| Analysis Name | Pyrus communis dAnjou Genome v2.3.a1 Assembly & Annotation |
| Sequencing technology | Illumina and Pacbio HiFi reads |
| Assembly method | Hifiasm (v0.16.0) |
| Release Date | 2024-03-18 |
Yocca A, Akinyuwa M, Bailey N, Cliver B, Estes H, Guillemette A, Hasannin O, Hutchison J, Jenkins W, Kaur I, Khanna RR, Loftin M, Lopes L, Moore-Pollard E, Olofintila O, Oyebode GO, Patel J, Thapa P, Waldinger M, Zhang J, Zhang Q, Goertzen L, Carey SB, Hargarten H, Mattheis J, Zhang H, Jones T, Boston L, Grimwood J, Ficklin S, Honaas L, Harkess A. A chromosome-scale assembly for 'd'Anjou' pear. G3 (Bethesda). 2024 Jan 8:jkae003. doi: 10.1093/g3journal/jkae003.
AbstractCultivated pear consists of several Pyrus species with Pyrus 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 'd'Anjou.' Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling 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.
Assembly statistics
| haplotype 1 | GenBank |
| Genome size | 534.7 Mb |
| Total ungapped length | 534.6 Mb |
| Number of chromosomes | 17 |
| Number of scaffolds | 352 |
| Scaffold N50 | 28.8 Mb |
| Scaffold L50 | 9 |
| Number of contigs | 413 |
| Contig N50 | 14.7 Mb |
| Contig L50 | 14 |
| GC percent | 38 |
| Genome coverage | 66.0x |
| Assembly level | Chromosome |
| haplotype 2 | GenBank |
| Genome size | 533.4 Mb |
| Total ungapped length | 533.4 Mb |
| Number of chromosomes | 17 |
| Number of scaffolds | 270 |
| Scaffold N50 | 29.6 Mb |
| Scaffold L50 | 9 |
| Number of contigs | 341 |
| Contig N50 | 13.4 Mb |
| Contig L50 | 16 |
| GC percent | 38 |
| Genome coverage | 66.0x |
| Assembly level | Chromosome |
The Pyrus communis dAnjou Genome v2.3.a1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Pyrus_hap1_v1.3.rename.fasta.gz | Pyrus_hap2_v1.3.rename.fasta.gz |
The Pyrus communis dAnjou Genome v2.3.a1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Pyrus_hap1_v2.3.a1.maker.gff.gz | Pyrus_hap2_v2.3.a1.maker.gff.gz |
| CDS sequences (FASTA file) | Pyrus_hap1_v2.3.a1.all.maker.transcripts.fasta.gz | Pyrus_hap2_v2.3.a1.all.maker.transcripts.fasta.gz |
| Protein sequences (FASTA file) | Pyrus_hap1_v2.3.a1.all.maker.proteins.fasta.gz | Pyrus_hap2_v2.3.a1.all.maker.proteins.fasta.gz |
Functional annotation for the Pyrus communis dAnjou Genome v2.3.a1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Pyrus_communis_v2.3.a1_hap1.Pfam.tsv.gz | Pyrus_communis_v2.3.a1_hap2.Pfam.tsv.gz |
Pyrus S genes Nucleotide
Pyrus S genes Protein