README

The content of the directory

data/
├── Marpol_135_accessions
│   ├── Marpol_135_accessions.txt
│   ├── Marpol_135_accessions.vcf.gz
│   └── Marpol_135_accessions.vcf.gz.tbi
├── Marpolmon_16_accessions
│   ├── Marpolmon_16_accessions.txt
│   ├── Marpolmon_16_accessions.vcf.gz
│   ├── Marpolmon_16_accessions.vcf.gz.tbi
│   ├── genomes.tar.gz
│   ├── GFFs.tar.gz
│   └── peptides.tar.gz
├── Marpolpol_13_accessions
│   ├── Marpolpol_13_accessions.txt
│   ├── Marpolpol_13_accessions.vcf.gz
│   ├── Marpolpol_13_accessions.vcf.gz.tbi
│   ├── genomes.tar.gz
│   ├── GFFs.tar.gz
│   └── peptides.tar.gz
├── Marpolrud_104_accessions
│   ├── Marpolrud_104_accessions.vcf.gz
│   ├── Marpolrud_104_accessions.vcf.gz.tbi
│   ├── Marpolrud_104_accessions.txt
│   ├── genomes.tar.gz
│   ├── GFFs.tar.gz
│   └── peptides.tar.gz
├── reference_genome
│   ├── MpTak_v6.1.genome.fasta
│   ├── MpTak_v6.1.genome.fasta.fai
│   ├── MpTak_v6.1r2.gff.gz
│   └── MpTak_v6.1r2.gff.gz.tbi
└── VCFs
    ├── Aberdeen.vcf.gz
    ├── Aberdeen.vcf.gz.tbi
    ├── Ale-A.vcf.gz
    ...

• Marpol_135_accessions

  • Marpol_135_accessions.txt: List of accessions included in the VCF file
  • Marpol_135_accessions.vcf.gz: Multi-sample VCF file (bgzipped) for all 3 subspecies of Marchantia polymorpha
  • Marpol_135_accessions.vcf.gz.tbi: The index file generated by tabix for the above VCF file .

• Marpolmon_16_accessions

  • Marpolmon_16_accessions.txt: List of accessions included in the VCF file
  • Marpolmon_16_accessions.vcf.gz: Multi-sample VCF files (bgzipped) for 16 accessions from Marchantia polymorpha subsp. montivagans.
  • Marpolmon_16_accessions.vcf.gz.tbi: The tabix index file for the VCF file above
  • genomes.tar.gz: Genomic FASTA files for subsp. montivagans 16 accessions, containing contigs generated by the de novo assembly of short reads
  • GFFs.tar.gz: Gene annotation in GFF format for subsp. montivagans 16 accessions.
  • peptides.tar.gz: Protein FASTA files for subsp. montivagans 16 accessions, generated from the genomic FASTA file and the GFF file.

• Marpolpol_13_accessions
  Same as above. For 13 accessions from M. polymorpha subsp. polymorpha.

• Marpolrud_104_accessions
  Same as above. For 104 accessions from M. polymorpha subsp. ruderalis.

• reference_genome
  The genome sequence for MpTak_v6.1 used as a reference genome and its faidx index file (.fai)
  MpTak_v6.1r2.gff.gz: Gene annotation in GFF format and its tabix index file (.tbi)

• VCFs
  Single-sample VCF files for each accession and their index files

Caveat

• Low quality data
  The data for the following accessions are of low quality and may need careful consideration when interpreting analytical results.

  RES36 *1
  RES37 *1, *2
  RES38
  RES40
  WT-M *1
  Tak1-HK *1
  Field-1 *1
  NILSC10 *1, *2
  NILSC17
  NILSC24
  NILSC20

  *1 Genome/protein FASTA and GFF are missing, since de novo assemblies for these accessions failed.
  *2 They are included in the VCF for all accessions (Marpol_135_accessions), but not included in the VCF files for each subspecies.

License

The data distributed in this directory is licensed under CC-BY (Creative Commons Attribution), which allows for the sharing and adaptation of the data, provided that proper attribution is given.

You are free to:
Share — copy and redistribute the material in any medium or format for any purpose, even commercially.
Adapt — remix, transform, and build upon the material for any purpose, even commercially.
The licensor cannot revoke these freedoms as long as you follow the license terms.

Under the following terms:
Attribution - You must give appropriate credit , provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
No additional restrictions - You may not apply legal terms or technological measures that legally restrict others > from doing anything the license permits.

See https://creativecommons.org/licenses/by/4.0/

Citation and contact

The Marchantia pangenome paper is under review.
If you want to use the data distributed in this directory, please cite our preprint at bioRxiv: DOI:10.1101/2023.10.27.564390

For inquiries about the data, please contact us at the following mail addresses:

• Pierre Marc (pierre-marc.delaux @ cnrs.fr)
• Maxime Bonhomme (maxime.bonhomme @ univ-tlse3.fr)