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Related Experiment Video

Updated: Jun 5, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.

Chaoqun Xu1, Ling-Yu Song1, Jing Li1

  • 1Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.

Plant, Cell & Environment
|December 11, 2024
PubMed
Summary
This summary is machine-generated.

MangroveDB provides a unified platform for analyzing mangrove omics data, offering 13 reference genomes and 40 transcriptomes. This resource empowers researchers with bioinformatics tools for deeper biological insights into these vital coastal plants.

Keywords:
databaseinteractive web‐based data analysismangrovesmulti‐omicsvisualization

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Area of Science:

  • Marine Biology
  • Genomics
  • Bioinformatics

Background:

  • Mangroves are crucial intertidal plants with significant ecological and economic importance.
  • Recent advancements have led to the sequencing of mangrove genomes and the generation of vast omics datasets.
  • Limited bioinformatics expertise and computational resources hinder experimental researchers from fully utilizing public omics data.

Purpose of the Study:

  • To address the challenge of accessing and analyzing mangrove omics data.
  • To create a centralized, user-friendly resource for mangrove research.
  • To facilitate new biological discoveries through reanalysis of existing data.

Main Methods:

  • Uniformly processed 942 transcriptome and 386 whole-genome sequencing datasets.
  • Developed MangroveDB, an interactive web-based database.
  • Integrated bioinformatics tools for data analysis and visualization.

Main Results:

  • Provided 13 reference genomes and 40 reference transcriptomes for 53 mangrove species.
  • Implemented online analysis tools including principal component analysis, differential gene expression, and GO/KEGG enrichment.
  • Included visualization functions like volcano plots, heatmaps, and PCA plots.

Conclusions:

  • MangroveDB serves as a valuable, accessible resource for the scientific community.
  • The platform enhances the efficient utilization of massive public omics datasets for mangrove research.
  • Facilitates exploration and discovery of new biological insights in mangroves.