marchantia

Genome data provided in this web site


This web site currently contains three versions of the Marchantia reference genome, JGI 3.1, MpTak1v5.1 (M. polymorpha subsp. ruderalis), and MpTak1_v6.1 (Standard genome for analytical use. Tak-1 autosome + Tak-1 V-chr + Tak-2 U-chr), as well as genomes from subsp. polymorpha (MppBR5) and subsp. montivagans (MpmSA2).
The data provided in this web site is freely available for academic purposes. Please cite our paper if you use the data obtained from the web site.

  • MpTak1_v7.1 and MpTak2_v7.1

    High-quality chromosome-level reference genomes asembled from PacBio HiFi sequencing reads.
    The gene annotation have been lifted over from MpTak_v6.1 with some manual curation.
    MpTak1_v7.1: chr1-8 and sex chromosome V derived from the male Tak-1 strain.
    MpTak2_v7.1: chr1-8 and sex chromosome U derived from the female Tak-2 strain.

    See README for more details.


  • MpTak_v7.1 (the default genome of MarpolBase)

    Standard reference genome for analytical use.
    Consists of a combination of chr1-8,V from male Tak-1 and chrU from female Tak-2

    See README for more details.


  • MpTak_v6.1

    Standard reference genome for analytical use. Created by combining the male Tak-1 genome (MpTak1v5.1) and the female Tak-2 U-chr sequence.
    Some of the uplaced scaffolds of MpTak1_v5.1 were removed (bacterial contamination, organellar sequences) and updated.


    Assembly and annotation version
    The latest annotation version is Revision 2 (MpTak_v6.1r2, 20230601).


    Citation
    Please site the following paper.
    Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochromatin (Montgomery, Tanizawa, Galic, et al. Current Biology, 30(4) P573-588, 2020.
    The paper describing Tak2 and the standard genome is also under preparation.

  • MpTak1_v5.1

    Chromosome-level genome assembly of the male Tak-1 strain obtained from PacBio long-read sequencing and Hi-C scaffolding. Consists of 9 chromosomal sequences and 435 unplaced scaffolds.


    Assembly and annotation version
    The latest annotation version is Revision 2 (MpTak1_v5.1r2).


    Changes from Revision1 to Revisio2
    The Genome Annotation Jamboree was held during Marchantia Workshop 2019 (Sendai, Japan) to improve gene annotation.
    We have incorporated the improved gene models curated by the participitants to create the Revision2 annotation. We would like to thank all the participitants in the Jamboree.
    This update also includes newly-identified gene models, removal of spurious gene models, merging of wrongly-separated gene models.

    Please note that the genome sequences of revision2 are the same as those of revision1. (Only annotations have been updated.)


    Citation
    Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochromatin (Montgomery, Tanizawa, Galic, et al. Current Biology, 30(4) P573-588, 2020.

  • JGI 3.1

    Draft genome sequences obtained under the initiative of DOE Joint Genome Institute (JGI) for the female BC4 strain. Consists of 2,957 scaffolds (4,454 contigs).
    The genomic data is also available at JGI Genome Portal.


    Citation
    Insights into land plant evolution garnered from the Marchantia polymorpha genome. (John L. Bowman, Takayuki Kohchi, Katsuyuki T. Yamato, et al. Cell 171(2) p287–304, 2017.

  • MppBR5 and MpmSA2

    MppBR5: Draft genome of M. polymprpha subsp. polymorpha BR5, consisting of 2,741 contigs.
    MpmSA2: Draft genome of M. polymprpha subsp. montivagans SA2, consisting of 2,710 contigs.
    Both genomes were assembled from PacBio long reads using HGAP.


    Citation
    Evolutionary History of the Marchantia polymorpha Complex. (Linde, et al.) Front. Plant Sci., 26 June 2020.

  • Contact

    If you have any questions, requests, or suggestions, please contact the E-mail address below.

    mpgdb [at] ynlab.info