An overview of the Phalaenopsisorchid genome through BAC end sequence analysis

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.

The genome sequence of the orchid Phalaenopsis equestris

“…We assessed the coverage of the genome assembly using BACs (Supplementary Note). First, 18,486 BAC-end sequences (>100 bp in length) from a previous study 61 and our data (W.-C. Tsai and H.-H. Chen, unpublished data) were downloaded and mapped back to the scaffolds using BLAT 62 . Of the BAC-end sequences, 92.9% could be mapped to the assembled genome.…”

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

“…High GC% in the genome helps to adapt to the different environmental conditions (cold/dry seasons) leading to more complex gene regulation (Smarda et al 2014). Partial genome sequence was carried out in one important orchid (Phalaenopsis equestris) (Hsu et al 2011) and then whole genome was completely sequenced for its characterization and phylogenetic analysis (Cai et al 2015). But reduced representation of the genomic segment has been sequenced in many organism using RAD, ddRAD, GBS methods based on NGS technology for genetic diversity and phylogenetic relationship using SNPs marker (Baird et al 2008;Etter et al 2011;Peterson et al 2012;Jiangfeng et al 2014;Wataru et al 2014).…”

“…Orchids are traded as cut flowers in the international markets. Orchidaceae is a largest family in the flowering plant, which includes approximately 25,000 species (Atwood 1986;Hsu et al 2011). Orchids can grow in the wide range of ecological habitats in the world and show maximum diversity among the species (Tremblay et al 2005).…”

DhEFL2, 3 and 4, the three EARLY FLOWERING4-like genes in a Doritaenopsis hybrid regulate floral transition

“…The distinct floral organs of orchids have made them a popular commercial crop with considerable economic value (Chao et al 2014). Among the many orchid species, Phalaenopsis (hybrids) is a highly commercially important orchid (Hsu et al 2011). Like most Phalaenopsis, flowering in Doritaenopsis, an intergeneric hybrid between Doritis and Phalaenopsis, is promoted by low temperature (Cui et al 2004;Qin et al 2012).…”