| Analysis Name | Pyrus communis Bartlett_DH_Genome_v2.0 Assembly & Annotation |
| Sequencing technology | PacBio, Illumina, Bionano and Hi-C |
| Assembly method | Canu |
| Release Date | 2019-05-28 |
Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience. 2019 Dec 1;8(12):giz138. doi: 10.1093/gigascience/giz138.
AbstractBackground: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same “Bartlett” reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. Findings: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. Conclusions: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
Assembly statistics
| Sequence coverage (×) | 123 |
| Sequenced genome size (Mb) | 496.9 |
| Contig Number | 501 |
| Contig N50 (Mb) | 5.3 |
| Assembly level | Chromosome |
The Pyrus communis Bartlett_DH_Genome_v2.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | PyrusCommunis_BartlettDHv2.0.fasta.gz |
The Pyrus communis Bartlett_DH_Genome_v2.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | PyrusCommunis_BartlettDHv2.0.gff.gz |
| CDS sequences (FASTA file) | PyrusCommunis_BartlettDHv2.0.cds.fasta.gz |
| Protein sequences (FASTA file) | PyrusCommunis_BartlettDHv2.0.pep.fasta.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | Domain |
| PcSFBB.XVI-S101 | Chr 17 | 26287332 | 23558421-23559608 | F-box; F_box_assoc |
| PcSFBB.XIV-S101 | Chr 17 | 26287332 | 23572019-23573239 | F-box; F_box_assoc |
| PcSFBB.XIII-S101 | Chr 17 | 26287332 | 23579896-23581077 | F-box; F_box_assoc |
| PcSFBB.Ib-S101 | Chr 17 | 26287332 | 23609154-23607952 | F-box; F_box_assoc |
| PcSFBB.VI-S101 | Chr 17 | 26287332 | 23643526-23642348 | F-box; F_box_assoc |
| PcSFBB.III-S101 | Chr 17 | 26287332 | 23712170-23713351 | F-box; F_box_assoc |
| PcSFBB.II-S101 | Chr 17 | 26287332 | 23749531-23750721 | F-box; F_box_assoc |
| PcSFBB.IV-S101 | Chr 17 | 26287332 | 23754546-23755730 | F-box; F_box_assoc |
| PcSFBB.XV.1-S101 | Chr 17 | 26287332 | 23772710-23771496 | F-box; F_box_assoc |
| PcSFBB.XV.2-S101 | Chr 17 | 26287332 | 23775896-23777110 | F-box; F_box_assoc |
| PcSFBB.X-S101 | Chr 17 | 26287332 | 23841628-23840447 | F-box; F_box_assoc |
| PcSFBB.XII-S101 | Chr 17 | 26287332 | 23990073-23991245 | F-box; F_box_assoc |
| PcS101-RNase | Chr 17 | 26287332 | 24015597-24015358,24014550-24014113 | RNase_T2 |
| PcSFBB.V-S101 | Chr 17 | 26287332 | 24092226-24091048 | F-box; F_box_assoc |
| PcSFBB.VII-S101 | Chr 17 | 26287332 | 24134599-24133427 | F-box; F_box_assoc |
| PcSFBB.XIX-S101 | Chr 17 | 26287332 | 24148173-24146941 | F-box; F_box_assoc |
| PcSFBB.XVIII-S101 | Chr 17 | 26287332 | 24161342-24160158 | F-box; F_box_assoc |
| PcSFBB.VIII-S101 | Chr 17 | 26287332 | 24199397-24198207 | F-box; F_box_assoc |
| PcSFBB.XXI-S101 | Chr 17 | 26287332 | 24650038-24651387 | F-box; F_box_assoc |
| PcSFBB.XXII-S101 | Chr 17 | 26287332 | 24907483-24906110 | F-box; F_box_assoc |
Pyrus communis Bartlett_DH_Genome_v2.0 S genes Nucleotide
Pyrus communis Bartlett_DH_Genome_v2.0 S genes Protein