Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

ChloroplastDB: the Chloroplast Genome Database.

Liying Cui1, Narayanan Veeraraghavan, Alexander Richter

  • 1Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802, USA.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary

ChloroplastDB offers unified annotations for chloroplast genomes, facilitating comparative evolutionary research. This database standardizes gene names and provides tools for analyzing sequence evolution and RNA editing across diverse organelle genomes.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.

bioRxiv : the preprint server for biology·2026
Same author

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca.

Journal of experimental botany·2026
Same author

Disease- and chemotherapy-associated salivary microbiome changes in breast cancer patients.

Breast cancer research and treatment·2026
Same author

Two independent origins of XY sex chromosomes in Asparagus.

Molecular biology and evolution·2026
Same author

Catch-Up Weight Gain and Gut Microbiota Development in Full-Term Small for Gestational Age Children During the First Year of Life-A Prospective Cohort Study.

American journal of human biology : the official journal of the Human Biology Council·2026
Same author

Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts.

BMC plant biology·2025

Area of Science:

  • Plant biology
  • Bioinformatics
  • Genomics

Background:

  • The rapid increase in sequenced organelle genomes necessitates standardized annotation.
  • Existing chloroplast genome databases lack uniform gene naming conventions and feature application.
  • Inconsistent annotations hinder comparative evolutionary studies.

Purpose of the Study:

  • To introduce ChloroplastDB, a unified, web-based database for chloroplast genomes.
  • To provide standardized annotations and facilitate comparative genomic research.
  • To offer tools for analyzing sequence evolution and RNA editing.

Main Methods:

  • Development of an interactive, web-based database (ChloroplastDB).
  • Integration of genomic, protein, DNA, and RNA sequences.

Related Experiment Videos

  • Implementation of unified annotations, gene name search, BLAST, and download functions.
  • Classification of orthologous protein sets using TribeMCL.

    • Main Results:

    • ChloroplastDB provides unified annotations for plastid genomes.
    • Enables retrieval of orthologous sequences regardless of original gene names.
    • Facilitates comparative analysis of gene content, codon usage, gene structure, and RNA editing.
    • Assigns standard gene names to orthologous protein sets.

    Conclusions:

    • ChloroplastDB addresses the challenge of inconsistent chloroplast genome annotations.
    • The database serves as a valuable resource for comparative genomics and evolutionary studies.
    • Future enhancements will support the growing volume of sequenced chloroplast genomes.