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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Organization of Genes02:07

Organization of Genes

Overview
Organization of Genes02:07

Organization of Genes

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Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

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Related Experiment Video

Updated: May 15, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Orchidstra: an integrated orchid functional genomics database.

Chun-lin Su1, Ya-Ting Chao, Shao-Hua Yen

  • 1Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.

Plant & Cell Physiology
|January 18, 2013
PubMed
Summary
This summary is machine-generated.

The Orchidstra database now provides extensive genomic and transcriptome data for orchid functional genomics. This resource facilitates research into the unique biological features of orchids, a highly diverse plant family.

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Last Updated: May 15, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Published on: June 17, 2012

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

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Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

Area of Science:

  • Plant genomics
  • Bioinformatics
  • Orchidaceae family studies

Background:

  • The Orchidaceae family is known for its exceptional biodiversity but lacks sufficient genomic information for detailed trait investigation.
  • Limited genomic data hinders research into the unique biological features of orchids.

Purpose of the Study:

  • To establish Orchidstra, a specialized database for collecting, annotating, and sharing orchid genomic information.
  • To support functional genomics studies within the Orchidaceae family.

Main Methods:

  • Integrated transcriptome data (>380,000 non-redundant sequences) from five orchid species and one hybrid.
  • Employed annotation pipelines (Gene Ontology, KEGG, Pfam) for protein-coding genes.
  • Performed deep sequencing of small RNA for Phalaenopsis aphrodite to identify microRNAs (miRNAs) and their targets.

Main Results:

  • Orchidstra houses over 380,000 non-redundant orchid transcript sequences, including more than 110,000 protein-coding genes.
  • Functional annotations and gene descriptions were assigned using established bioinformatics pipelines.
  • Identified miRNAs, precursors, and putative target genes in Phalaenopsis aphrodite, with data integrated into the database.

Conclusions:

  • Orchidstra serves as a valuable centralized resource for orchid genomic and functional genomics research.
  • The database facilitates the study of orchid biodiversity and unique biological traits.
  • Future expansion will include more species and genomic data to further enhance orchid research.