White Lupin Genome

Here you will find the Lupin genome in fasta format along with the associated data. This includes annotation, protein sequences, sequencing data...

Lupin Genome version 1.0 (latest)

Genome data

Here you will find the latest genomic sequence of white lupin, including the annotation of 38258 Genes and 3129 non coding RNA. You can also download the sequences of all the annoted elements. The sequencing data that have been used for the genome assembly are also available.

Genome

Lupin genome version 1.0 : Lalbus.fasta
Lupin chloroplast + annotation : Lalbus_chloroplast.zip
Lupin mitochondrion + annotation : Lalbus_mitochondrion.zip

Annotations

Gene annotations in gff3 : Lalbus_genes.gff3
miRNA Clusters : Lalbus_shortstack_miRNA_clusters.gff3
Transposable elements (DANTE) : Lalbus_dante_transposable_elements.gff
Satellites : Lalbus_satelites.gff
Ribosomal DNA : Lalbus_rDNA.gff
GO annotation (update 2024) : Lalbus-GO-annotation.zip

Fasta sequences

Gene sequences : Lalbus_genes.fasta
Protein sequences : Lalbus_protein.fasta
CDS sequences : Lalbus_cds.fasta
mRNA sequences : Lalbus_mRNA.fasta
ncRNA sequences : Lalbus_ncRNA.fasta

pangenome sequences

Pangenome assembly

Variety	Genome	Annotation	Genes	mRNA	CDS	Proteins
P21525	P21525.fasta.gz	P21525.gff3.gz	genes	mRNA	CDS	proteins
Volodia	Volodia.fasta.gz	Volodia.gff3.gz	genes	mRNA	CDS	proteins
ALB01	ALB01.fasta.gz	ALB01.gff3.gz	genes	mRNA	CDS	proteins
Amiga	Amiga.fasta.gz	Amiga.gff3.gz	genes	mRNA	CDS	proteins
Badajoz	Badajoz.fasta.gz	Badajoz.gff3.gz	genes	mRNA	CDS	proteins
Batsi_Wild	Batsi_Wild.fasta.gz	Batsi_Wild.gff3.gz	genes	mRNA	CDS	proteins
Clovis	Clovis.fasta.gz	Clovis.gff3.gz	genes	mRNA	CDS	proteins
Dieta	Dieta.fasta.gz	Dieta.gff3.gz	genes	mRNA	CDS	proteins
Dogan	Dogan.fasta.gz	Dogan.gff3.gz	genes	mRNA	CDS	proteins
EGY6484B	EGY6484B.fasta.gz	EGY6484B.gff3.gz	genes	mRNA	CDS	proteins
Energy	Energy.fasta.gz	Energy.gff3.gz	genes	mRNA	CDS	proteins
Feodora	Feodora.fasta.gz	Feodora.gff3.gz	genes	mRNA	CDS	proteins
Figaro	Figaro.fasta.gz	Figaro.gff3.gz	genes	mRNA	CDS	proteins
Gerelta-2	Gerelta-2.fasta.gz	Gerelta-2.gff3.gz	genes	mRNA	CDS	proteins
GR38	GR38.fasta.gz	GR38.gff3.gz	genes	mRNA	CDS	proteins
GRC5262B	GRC5262B.fasta.gz	GRC5262B.gff3.gz	genes	mRNA	CDS	proteins
Gyulatanya	Gyulatanya.fasta.gz	Gyulatanya.gff3.gz	genes	mRNA	CDS	proteins
Hansa	Hansa.fasta.gz	Hansa.gff3.gz	genes	mRNA	CDS	proteins
Kalina	Kalina.fasta.gz	Kalina.gff3.gz	genes	mRNA	CDS	proteins
Kiev	Kiev.fasta.gz	Kiev.gff3.gz	genes	mRNA	CDS	proteins
LD37	LD37.fasta.gz	LD37.gff3.gz	genes	mRNA	CDS	proteins
Lucky	Lucky.fasta.gz	Lucky.gff3.gz	genes	mRNA	CDS	proteins
Luxe	Luxe.fasta.gz	Luxe.gff3.gz	genes	mRNA	CDS	proteins
Magnus	Magnus.fasta.gz	Magnus.gff3.gz	genes	mRNA	CDS	proteins
Murringo	Murringo.fasta.gz	Murringo.gff3.gz	genes	mRNA	CDS	proteins
N3507	N3507.fasta.gz	N3507.gff3.gz	genes	mRNA	CDS	proteins
Nahrquell	Nahrquell.fasta.gz	Nahrquell.gff3.gz	genes	mRNA	CDS	proteins
Neuland	Neuland.fasta.gz	Neuland.gff3.gz	genes	mRNA	CDS	proteins
Neutra	Neutra.fasta.gz	Neutra.gff3.gz	genes	mRNA	CDS	proteins
Orus	Orus.fasta.gz	Orus.gff3.gz	genes	mRNA	CDS	proteins
P27174-4	P27174-4.fasta.gz	P27174-4.gff3.gz	genes	mRNA	CDS	proteins
Poutignano	Poutignano.fasta.gz	Poutignano.gff3.gz	genes	mRNA	CDS	proteins
Primorsky	Primorsky.fasta.gz	Primorsky.gff3.gz	genes	mRNA	CDS	proteins
Shinfield	Shinfield.fasta.gz	Shinfield.gff3.gz	genes	mRNA	CDS	proteins
Start	Start.fasta.gz	Start.gff3.gz	genes	mRNA	CDS	proteins
SYR6258B	SYR6258B.fasta.gz	SYR6258B.gff3.gz	genes	mRNA	CDS	proteins
Tombowskij	Tombowskij.fasta.gz	Tombowskij.gff3.gz	genes	mRNA	CDS	proteins
Ulysses	Ulysses.fasta.gz	Ulysses.gff3.gz	genes	mRNA	CDS	proteins
Wado-2	Wado-2.fasta.gz	Wado-2.gff3.gz	genes	mRNA	CDS	proteins

