ArticlePlant biotechnology journal2018
Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding.
Article in Plant biotechnology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 108 citations in OpenAlex.
- Orchid genome evolution and trait innovation.Journal of integrative plant biology · 2026Review
- Heat-Stress Induced Apoptosis: A New Biotechnological Strategy to Enhance Ganoderic Acids Production inJournal of fungi (Basel, Switzerland) · 2026Article
- Efficient Regeneration and Genetic Transformation System for Cymbidium kanran 'Zhushalan'.Genes · 2026Article
- Molecular mechanisms underlying floral trait formation inHorticulture research · 2026Article
- A novel CsbZIP26-CsSEP4-CsSPL18 regulatory module governs gynostemium morphology and floral architecture inHorticulture research · 2026Article
- Identification and characterization of the structure genes involved in anthocyanin biosynthesis in flowers ofFrontiers in plant science · 2026Article
- Multi-Omics Analysis Unravels the Biosynthesis and Regulatory Mechanisms of Floral Scent Across Various Cultivars and Developmental Stages inPlants (Basel, Switzerland) · 2025Article
- The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation.Molecular ecology · 2025Article
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
- Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions.Functional & integrative genomics · 2025Review
- Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum.Plant biotechnology journal · 2025Article
- Transcriptome analysis reveals the mechanisms underlying petal growth during the flower opening process in Phalaenopsis orchids.BMC plant biology · 2025Article
- A chromosome-levelActa pharmaceutica Sinica. B · 2025Article
- OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis.BMC plant biology · 2025Article
- High-density genetic map construction using whole-genome resequencing of theFrontiers in plant science · 2025Article
- The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee-pollinated orchids.G3 (Bethesda, Md.) · 2024Article
- Integrating Physiology, Cytology, and Transcriptome to Reveal the Leaf Variegation Mechanism inBiomolecules · 2024Article
- Progress in systematics and biogeography of Orchidaceae.Plant diversity · 2024Review
- Genome-Wide Identification and Expression Pattern Analysis ofInternational journal of molecular sciences · 2024Article
- Identification and Characterization of thePlants (Basel, Switzerland) · 2024Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
Abstract
The Orchidaceae is a diverse and ecologically important plant family. Approximately 69% of all orchid species are epiphytes, which provide diverse microhabitats for many small animals and fungi in the canopy of tropical rainforests. Moreover, many orchids are of economic importance as food flavourings or ornamental plants. Phalaenopsis aphrodite, an epiphytic orchid, is a major breeding parent of many commercial orchid hybrids. We provide a high-quality chromosome-scale assembly of the P. aphrodite genome. The total length of all scaffolds is 1025.1 Mb, with N50 scaffold size of 19.7 Mb. A total of 28 902 protein-coding genes were identified. We constructed an orchid genetic linkage map, and then anchored and ordered the genomic scaffolds along the linkage groups. We also established a high-resolution pachytene karyotype of P. aphrodite and completed the assignment of linkage groups to the 19 chromosomes using fluorescence in situ hybridization. We identified an expansion in the epiphytic orchid lineage of FRS5-like subclade associated with adaptations to the life in the canopy. Phylogenetic analysis further provides new insights into the orchid lineage-specific duplications of MADS-box genes, which might have contributed to the variation in labellum and pollinium morphology and its accessory structure. To our knowledge, this is the first orchid genome to be integrated with a SNP-based genetic linkage map and validated by physical mapping. The genome and genetic map not only offer unprecedented resources for increasing breeding efficiency in horticultural orchids but also provide an important foundation for future studies in adaptation genomics of epiphytes.
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