Prunus cerasus cv.Montmorency v1.0.a2 Assembly & Annotation

Overview

Analysis Name Prunus cerasus cv.Montmorency v1.0.a2 Assembly & Annotation
Sequencing technology PacBio long-reads, Illumina short-reads
Assembly method Canu
Release Date 2024-02-21
Reference Publication(s)

Goeckeritz CZ, Rhoades KE, Childs KL, Iezzoni AF, VanBuren R, Hollender CA. Genome of tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes. Hortic Res. 2023 May 10;10(7):uhad097. doi: 10.1093/hr/uhad097.

Abstract

Sour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa (ground cherry) and Prunus avium (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the USA. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for 'Montmorency' and provide compelling evidence P. fruticosa is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show 'Montmorency' is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A') and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). The genome composition of 'Montmorency' is AA'BB and little-to-no recombination has occurred between progenitor subgenomes (A/A' and B). In Prunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. The S-alleles and DAMs in 'Montmorency' and P. fruticosa were manually annotated and support subgenome assignments. Lastly, the hybridization event 'Montmorency' is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The 'Montmorency' genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.

Assembly statistics

Assembly

The Prunus cerasus cv.Montmorency v1.0.a2 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Pcerasus_montmorency_final.fasta.gz

Gene Predictions

The Prunus cerasus cv.Montmorency v1.0.a2 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Pcer_mont_QTL_update2_CORRECTED.sortedb.gff3.gz
CDS sequences (FASTA file) Pcer_mont_QTL_update2_cds.fasta.gz
Protein sequences (FASTA file) Pcer_mont_QTL_update2_proteins.fasta.gz

Functional Analysis

Functional annotation for the Prunus cerasus cv.Montmorency v1.0.a2 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Prunus_cerasus_cv.Montmorency_v1.0.a2.Pfam.tsv.gz

S genes

Prunus S genes Nucleotide

Prunus S genes Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences