Database Commons

a catalog of worldwide biological databases

BACKGROUND: The 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.
DESCRIPTION: Recently, 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.
CONCLUSIONS: OrchidBase 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/.

Orchids are one of the most ecological and evolutionarily significant plants, and the Orchidaceae is one of the most abundant families of the angiosperms. Genetic databases will be useful not only for gene discovery but also for future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting in 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of the database is an automated system written in Perl and C#, and consists of the following components: automatic pre-processing of EST reads, assembly of raw sequences, annotation of the assembled sequences and storage of the analyzed information in SQL databases. A web application was implemented with HTML and a Microsoft .NET Framework C# program for browsing and querying the database, creating dynamic web pages on the client side, analyzing gene ontology (GO) and mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers with a high-quality genetic resource for data mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.