EyeChrom and CCDBcurator: Visualizing chromosome count data from plants.

Area of Science:

• Plant Biology
• Evolutionary Biology
• Bioinformatics

Background:

• Chromosome count data for numerous plant species are accessible via the Chromosome Counts Database (CCDB).
• Exploring this data in its current text-only format can be challenging for detailed analysis.
• Understanding chromosome number variation is crucial for plant evolutionary studies, especially concerning polyploidy.

Purpose of the Study:

• To develop user-friendly tools for curating and visualizing plant chromosome count data.
• To facilitate the summarization and display of intra- and interspecific chromosome number variation.
• To provide accessible data for evolutionary analyses, publications, and teaching.

Main Methods:

• Development of an R package (CCDBcurator) for data cleaning and summarization.
• Creation of a web application (EyeChrom) for graphical visualization of chromosome data.
• Utilizing the Chromosome Counts Database as the primary data source.

Main Results:

• CCDBcurator and EyeChrom enable efficient cleaning, curation, and summarization of chromosome count data.
• The tools generate various formats for data and figures, suitable for export.
• Graphical displays allow for easy summarization of chromosome number variation within and between species.

Conclusions:

• CCDBcurator and EyeChrom offer a fast, easy, and reproducible method for managing plant chromosome data.
• These tools enhance the accessibility and utility of chromosome count data for research and education.
• The visualization capabilities support the growing importance of polyploidy research in plant evolution.