Orchidstra: An Integrated Orchid Functional Genomics Database

Abstract

A specialized orchid database, named Orchidstra (URL: http://orchidstra.abrc.sinica.edu.tw), has been constructed to collect, annotate and share genomic information for orchid functional genomics studies. The Orchidaceae is a large family of Angiosperms that exhibits extraordinary biodiversity in terms of both the number of species and their distribution worldwide. Orchids exhibit many unique biological features; however, investigation of these traits is currently constrained due to the limited availability of genomic information. Transcriptome information for five orchid species and one commercial hybrid has been included in the Orchidstra database. Altogether, these comprise >380,000 non-redundant orchid transcript sequences, of which >110,000 are protein-coding genes. Sequences from the transcriptome shotgun assembly (TSA) were obtained either from output reads from next-generation sequencing technologies assembled into contigs, or from conventional cDNA library approaches. An annotation pipeline using Gene Ontology, KEGG and Pfam was built to assign gene descriptions and functional annotation to protein-coding genes. Deep sequencing of small RNA was also performed for Phalaenopsis aphrodite to search for microRNAs (miRNAs), extending the information archived for this species to miRNA annotation, precursors and putative target genes. The P. aphrodite transcriptome information was further used to design probes for an oligonucleotide microarray, and expression profiling analysis was carried out. The intensities of hybridized probes derived from microarray assays of various tissues were incorporated into the database as part of the functional evidence. In the future, the content of the Orchidstra database will be expanded with transcriptome data and genomic information from more orchid species.

Orchidstra 2.0—A Transcriptomics Resource for the Orchid Family

“…Several web-based databases provide transcriptome information for orchid species, e.g. OOGB , OrchidBase (Tsai et al 2013) and Orchidstra (Su et al 2013a). These databases host a large collection of NGS-based orchid transcriptome assemblies and EST data, and provide search options for gene annotation.…”

“…The transcriptome sequence information and annotation from related orchid species can be used to develop genetic markers or phylogenetic markers that will be useful in the fields of functional genomics, genetic mapping and phylogenetic analysis. While Orchidstra 2.0 is an orchid-focused resource, we believe that Su et al 2013aTsai et al 2013our database deserves to be utilized by all users who have an interest in plant gene families and comparative genomics. We welcome feedback and suggestions from all users for further improvement of the database.…”

“…To assign the GO term annotation (Ashburner et al 2000) for each unigene, the BLAST XML files were generated using the E-value cutoff of 1EÀ10 with the number of top BLASTX hits output set to 20, and then the resulting output files were subjected to Blast2GO (v3.3) analysis (Conesa et al 2005). Moreover, rather than using one-way BLAST in the previous study (Su et al 2013a), we performed OrthoMCL (Li et al 2003) clustering to identify the orthologous sequences of protein-coding genes. In total, 593,709 amino acid sequences were collected from the 18 orchid species, Arabidopsis and rice.…”

“…Whole-transcriptome sequencing is an efficient way of reducing genome complexity to obtain functional information, and therefore it often serves as a starting point for large-scale sequencing and the development of genomics tools. We published the Orchidstra database in 2013 (Su et al 2013a) to accommodate the annotated transcriptome shotgun assembly and expressed sequence tag (EST) data for five orchid species and one hybrid, all belonging to the subfamily Epidendroideae. In this study we designed a new database schema for the transcriptomics database system and built a new database with a completely new user interface, Orchidstra 2.0, which is more comprehensive in terms of data richness and database functionality.…”

Recent Progress in Genomic Analysis of Ornamental Plants, with a Focus on Carnation

“…EST databases for Phalaenopsis Hsiao et al, 2011;Su et al, 2011;Tsai et al, 2013) and Oncidium have been obtained using NGS technology. An integrated database, Orchidstra, has recently been constructed (http://orchidstra.abrc.sinica.edu.tw/; Su et al, 2013a). The Orchidstra database contains transcriptome information for five orchid species and one commercial hybrid as well as microRNA (Chao et al, 2014) and microarray-based expression profiling data for a potential orchid model species, P. aphrodite (Su et al, 2013b).…”