ArticleBMC plant biology2011
An overview of the Phalaenopsis orchid genome through BAC end sequence analysis.
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- The Breeding, Cultivation, and Potential Applications of Ornamental Orchids with a Focus onPlants (Basel, Switzerland) · 2025Review
- PeCIN8 expression correlates with flower size and resistance to yellow leaf disease in Phalaenopsis orchids.BMC plant biology · 2023Article
- In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing.Frontiers in plant science · 2022Review
- Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids.BMC genomics · 2020Article
- The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids.PloS one · 2018Article
- Post genomics era for orchid research.Botanical studies · 2017Review
- Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2017Article
- Field Guide to Plant Model Systems.Cell · 2016Review
- Direct somatic embryogenesis ofJournal, genetic engineering & biotechnology · 2016Article
- Application of a modified drop method for high-resolution pachytene chromosome spreads in two Phalaenopsis species.Molecular cytogenetics · 2016Article
- DhEFL2, 3 and 4, the three EARLY FLOWERING4-like genes in a Doritaenopsis hybrid regulate floral transition.Plant cell reports · 2015Article
- Article
- Genome-wide transcriptome and expression profile analysis of Phalaenopsis during explant browning.PloS one · 2015Article
- RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae).PloS one · 2015Article
- Article
- Engineering crassulacean acid metabolism to improve water-use efficiency.Trends in plant science · 2014Review
- Article
- De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts.PloS one · 2014Article
- Genome-wide annotation, expression profiling, and protein interaction studies of the core cell-cycle genes in Phalaenopsis aphrodite.Plant molecular biology · 2014Article
- Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis.Plant molecular biology · 2013Article
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10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundPhalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.
resultsWe used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes) of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.
conclusionUsing BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the Phalaenopsis genome and advances our knowledge thereof.
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