Prunus dulcis Lauranne Genome v1.0

Overview
Analysis NamePrunus dulcis Lauranne Genome v1.0
MethodIllumina and PacBio
SourcePrunus dulcis Lauranne Genome v1.0
Date performed2019-06-21

Publication

Sánchez-Pérez R, Pavan S, Mazzeo R, Moldovan C, Aiese Cigliano R, Del Cueto J, Ricciardi F, Lotti C, Ricciardi L, Dicenta F, López-Marqués RL, Møller BL. Mutation of a bHLH transcription factor allowed almond domestication. Science. 2019 Jun 14;364(6445):1095-1098. doi: 10.1126/science.aav8197.

Abstract

Wild almond species accumulate the bitter and toxic cyanogenic diglucoside amygdalin. Almond domestication was enabled by the selection of genotypes harboring sweet kernels. We report the completion of the almond reference genome. Map-based cloning using an F1 population segregating for kernel taste led to the identification of a 46-kilobase gene cluster encoding five basic helix-loop-helix transcription factors, bHLH1 to bHLH5. Functional characterization demonstrated that bHLH2 controls transcription of the P450 monooxygenase-encoding genes PdCYP79D16 and PdCYP71AN24, which are involved in the amygdalin biosynthetic pathway. A nonsynonymous point mutation (Leu to Phe) in the dimerization domain of bHLH2 prevents transcription of the two cytochrome P450 genes, resulting in the sweet kernel trait.

Genome facts and statistics

The genome (2n =2x = 16, haploid genome size=246Mb) of the sweet homozygous almond cultivar Lauranne was sequenced with a combination of Illumina (paired-end and 5-kb mate pairs) and Pac Biotechnologies.The long PacBio reads were used to perform the genome assembly, whereas the Illumina reads were used to perform gap filling and scaffolding. The scaffolds obtained were organized in pseudomolecules using the P. persica reference genome, as the genomes across the Prunus genus are essentially collinear (23–25). The final assembly constitutes 4078 scaffolds, of which 2572 are organized in eight pseudomolecules, with a final N50 of 21.8Mb (where N50 ist heminimum contig length needed to cover 50% of the genome) and a L90 of 306 (where L90 is the smallest number of contigs whose length sum makes up 90% of genome size).

Assembly

The Prunus dulcis Lauranne Genome v1.0 assembly files are available in FASTA format.

Downloads

Pseudomolecule (FASTA file) pdulcis_lauranne_v1.0.fasta.gz

 

Gene Predictions

The Prunus dulcis lauranne v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) pdulcis_lauranne_v1.0.proteins.fasta.gz
Genes (GFF3 file) pdulcis_lauranne_v1.0.genes.gff3.gz

 

Downloads

All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.

Homology

Homology of the Prunus dulcis Lauranne genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus dulcis Lauranne v1.0 proteins with NCBI nr homologs (EXCEL file) Pd_lauranne_v1.0_vs_nr.xlsx.gz
Prunus dulcis Lauranne v1.0 proteins with NCBI nr (FASTA file) Pd_lauranne_v1.0_vs_nr_hit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins without NCBI nr (FASTA file) Pd_lauranne_v1.0_vs_nr_noHit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) Pd_lauranne_v1.0_vs_arabidopsis.xlsx.gz
Prunus dulcis Lauranne v1.0 proteins with arabidopsis (TAIR10) (FASTA file) Pd_lauranne_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins without arabidopsis (TAIR10) (FASTA file) Pd_lauranne_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins with SwissProt homologs (EXCEL file) Pd_lauranne_v1.0_vs_swissprot.xlsx.gz
Prunus dulcis Lauranne v1.0 proteins with SwissProt (FASTA file) Pd_lauranne_v1.0_vs_swissprot_hit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins without SwissProt (FASTA file) Pd_lauranne_v1.0_vs_swissprot_noHit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins with TrEMBL homologs (EXCEL file) Pd_lauranne_v1.0_vs_trembl.xlsx.gz
Prunus dulcis Lauranne v1.0 proteins with TrEMBL (FASTA file) Pd_lauranne_v1.0_vs_trembl_hit.fasta.gz
Prunus dulcis Lauranne v1.0 proteins without TrEMBL (FASTA file) Pd_lauranne_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation for the Prunus dulcis Lauranne genome v1.0 are available for download below. The Prunus dulcis Lauranne genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan pdulcis_lauranne_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pdulcis_lauranne_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pdulcis_lauranne_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pdulcis_lauranne_v1.0_KEGG-pathways.xlsx.gz

 

Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus dulcis genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.

 

Fragaria x ananassa GDR RefTrans v1 Prunus dulcis_Lauranne_v1.0_f.x.ananassa_GDR_reftransV1
Malus x domestica GDR RefTrans v1 Prunus dulcis_Lauranne_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus dulcis_Lauranne_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus dulcis_Lauranne_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus dulcis_Lauranne_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus dulcis_Lauranne_v1.0_rubus_GDR_reftransV2