Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Background: Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study.
Description: Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses.
Conclusion: OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697506 | PMC |
| http://dx.doi.org/10.1186/s12870-024-06024-1 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Reticulate evolutionary history underpins a revised generic circumscription of Paphiopedilum (Orchidaceae): insights from integrative phylogenomics and historical biogeography.
BMC Plant Biol
August 2025
Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, The University of Gdańsk, Wita Stwosza 59, 80-308, Gdansk, Poland.
Background: The taxonomy of Paphiopedilum-a diverse group of slipper orchids-has long posed challenges due to high morphological variability and conflicting phylogenetic signals. Despite intensive research, a clear and stable infrageneric classification remains unresolved.
Results: We present an integrative phylogenetic framework based on multiple nuclear low-copy genes (XDH, PHYC, LFY, RAD51, ACO, DEF4), ITS and plastid (matK) sequences, supported by morphological and biogeographical data.
Integrated Multi-Omics Investigation of Gypenosides' Mechanisms in Lowering Hepatic Cholesterol.
Biomolecules
August 2025
Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Guizhou Engineering Research Center for Orchid Medicinal Plant Breeding and Efficient Application, Zunyi Medical University, Zunyi 563000, China.
(1) Objective: This study aimed to systematically elucidate the molecular mechanisms by which gypenosides (GP), a major active component of , ameliorate hypercholesterolemia by modulating the hepatic steroidogenesis pathway, and to identify key therapeutic targets. (2) Methods: We established a high-fat diet (HFD)-induced hypercholesterolemia (HC) mouse model and performed GP intervention. An integrated multi-omics approach, combining transcriptomics and proteomics, was utilized to comprehensively analyze GP's effects on the expression of genes and proteins associated with hepatic cholesterol synthesis, transport, and steroid hormone metabolism.
View Article and Find Full Text PDFAn enhanced gene function analysis platform for Gastrodia Elata integrating further omics data and analysis tools.
BMC Plant Biol
August 2025
Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, China.
Gastrodia elata, the dried tuber of the Gastrodia orchid, is a valued traditional Chinese medicine with important medicinal and dietary benefits. The growing multi-omics data demands an updated platform to include the latest G.elata genome and transcriptome, thereby enhancing gene function analysis for researchers.
View Article and Find Full Text PDFGenome-Wide Identification and Characterisation of the Gene Family in and Their Transcriptional Response to Fungal Infection.
Int J Mol Sci
August 2025
Pharmacy School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China.
Blume is an important medicinal orchid, yet its large-scale cultivation is increasingly threatened by fungal diseases. The 4-coumarate-CoA ligase (4CL) gene family directs a key step in phenylpropanoid metabolism and plant defence, but its composition and function in have not been investigated. We mined the genome for 4CL homologues, mapped their chromosomal locations, and analysed their gene structures, conserved motifs, phylogenetic relationships, promoter cis-elements and codon usage bias.
View Article and Find Full Text PDFClimate change-driven northward expansion of the mediterranean orchid Ophrys apifera from genetic and ecological perspectives.
Sci Rep
August 2025
Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland.
Ophrys apifera, commonly known as the bee orchid, is a species of orchid that has expanded its range northwards in recent decades. The present study focuses on its occurrence in Poland and analyses possible causes of this expansion, including climate change, autogamy and genetic diversity of new populations. Genetic analyses using nuclear microsatellite markers and plastid DNA revealed low overall population variability in Poland and neighbouring countries (the Czech Republic, Germany), probably caused by the founder effect and bottleneck, as well as the autogamous reproductive strategy of this species.
View Article and Find Full Text PDF