Data

All data files associated with the Lactuca (super-)pangenome are available for download on this page. The sequences and their annotations listed here can be explored interactively using the available genome browser.

Species-specific data

For each species, linear pangenomes were created and analysed. Since these linear pangenomes are extended reference genomes, they also contain all sequences of already publicly available genomes.
The following data files are available for each of the four species:

L. sativa	L. serriola	L. saligna	L. virosa
L. sativa basis (NCBI: GCF_002870075.2)	L. sativa basis (NCBI: GCF_002870075.2)	L. saligna basis (NCBI: PRJEB56287)	L. virosa basis (NCBI: PRJEB50301)
Pangenome sequence	Pangenome sequence	Pangenome sequence	Pangenome sequence
Pangenome sequence index	Pangenome sequence index	Pangenome sequence index	Pangenome sequence index
Pangenome annotation	Pangenome annotation	Pangenome annotation	Pangenome annotation
Pangenome annotation overview	Pangenome annotation overview	Pangenome annotation overview	Pangenome annotation overview
Functional annotation (raw data)	Functional annotation (raw data)	Functional annotation (raw data)	Functional annotation (raw data)
PAV overview	PAV overview	PAV overview	PAV overview
Binary PAV overview	Binary PAV overview	Binary PAV overview	Binary PAV overview
CNV overview	CNV overview	CNV overview	CNV overview

Species-integrated data

The following data files integrate across species:

• Homology table
• PAV overview integrated across species based on homology

Notes

The following files are associated with the above links:

• Pangenome sequence: the pangenome sequence in FASTA format
• Pangenome sequence index: the index of the pangenome sequence in FASTA format
• Pangenome annotation: the pangenome annotation in GFF3 format
• Pangenome annotation overview: an overview of all genes in the pangenome and their characteristics in TSV format
• Functional annotation (raw data): the raw output of InterProScan (functional domain annotation) for the pangenome in TSV format
• PAV overview: the overview of raw (continuous) PAV values in the pangenome in TSV format: between 0 and 1
• Binary PAV overview: the overview of binarised (threshold of 0.8) PAV values in the pangenome in TSV format: either 0 or 1
• CNV overview: the overview of raw (continuous, normalised) CNV values in the pangenome in TSV format: higher than 0 and centered around 1
• Homology table: the homology table in human-readable format
• PAV overview integrated across species based on homology: for all accessions, the number of present copies of each homology group based on the binary PAV overview