Sequencing data

Genome assembly data

Illumina Reads

Illumina reads R1 : Lupin_NoIndex_L004_R1.fastq.gz
Illumina reads R2 : Lupin_NoIndex_L004_R2.fastq.gz

PacBio Reads

Pacbio Reads : PacBio data

Bionano Genomics Irys :

Optical map : OptMAP_Lal_amiga_171127.cmap

For convenience, all the Pacbio reads (from the subreads.bam files) have been merged into a single big fasta file.

Varieties Resequencing

Illumina Sequencing data (First 15 Varieties batch)

Amiga_R1 : Amiga_R1.fastq.gz
Amiga_R2 : Amiga_R2.fastq.gz
Clovis_R1 : Clovis_R1.fastq.gz
Clovis_R2 : Clovis_R2.fastq.gz
Dieta_R1 : Dieta_R1.fastq.gz
Dieta_R2 : Dieta_R2.fastq.gz
Energy_R1 : Energy_R1.fastq.gz
Energy_R2 : Energy_R2.fastq.gz
Feodora_R1 : Feodora_R1.fastq.gz
Feodora_R2 : Feodora_R2.fastq.gz
Figaro_R1 : Figaro_R1.fastq.gz
Figaro_R2 : Figaro_R2.fastq.gz
GR38_R1 : GR38_R1.fastq.gz
GR38_R2 : GR38_R2.fastq.gz
Kiev_R1 : Kiev_R1.fastq.gz
Kiev_R2 : Kiev_R2.fastq.gz
LD37_R1 : LD37_R1.fastq.gz
LD37_R2 : LD37_R2.fastq.gz
Lucky_R1 : Lucky_R1.fastq.gz
Lucky_R2 : Lucky_R2.fastq.gz
Luxe_R1 : Luxe_R1.fastq.gz
Luxe_R2 : Luxe_R2.fastq.gz
Magnus_R1 : Magnus_R1.fastq.gz
Magnus_R2 : Magnus_R2.fastq.gz
Orus_R1 : Orus_R1.fastq.gz
Orus_R2 : Orus_R2.fastq.gz
P27174-4_R1 : P27174-4_R1.fastq.gz
P27174-4_R2 : P27174-4_R2.fastq.gz
Ulysses_R1 : Ulysses_R1.fastq.gz
Ulysses_R2 : Ulysses_R2.fastq.gz

