based fruit transcriptome data, constructed anthocyanin biosynthesis pathway identified 19 candidate structural seven transcription factors regulate in developmental stage ruthenicum, highly expressed at a later development. Furthermore, 154 potential disease resistance-related nucleotide-binding been genome. whole-genome proximal, dispersed, tandem duplication enriched number involved synthesis pathways. These results provide genetic basis understanding evolution pharmacologically active components genus.

Language: Английский

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Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(5)

Published: Feb. 1, 2025

Abstract Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory hepatoprotective properties. P. important clinical value the active triterpenoid saponins roots. However, biosynthetic pathway remains unclear, related genes remain unknown. Therefore, this study, we assembled high-quality integrated telomere-to-telomere reference genome combined time-specific transcriptome metabolome profiling to identify cytochrome P450s (CYPs) responsible for hydroxylation processes involved saponin biosynthesis. Nine chromosomes were without gaps or mismatches, nine centromeres 18 telomere regions identified. This eliminated redundant sequences from previous versions incorporated structural variation information. Comparative analysis revealed that underwent core eudicot γ-WGT event. We screened 211 CYPs found tandem proximal duplications may be crucial expansion CYP families. outlined proposed steps, likely catalyzed by CYP716A/72A/749A families, platycodin biosynthesis identified three PgCYP716A, seven PgCYP72A, PgCYP749A showed positive correlation with By establishing T2T assembly genome, transcriptome, resource grandiflorus, provide foundation complete elucidation platycodins pathway, which consequently leads heterologous bioproduction, serves fundamental genetic molecular-assisted breeding improvement grandiflorus.

Language: Английский

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The chromosome-level genome of Centella asiatica provides insights into triterpenoid biosynthesis

Plant Physiology and Biochemistry, Journal Year: 2025, Volume and Issue: 222, P. 109710 - 109710

Published: Feb. 25, 2025

Language: Английский

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Chromosome-level genome assembly of an important ethnic medicinal plant Callicarpa nudiflora

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: April 18, 2025

Callicarpa nudiflora is one of high medicinal and economic value plants in China, which was recorded Chinese pharmacopoeia (2020 edition) widely used to treat tropical bacterial infections, acute infectious hepatitis, internal external bleeding. In this study, we assembled the C. genome with a size approximately 597.82 Mb contig N50 length 34.14 Mb. A total 98.61% sequences were anchored 17 pseudo-chromosomes by using PacBio long reads Hi-C sequencing data. We totally predicted 31,266 protein-coding genes, 92.45% could be annotated databases such as NR, GO, KOG, KEGG. addition, identified 2,303 rRNAs, 884 MicroRNAs 531 tRNAs from genome. The chromosome-scale represents crucial resource for investigating molecular mechanisms underlying biosynthesis components facilitates exploration conservation nudiflora.

Language: Английский

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Comparative genome-wide analysis of low-temperature responses during perennating bud dormancy in cold-sensitive and -insensitive Panax ginseng cultivars

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: May 13, 2025

Language: Английский

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Multiple Transcriptomic Networks Regulate the Callus Development Process in Panax ginseng

Agronomy, Journal Year: 2025, Volume and Issue: 15(5), P. 1244 - 1244

Published: May 20, 2025

Callus induction is one of the most important techniques in plant-based industries. Important features use callus are maintenance pluripotency and proliferation cells. Although importance also understood ginseng, there no studies on genetic modules associated with growth regulation. Panax ginseng embryo tissue was wounded cultured callus-inducing media, its time-course physiology observed. Time-course samples were collected for total RNA extraction RNA-Seq analysis using Illumina HiSeq X Ten platform. P. treated varying amounts gamma radiation analysis. A combinatory various network analyses used to reveal regulatory underlying development. We able determine development dose-dependent effect Network revealed two networks correlated growth. Our research provides a illustrating how induced regulated ginseng. This result would be helpful cell culture system or clonal propagation protocol

Language: Английский

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Phylogenetic Analysis and Expression Patterns of Triterpenoid Saponin Biosynthesis Genes in 19 Araliaceae Plants

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 3439 - 3439

Published: April 7, 2025

The Araliaceae family has significant economic and medicinal value. However, the phylogenetic relationships expression patterns of key genes active triterpenoid substance within this are still unclear. In study, we employed comparative transcriptomics to analyze transcriptomes 19 species from 11 genera Araliaceae, aiming elucidate evolutionary history in ginsenoside biosynthesis pathway. Our results divide into two subfamilies: Aralioideae Hydrocotyloideae. is further classified three groups: Aralia-Panax group, Polyscias-Pseudopanax Asian Palmate group. PhyloNet analysis reveals that common ancestor Panax ginseng, quinquefolius, japonicus was an allopolyploid, likely resulting hybridization between notoginseng pseudoginseng. Additionally, all underwent pg-β event, which may be critical for biosynthesis. We discovered exhibit distinct enzyme (β-AS, DDS, CYP450, UGTs) compared other species. These show independent lineages gene trees, suggesting unique functional adaptations enable efficiently synthesize ginsenosides. This study provides a theoretical foundation conservation utilization germplasm resources.

Language: Английский

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High-resolution genetic map and SNP chip for molecular breeding in Panax ginseng, a tetraploid medicinal plant

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(12)

Published: Sept. 9, 2024

Language: Английский

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High-quality genome of black wolfberry (Lycium ruthenicum Murr.) provides insights into the genetics of anthocyanin biosynthesis regulation

Horticulture Research, Journal Year: 2024, Volume and Issue: 12(2)

Published: Oct. 23, 2024

Abstract Black wolfberry (Lycium ruthenicum Murr.) is an important plant for ecological preservation. In addition, its fruits are rich in anthocyanins and have edible medicinal value. However, a high-quality chromosome-level genome this species not yet available, the regulatory mechanisms involved biosynthesis of unclear. study, haploid material was used to assemble reference Lycium ruthenicum, resulting size 2272 Mb with contig N50 92.64 Mb, 38 993 annotated gene models. evolution large-scale variations compared Ningxia barbarum were determined. Importantly, homology annotation identified 86 genes pathway anthocyanin biosynthesis, five which [LrCHS1 (evm.TU.Chr05.295), LrCHS2 (evm.TU.Chr09.488), LrAOMT (evm.TU.Chr09.809), LrF3’5’H (evm.TU.Chr06.177), LrAN2.1 (evm.TU.Chr05.2618)] screened by differential expression analysis correlation using combination transcriptome metabolome testing. Overexpression these could significantly up- or downregulate anthocyanin-related metabolites. These results will help accelerate functional genomic research L. elucidation synthesis be beneficial breeding new varieties further exploring conservation potential.

Language: Английский

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