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.
Highlights
Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide
Bacterial artificial chromosome (BAC) end sequencing Two large-insert bacterial artificial chromosome (BAC) libraries were used for end-sequencing in the present study
DNA samples extracted from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively) were sequenced from both ends using Applied Biosystems (ABI) Big Dye terminator chemistry followed by analysis on ABI 3730 machines
Summary
Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. The family Orchidaceae, which contains at least 25,000 species, is one of the largest families of flowering plants [1]. Orchids show a wide diversity of epiphytic and terrestrial growth forms, and these plants have successfully colonized almost every habitat on earth. The factors promoting the richness of Expansion of diversity may have taken place more quickly in the orchid family than in most other flowering plant families, which had already started to diversify in the mid-Cretaceous [6]. The time at which orchids originated is disputed, but it has been suggested to be 80-40 million years ago (Mya) ( in the late Cretaceous to late Eocene) [7]. The most recent common ancestor of extant orchids is believed to have lived in the late Cretaceous (76-84 Mya) [8]. Perhaps the only general statement that can be made about the origin of orchids is that most extant groups are probably very young
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