Illumina Sequencing data (Second 24 Varieties batch)

P21525 : P21525_R1.fastq.gz P21525_R2.fastq.gz
Volodia : Volodia_R1.fastq.gz Volodia_R2.fastq.gz
Tombowskij : Tombowskij_R1.fastq.gz Tombowskij_R2.fastq.gz
ALB01 : ALB01_R1.fastq.gz ALB01_R2.fastq.gz
Badajoz : Badajoz_R1.fastq.gz Badajoz_R2.fastq.gz
Batsi : Batsi_R1.fastq.gz Batsi_R2.fastq.gz
Dogan : Dogan_R1.fastq.gz Dogan_R2.fastq.gz
EGY6484B : EGY6484B_R1.fastq.gz EGY6484B_R2.fastq.gz
Gerelta : Gerelta_R1.fastq.gz Gerelta_R2.fastq.gz
GRC5262B : GRC5262B_R1.fastq.gz GRC5262B_R2.fastq.gz
Gyulatanya : Gyulatanya_R1.fastq.gz Gyulatanya_R2.fastq.gz
Hansa : Hansa_R1.fastq.gz Hansa_R2.fastq.gz
Kalina : Kalina_R1.fastq.gz Kalina_R2.fastq.gz
Murringo : Murringo_R1.fastq.gz Murringo_R2.fastq.gz
N3507 : N3507_R1.fastq.gz N3507_R2.fastq.gz
Nahrquell : Nahrquell_R1.fastq.gz Nahrquell_R2.fastq.gz
Neuland : Neuland_R1.fastq.gz Neuland_R2.fastq.gz
Neutra : Neutra_R1.fastq.gz Neutra_R2.fastq.gz
Poutignano : Poutignano_R1.fastq.gz Poutignano_R2.fastq.gz
Primorsky : Primorsky_R1.fastq.gz Primorsky_R2.fastq.gz
Shinfield : Shinfield_R1.fastq.gz Shinfield_R2.fastq.gz
Start : Start_R1.fastq.gz Start_R2.fastq.gz
SYR6258B : SYR6258B_R1.fastq.gz SYR6258B_R2.fastq.gz
Wado : Wado_R1.fastq.gz Wado_R2.fastq.gz

Raw genomic variation from 39 accessions

VCF : 39_lupin_varieties.vcf.gz 39_lupin_varieties.vcf.gz.tbi

Oxford Nanopore Sequencing data

Graecus : Graecus nanopore reads
P27174-4 : P27174-4 nanopore reads

Other genome assembly

Graecus assembly : Graecus assembly
P27174-4 assembly : P27174-4 assembly

ChIP-Seq data

ChIP-Seq Data

Input DNA (1) : CL100100938_L1_B5CLUPmnbCAAADABA-531_1.fq.gz
Input DNA (2) : CL100105475_L2_B5CLUPmnbCAAADABA-531_1.fq.gz
CENH3-ChIP : CL100105475_L2_B5CLUPmnbCAAAAABA-521_1.fq.gz

Expression data

Here you will find all the raw sequencing data that were used for this study. In addition, for RNA-seq, the raw count table is provided. Just click on the button you are intereted in to display the downloadable corresponding data.

Secco RNA-seq Data

Sequencing Data