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April 3rd, 2025
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Department of Informatics, National Institute of Genetics, Japan
genomics
biorxiv

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

Tanizawa, Y.Open in Google Scholar•Mochizuki, T.Open in Google Scholar•Yagura, M.Open in Google Scholar•Sakamoto, M.Open in Google Scholar•Fujisawa, T.Open in Google Scholar•Kawamura, S.Open in Google Scholar•Shimokawa, E.Open in Google Scholar•Yamaoka, S.Open in Google Scholar•Nishihama, R.Open in Google Scholar•Bowman, J. L.Open in Google Scholaret al.

The liverwort Marchantia polymorpha is a key model organism for understanding land plant evolution, development, and gene regulation. To support the growing demand for high-quality genomic resources, we present MarpolBase, a comprehensive and integrated genome database that hosts newly assembled, high-accuracy reference genomes for both the male Tak-1 and female Tak-2 accessions, designated as ver. 7.1 reference genomes. These new assemblies, generated using PacBio HiFi long-read sequencing, represent nearly telomere-to-telomere chromosome-level genomes, with improvements in assembly continuity, annotation accuracy, and structural resolution, especially for repeat-rich regions and sex chromosomes. MarpolBase offers not only access to genome sequences and gene annotations but also provides a unified platform for data exploration, comparative analysis, and community-driven gene nomenclature. It includes keyword-searchable gene pages with structural and functional annotations, expression data integration, genome browser visualization, and online analytical and utility tools. By unifying genome assembly, annotation, nomenclature, and analysis tools in a single platform, MarpolBase serves as a central resource for functional genomics and evolutionary studies in M. polymorpha, and a model for future plant genome databases.

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