Abstract
BackgroundThe Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae.DescriptionRecently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species.ConclusionsOrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/
Highlights
The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide
The second version of OrchidBase included the floral transcriptomes of 10 orchid species from each of the five Orchidaceae subfamilies: Neuwiedia malipoensis and Apostasia shenzhenica (Apostasioideae); Paphiopedilum armeniacum and Cypripedium singchii (Cypripedioideae); Cymbidium sinense and Phalaenopsis equestris (Epidendroideae); Hemipilia forrestii and Habenaria delavayi (Orchidoideae); Vanilla shenzhenica and Galeola faberi (Vanilloideae) [17]
The OrchidBase 4.0 enables using genomic data to understand the fundamental biology of orchids
Summary
The addition and integration of orchid whole genomic sequences with detailed annotation information and easy-to-use web interfaces in OrchidBase 4.0 allow users to efficiently find target genes, such as floral development-related genes [24], floral pigmentation pattern-related genes [25], TCP transcription factor genes [11], and transposable element [26]. The orchid genome sequence has been supplied valuable information for plant genome evolution and comparative genomic studies [15, 27]. OrchidBase 4.0 will be updated continuously and more -omic information and analysis tools will be included for comprehensive analysis of the orchid gene function and genome evolution. Availability and requirements Project name: OrchidBase 4.0. Abbreviations A. shenzhenica: Apstasia shenzhenica; CAM: Crassulacean Acid Metabolism; D. catenatum: Dendrobium catenatum; ESTs: Expressed Sequence Tags; FPKM: Fragments Per Kilobase of transcript per Millions mapped reads; KEGG: Kyoto Encyclopedia of Genes and Genomes; GO: Gene Ontology; P. equestris: Phalaenopsis equestris; SQL: Structured Query Language
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