Pyrus communis d'Anjou Genome v2.3.a1 Assembly & Annotation

Analysis NamePyrus communis d'Anjou Genome v2.3.a1 Assembly & Annotation
MethodHifiasm (v0.16.0)
SourceIllumina and Pacbio HiFi reads
Date performed2023-08-31


Yocca, A., Akinyuwa, M., Bailey, N., Cliver, B., Estes, H., Guillemette, A., Hasannin, O., Hutchison, J., Jenkins, W., Kaur, I., Khanna, R. R., Loftin, M., Lopes, L., Moore-Pollard, E., Olofintila, O., Oyebode, G. O., Patel, J., Thapa, P., Waldinger, M., Zhang, J., Zhang, Q., Goertzen, L., Carey, S., Hargarten, H., Mattheis, J., Zhang, H., Jones, T., Boston, L., Grimwood, J., Ficklin, S., Honaas, L., & Harkess A. (2024). A chromosome-scale assembly for 'd'Anjou' pear.  G3|Genes|Genomes|Genetics


Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully-phased chromosome-scale genome assembly of P. communis cv. ‘d’Anjou’. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other, and to the Malus domestica ‘Honeycrisp’ apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d’Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.



Homology of the Pyrus communis DAnjou genome v2.3.a1 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

P. communis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pcommunis_DAnjou_v2.3.a1_vs_arabidopsis.xlsx.gz
P. communis v1.0 proteins with arabidopsis (Araport11) (FASTA file) Pcommunis_DAnjou_v2.3.a1_vs_arabidopsis_hit.fasta.gz
P. communis v1.0 proteins without arabidopsis (Araport11) (FASTA file) Pcommunis_DAnjou_v2.3.a1_vs_arabidopsis_noHit.fasta.gz
P. communis v1.0 proteins with SwissProt homologs (EXCEL file) Pcommunis_DAnjou_v2.3.a1_vs_swissprot.xlsx.gz
P. communis v1.0 proteins with SwissProt (FASTA file) Pcommunis_DAnjou_v2.3.a1_vs_swissprot_hit.fasta.gz
P. communis v1.0 proteins without SwissProt (FASTA file) Pcommunis_DAnjou_v2.3.a1_vs_swissprot_noHit.fasta.gz
P. communis v1.0 proteins with TrEMBL homologs (EXCEL file) Pcommunis_DAnjou_v2.3.a1_vs_trembl.xlsx.gz
P. communis v1.0 proteins with TrEMBL (FASTA file) Pcommunis_DAnjou_v2.3.a1_vs_trembl_hit.fasta.gz
P. communis v1.0 proteins without TrEMBL (FASTA file) Pcommunis_DAnjou_v2.3.a1_vs_trembl_noHit.fasta.gz

The Pyrus communis d’Anjou v2.3 genome assembly files are available in GFF3 and FASTA format.


Chromosomes (HAP 1) (FASTA file) Pcommunis_DAnjou_Hap1.v2.3.a1.fasta.gz
Chromosomes (HAP 2) (FASTA file) Pcommunis_DAnjou_Hap2.v2.3.a1.fasta.gz
Gene Predictions

The Pyrus communis d’Anjou v2.3 genome gene prediction files are available in GFF3 and FASTA format.


Genes (HAP 1) (GFF3 file) Pcommunis_DAnjou_hap1_v2.3.a1.genes.gff3.gz
Genes (HAP 2) (GFF3 file) Pcommunis_DAnjou_hap2_v2.3.a1.genes.gff3.gz
Protein sequences (HAP 1) (FASTA file) Pcommunis_DAnjou_hap1_v2.3.a1.protein.fasta.gz
Protein sequences (HAP 2) (FASTA file) Pcommunis_DAnjou_hap2_v2.3.a1.protein.fasta.gz
Transcript sequences (HAP 1) (FASTA file) Pcommunis_DAnjou_hap1_v2.3.a1.transcripts.fasta.gz
Transcript sequences (HAP 2) (FASTA file) Pcommunis_DAnjou_hap2_v2.3.a1.transcripts.fasta.gz
Functional Analysis

Functional annotation for the Pyrus communis d'Anjou genome v2.3 are available for download below. The Pyrus communis d'Anjou genome v2.3.a1 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).


GO assignments from InterProScan Pcommunis_DAnjou_v2.3.a1_genes2GO.xlsx.gz
IPR assignments from InterProScan Pcommunis_DAnjou_v2.3.a1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Pcommunis_DAnjou_v2.3.a1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Pcommunis_DAnjou_v2.3.a1_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 Pyrus communisd'Anjou Genome v2.3.a1 assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.


Fragaria x ananassa GDR RefTrans v1 Pcommunis_DAnjou_v2.3.a1_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pcommunis_DAnjou_v2.3.a1_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pcommunis_DAnjou_v2.3.a1_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pcommunis_DAnjou_v2.3.a1_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pcommunis_DAnjou_v2.3.a1_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Pcommunis_DAnjou_v2.3.a1_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Pcommunis_DAnjou_v2.3.a1_pyrus_GDR_reftransV1