MarpolBase: genome database for Marchantia polymorpha featuring high quality reference genome sequences

Area of Science:

• Plant biology
• Genomics
• Evolutionary biology

Background:

• Marchantia polymorpha is a crucial model organism for plant evolution and development research.
• Existing genomic resources require enhancement for comprehensive analysis.

Purpose of the Study:

• To develop MarpolBase, an integrated genome database for Marchantia polymorpha.
• To provide high-accuracy, telomere-to-telomere reference genomes for M. polymorpha.
• To establish a unified platform for genome analysis and community-driven nomenclature.

Main Methods:

• PacBio HiFi long-read sequencing for genome assembly.
• Development of a comprehensive database integrating genome sequences, annotations, and expression data.
• Implementation of genome browsers and analytical tools.

Main Results:

• Newly assembled, high-accuracy reference genomes (ver. 7.1) for male (Tak-1) and female (Tak-2) M. polymorpha accessions.
• Improved assembly continuity, annotation accuracy, and structural resolution, particularly for repeat-rich regions and sex chromosomes.
• MarpolBase offers integrated data exploration, comparative analysis, and gene nomenclature functionalities.

Conclusions:

• MarpolBase serves as a central, freely accessible resource for Marchantia polymorpha functional genomics and evolutionary studies.
• The database sets a precedent for future plant genome database development.
• Enhanced genomic data facilitates deeper understanding of land plant evolution and gene regulation.