| Analysis Name | Pyrus pyrifolia PPY_r1.0 Assembly & Annotation |
| Sequencing technology | Sequel |
| Assembly method | FALCON v. 1.8.1 |
| Release Date | 2020-12-23 |
Shirasawa K, Itai A, Isobe S. Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki'. DNA Res. 2021 May 2;28(2):dsab001. doi: 10.1093/dnares/dsab001.
AbstractWe analyzed the genome sequence of a Japanese pear (Pyrus pyrifolia) to facilitate its genetics and genomics as well as breeding programs, in which a variety 'Nijisseiki' with superior flesh texture has been used as a parent for most Japanese pear cultivars. De novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6 Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 high-confidence protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of genome-wide duplication was observed, consistent with related species. This is the first chromosome-scale genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.
Assembly statistics
| Genome size | 503.9 Mb |
| Total ungapped length | 503.9 Mb |
| Number of contigs | 114 |
| Contig N50 | 7.7 Mb |
| Contig L50 | 21 |
| GC percent | 37.5 |
| Genome coverage | 136.0x |
| Assembly level | Contig |
The Pyrus pyrifolia PPY_r1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | PPY_r1.0.pmol.fasta.gz |
The Pyrus pyrifolia PPY_r1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | PPY_r1.0.pmol.gene.gff.gz |
| CDS sequences (FASTA file) | PPY_r1.0.cds.fasta.gz |
| Protein sequences (FASTA file) | PPY_r1.0.pep.fasta.gz |
Functional annotation for the Pyrus pyrifolia PPY_r1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Pyrus_pyrifolia_PPY_r1.0.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| PpySFBB.XVI | PPY_r1.0chr17 | 31990591 | 29400500-29401687 | ON918627.1, PbrSFBB.XVI-S17 | 98.91 | F-box; F_box_assoc |
| PpySFBB.XIV | PPY_r1.0chr17 | 31990591 | 29417387-29418607 | ON918625.1, PbrSFBB.XIV-S17 | 98.85 | F-box; F_box_assoc |
| PpySFBB.XIII | PPY_r1.0chr17 | 31990591 | 29427360-29428541 | ON918624.1, PbrSFBB.XIII-S17 | 99.58 | F-box; F_box_assoc |
| PpySFBB.IX | PPY_r1.0chr17 | 31990591 | 29453987-29452785 | ON918620.1, PbrSFBB.IX-S17 | 97.1 | F-box; F_box_assoc |
| PpySFBB.VI | PPY_r1.0chr17 | 31990591 | 29486571-29485393 | ON918617.1, PbrSFBB.VI-S17 | 98.56 | F-box; F_box_assoc |
| PpySFBB.III | PPY_r1.0chr17 | 31990591 | 29531116-29532297 | ON918615.1, PbrSFBB.III-S17 | 95.99 | F-box; F_box_assoc |
| PpySFBB.II | PPY_r1.0chr17 | 31990591 | 29569337-29570527 | ON918614.1, PbrSFBB.II-S17 | 95.14 | F-box; F_box_assoc |
| PpySFBB.IV | PPY_r1.0chr17 | 31990591 | 29575064-29576248 | ON918616.1, PbrSFBB.IV-S17 | 94.6 | F-box; F_box_assoc |
| PpySFBB.VII | PPY_r1.0chr17 | 31990591 | 29624823-29626001 | ON918618.1, PbrSFBB.VII-S17 | 95.67 | F-box; F_box_assoc |
| PpySFBB.VII.2 | PPY_r1.0chr17 | 31990591 | 29655787-29656965 | ON918618.1, PbrSFBB.VII-S17 | 91.1 | F-box; F_box_assoc |
| PpySFBB.XI | PPY_r1.0chr17 | 31990591 | 29687115-29685931 | ON918622.1, PbrSFBB.XI-S17 | 93.84 | F-box; F_box_assoc |
| PpySFBB.XVIII | PPY_r1.0chr17 | 31990591 | 29733172-29731985 | ON918628.1, PbrSFBB.XVIII-S17 | 87.5 | F-box; F_box_assoc |
| PpySFBB.I | PPY_r1.0chr17 | 31990591 | 29796689-29797891 | ON918613.1, PbrSFBB.I-S17 | 94.02 | F-box; F_box_assoc |
| PpySFBB.X | PPY_r1.0chr17 | 31990591 | 29814701-29813520 | ON918621.1, PbrSFBB.X-S17 | 95.35 | F-box; F_box_assoc |
| PpySFBB.XII | PPY_r1.0chr17 | 31990591 | 29835171-29833999 | ON918623.1, PbrSFBB.XII-S17 | 95.31 | F-box; F_box_assoc |
| PpySFBB.XV | PPY_r1.0chr17 | 31990591 | 29926426-29925194 | ON918626.1, PbrSFBB.XV-S17 | 94.73 | F-box; F_box_assoc |
| PpySFBB.XIX | PPY_r1.0chr17 | 31990591 | 29982617-29981385 | ON918629.1, PbrSFBB.XIX-S17 | 97.08 | F-box; F_box_assoc |
| PpySFBB.VIII | PPY_r1.0chr17 | 31990591 | 30046349-30045159 | ON918619.1, PbrSFBB.VIII-S17 | 98.99 | F-box; F_box_assoc |
| S-RNase | PPY_r1.0chr17 | 31990591 | 29677347-29677592,29678746-29679180 | D49527.1 | 100 | RNase_T2 |
Pyrus pyrifolia PPY_r1.0 S genes Nucleotide
Pyrus pyrifolia PPY_r1.0 S genes Protein