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1.
Plant Cell Physiol ; 54(2): e7, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23314755

RESUMO

Both floral development and evolutionary trends of orchid flowers have long attracted the interest of biologists. However, expressed sequences derived from the flowers of other orchid subfamilies are still scarce except for a few species in Epidendroideae. In order to broadly increase our scope of Orchidaceae genetic information, we updated the OrchidBase to version 2.0 which has 1,562,071 newly added floral non-redundant transcribed sequences (unigenes) collected comprehensively from 10 orchid species across five subfamilies of Orchidaceae. A total of 662,671,362 reads were obtained by using next-generation sequencing (NGS) Solexa Illumina sequencers. After assembly, on average 156,207 unigenes were generated for each species. The average length of a unigene is 347 bp. We made a detailed annotation including general information, relative expression level, gene ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping and gene network prediction. 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. We have re-designed the user interface in the new version. Users can enter the Phalaenopsis transcriptome or Orchidaceae floral transcriptome to browse or search the unigenes. OrchidBase 2.0 is freely available at http://orchidbase.itps.ncku.edu.tw/.


Assuntos
Bases de Dados Genéticas , Flores/metabolismo , Genes de Plantas , Orchidaceae/metabolismo , Software , Transcriptoma , Etiquetas de Sequências Expressas , Flores/genética , Biblioteca Gênica , Internet , Anotação de Sequência Molecular , Orchidaceae/classificação , Orchidaceae/genética , Filogenia
2.
Gene ; 518(1): 91-100, 2013 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-23262337

RESUMO

Orchids are one of the most species rich of all angiosperm families. Their extraordinary floral diversity, especially conspicuous labellum morphology, makes them the successful species during evolution process. Because of the fine and delicate development of the perianth, orchid provides a rich subject for studying developmental biology. However, study on molecular mechanism underling orchid floral development is still in its infancy. In this study, we developed an oligomicroarray containing 14,732 unigenes based on the information of expressed sequence tags derived from Phalaenopsis orchids. We applied the oligomicroarray to compare transcriptome among different types of floral organs including sepal, petal and labellum. We discovered that 173, 11, and 285 unigenes were highly differentially expressed in sepal, petal, and labellum, respectively. These unigenes were annotated with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and transcription factor family. Unigenes involved in energy metabolism, lipid metabolism, and terpenoid metabolism are significantly differentially distributed between labellum and two types of tepal (sepal and petal). Labellum-dominant unigenes encoding MADS-box and sepal-dominant unigenes encoding WRKY transcription factors were also identified. Further studies are required but data suggest that it will be possible to identify genes better adapted to sepal, petal and labellum function. The developed functional genomic tool will narrow the gap between approaches based on model organisms with plenty genomic resources and species that are important for developmental and evolutionary studies.


Assuntos
Flores/genética , Perfilação da Expressão Gênica/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Orchidaceae/genética , Metabolismo Energético/genética , Etiquetas de Sequências Expressas , Flores/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Metabolismo dos Lipídeos/genética , Proteínas de Domínio MADS/genética , Proteínas de Domínio MADS/metabolismo , Redes e Vias Metabólicas/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
3.
BMC Genomics ; 12: 360, 2011 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-21749684

RESUMO

BACKGROUND: Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economically important floriculture industry worldwide. We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome. RESULTS: To maximize sequence diversity, we pooled RNA from 10 samples of different tissues, various developmental stages, and biotic- or abiotic-stressed plants. We obtained 206,960 expressed sequence tags (ESTs) with an average read length of 228 bp. These reads were assembled into 8,233 contigs and 34,630 singletons. The unigenes were searched against the NCBI non-redundant (NR) protein database. Based on sequence similarity with known proteins, these analyses identified 22,234 different genes (E-value cutoff, e-7). Assembled sequences were annotated with Gene Ontology, Gene Family and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these annotations, over 780 unigenes encoding putative transcription factors were identified. CONCLUSION: Pyrosequencing was effective in identifying a large set of unigenes from Phalaenopsis. The informative EST dataset we developed constitutes a much-needed resource for discovery of genes involved in various biological processes in Phalaenopsis and other orchid species. These transcribed sequences will narrow the gap between study of model organisms with many genomic resources and species that are important for ecological and evolutionary studies.


Assuntos
Etiquetas de Sequências Expressas , Estudos de Associação Genética , Orchidaceae/genética , Mapeamento de Sequências Contíguas , Bases de Dados de Proteínas , Perfilação da Expressão Gênica , Proteínas de Plantas/genética , Análise de Sequência de DNA , Fatores de Transcrição/genética
4.
Plant Cell Physiol ; 52(2): 238-43, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21245031

RESUMO

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.


Assuntos
Bases de Dados Genéticas , Perfilação da Expressão Gênica , Orchidaceae/genética , Mineração de Dados , Etiquetas de Sequências Expressas , Biblioteca Gênica , Internet , Anotação de Sequência Molecular , Análise de Sequência de DNA , Interface Usuário-Computador
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