Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

Nature Plants, Journal Year: 2022, Volume and Issue: 8(4), P. 373 - 388

Published: April 21, 2022

Abstract To improve our understanding of the origin and evolution mycoheterotrophic plants, we here present chromosome-scale genome assemblies two sibling orchid species: partially Platanthera zijinensis holomycoheterotrophic guangdongensis . Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates gene loss, deletion most photoreceptor genes auxin transporter might be linked to unique phenotypes fully orchids. Conversely, trehalase catalyse conversion trehalose into glucose have expanded in sequenced orchids, line fact germination non-endosperm seeds needs carbohydrates from fungi during protocorm stage. We further show mature plant P. , different photosynthetic keeps expressing hijack fungi. Therefore, propose orchids a continuation stage by sustaining expression genes. Our results shed light on molecular mechanism underlying initial, partial full mycoheterotrophy.

Language: Английский

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Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: March 1, 2022

Orchids constitute approximately 10% of flowering plant species. However, only about 10 orchid genomes have been published. Metabolites are the main way through which orchids respond to their environment. Dendrobium nobile, belonging Dendrobium, second largest genus in Orchidaceae, has high ornamental, medicinal, and ecological value. D. nobile is source many popular horticultural varieties. Among species, highest amount dendrobine, regarded as one criteria for evaluating medicinal quality. Due lack data analysis at genomic level, biosynthesis pathways dendrobine other related ingredients unknown. In this paper, we report a chromosome-scale reference genome facilitate investigation its characteristics comparison with The assembled size was 1.19 Gb. Of sequences, 99.45% were anchored 19 chromosomes. Furthermore, identified differences gene number expression patterns compared two species by integrating whole-genome sequencing transcriptomic [e.g., genes polysaccharide pathway upstream alkaloid (dendrobine) pathway]. Differences TPS CYP450 families also found among All above might contribute species-specific ingredient pathways. metabolic pathway-related will provide further insight into responses Additionally, important insights molecular elucidation active enhance understanding evolution.

Language: Английский

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Haplotype‐resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value

The Plant Journal, Journal Year: 2022, Volume and Issue: 111(5), P. 1340 - 1353

Published: July 4, 2022

Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it highly regarded for its medicinal applications and therefore has high economic value. Here, we report high-quality haplotype-resolved genome of B. haplotype A (2.37 Gb, with scaffold N50 146.39 Mb contig 1.65 Mb) B (2.43 150.22 1.66 Mb), assembled from high-fidelity (HiFi) reads chromosome conformation capture (Hi-C) reads. We find evidence that striata undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots recent unique to all orchids. also reconstructed the ancestral orchid karyotype (AOK) 18 chromosomes evolutionary trajectories 16 modern chromosomes. Comparative genomic analysis suggests expanded gene families might play important roles secondary metabolite biosynthesis environmental adaptation. By combining transcriptomic data, identified 10 core members nine were probably involved polysaccharide (BSP) biosynthesis. Based on virus-induced silencing (VIGS) yeast two-hybrid experiments, present MYB transcription factor (TF), BsMYB2, can regulate BSP directly interacting eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 UGP2_1. Our study will enhance understanding evolution accelerate molecular-assisted breeding improving traits

Language: Английский

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Advances and prospects of orchid research and industrialization

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together human influences also make it a keystone group biodiversity conservation. The advent sequencing technologies transgenic techniques represents quantum leap orchid research, enabling molecular approaches to be employed resolve historically interesting puzzles basic applied biology. To date, 16 different genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, Orchidoideae) been released. genome projects given rise massive data greatly empowers studies pertaining key innovations evolutionary mechanisms for breadth species. extensive exploration transcriptomics, comparative genomics, recent advances gene engineering linked important traits orchids multiplicity regulating networks, providing great potential genetic enhancement improvement. In this review, we summarize progress achievement fundamental research industrialized application particular focus tools, future prospects breeding post-genomic comprehensive assemblage state art knowledge industrialization.

Language: Английский

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The CAM lineages of planet Earth

Annals of Botany, Journal Year: 2023, Volume and Issue: 132(4), P. 627 - 654

Published: Sept. 12, 2023

Abstract Background and Scope The growth of experimental studies crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances molecular systematics, presents an opportunity to re-assess the phylogenetic distribution diversity species capable CAM. It has been more than two decades since last comprehensive lists CAM taxa were published, updated survey occurrence is needed facilitate guide future research. We aimed these taxa, their morphology, physiology ecology, likely number evolutionary origins based on currently known lineages. Results Conclusions found direct evidence (in form or field observations gas exchange, day–night fluctuations organic acids, carbon isotope ratios enzymatic activity) for 370 genera vascular plants, representing 38 families. Further assumptions about frequency clades Cactaceae Crassulaceae bring estimated CAM-capable nearly 7 % all plants. suggests a minimum 66 independent possibly dozens more. To achieve further insight into origins, there need extensive systematic surveys previously unstudied lineages, particularly living material identify low-level activity, denser sampling increase resolution CAM-evolving clades. This should allow progress understanding functional significance this pathway by integration evolution genomics its many forms.

Language: Английский

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Chromosome-level genomes of three key Allium crops and their trait evolution

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(11), P. 1976 - 1986

Published: Nov. 1, 2023

Language: Английский

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Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium

Nature Plants, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Language: Английский

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Natural Composition and Biosynthetic Pathways of Alkaloids in Medicinal Dendrobium Species

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: May 6, 2022

Dendrobium is the second biggest genus in Orchidaceae family, some of which have both ornamental and therapeutic values. Alkaloids are a group active chemicals found plants. Dendrobine has emerged specific pharmacological properties. Although alkaloids been isolated identified since 1930s, composition their biosynthesis pathways, including metabolic intermediates, alkaloid transporters, concrete genes involved downstream associated gene clusters, remained unresolved scientific issues. This paper comprehensively reviews currently tentative from aspect biogenic pathways or uncovered based on genome annotations. The each class highlighted. Moreover, advances high-throughput sequencing technologies discovery addressed. Applications synthetic biology large-scale production also described. would serve as basis for further investigation into alkaloids.

Language: Английский

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Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 28, 2022

The GRAS gene family encodes transcription factors that participate in plant growth and development phases. They are crucial regulating light signal transduction, hormone (e.g. gibberellin) signaling, meristem growth, root radial development, response to abiotic stress, etc. However, little is known about the features functions of genes Orchidaceae, largest most diverse angiosperm lineage. In this study, genome-wide analysis was conducted Dendrobium chrysotoxum (Epidendroideae, Orchidaceae) investigate its physicochemical properties, phylogenetic relationships, structure, expression patterns under stress orchids. Forty-six DchGRAS were identified from D. genome divided into ten subfamilies according their relationships. Sequence showed proteins contained conserved VHIID SAW domains. Gene structure intronless accounted for approximately 70% genes, structures same subfamily same, motifs also similar. K a/ s ratios 12 pairs all less than 1, indicating underwent negative selection. results cis -acting element 46 a large number hormone-regulated light-responsive elements as well environmental stress-related elements. addition, real-time reverse quantitative PCR (RT−qPCR) experimental significant differences levels high temperature, drought salt treatment, among which two members LISCL ( DchGRAS13 DchGRAS15 ) sensitive stress. Taken together, paper provides insights regulatory roles

Language: Английский

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A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly

Plant Communications, Journal Year: 2022, Volume and Issue: 3(5), P. 100330 - 100330

Published: May 5, 2022

Language: Английский

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