| Analysis Name | Pyrus betulifolia ASM784424v1 Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | HGAP v. 1.0 |
| Release Date | 2019-08-08 |
Dong X, Wang Z, Tian L, Zhang Y, Qi D, Huo H, Xu J, Li Z, Liao R, Shi M, Wahocho SA, Liu C, Zhang S, Tian Z, Cao Y. De novo assembly of a wild pear (Pyrus betuleafolia) genome. Plant Biotechnol J. 2020 Feb;18(2):581-595. doi: 10.1111/pbi.13226.
AbstractChina is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.
Assembly statistics
| Genome size | 532.2 Mb |
| Total ungapped length | 496.5 Mb |
| Number of chromosomes | 17 |
| Number of organelles | 1 |
| Number of scaffolds | 136 |
| Scaffold N50 | 28.1 Mb |
| Scaffold L50 | 8 |
| Number of contigs | 592 |
| Contig N50 | 1.6 Mb |
| Contig L50 | 93 |
| GC percent | 37.5 |
| Genome coverage | 95.9x |
| Assembly level | Chromosome |
The Pyrus betulifolia ASM784424v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHAAYT00000000.genome.fasta.gz |
The Pyrus betulifolia ASM784424v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHAAYT00000000.gff.gz |
| CDS sequences (FASTA file) | GWHAAYT00000000.CDS.fasta.gz |
| Protein sequences (FASTA file) | GWHAAYT00000000.Protein.faa.gz |
Functional annotation for the Pyrus betulifolia ASM784424v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Pyrus_betulifolia_ASM784424v1.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | Domain |
| PbeSFBB.XVI-S67 | Chr 17 | 29412830 | 26093227-26094414 | F-box; F_box_assoc |
| PbeSFBB.X-S67 | Chr 17 | 29412830 | 26110389-26111567 | F-box; F_box_assoc |
| PbeSFBB.XI-S67 | Chr 17 | 29412830 | 26131630-26132814 | F-box; F_box_assoc |
| PbeSFBB.III-S67 | Chr 17 | 29412830 | 26250993-26252174 | F-box; F_box_assoc |
| PbeSFBB.IV-S67 | Chr 17 | 29412830 | 26336706-26337890 | F-box; F_box_assoc |
| PbeSFBB.Ia-S67 | Chr 17 | 29412830 | 26371301-26372503 | F-box; F_box_assoc |
| PbeSFBB.XV-S67 | Chr 17 | 29412830 | 26397872-26399086 | F-box; F_box_assoc |
| PbeSFBB.VI-S67 | Chr 17 | 29412830 | 26403481-26404659 | F-box; F_box_assoc |
| PbeSFBB.Ib-S67 | Chr 17 | 29412830 | 26563583-26564785 | F-box; F_box_assoc |
| PbeSFBB.XIII-S67 | Chr 17 | 29412830 | 26708911-26710092 | F-box; F_box_assoc |
| PbeSFBB.XII-S67 | Chr 17 | 29412830 | 26783023-26784195 | F-box; F_box_assoc |
| PbeSFBB.XIV-S67 | Chr 17 | 29412830 | 26856722-26857942 | F-box; F_box_assoc |
| S67-RNase | Chr 17 | 29412830 | 26886516-26886767,26886918-26887352 | RNase_T2 |
| PbeSFBB.IX-S67 | Chr 17 | 29412830 | 26965220-26966398 | F-box; F_box_assoc |
| PbeSFBB.VII-S67 | Chr 17 | 29412830 | 27014738-27015910 | F-box; F_box_assoc |
| PbeSFBB.XIX-S67 | Chr 17 | 29412830 | 27098826-27100058 | F-box; F_box_assoc |
| PbeSFBB.XVIII-S67 | Chr 17 | 29412830 | 27111438-27112622 | F-box; F_box_assoc |
| PbeSFBB.VIII-S67 | Chr 17 | 29412830 | 27139919-27141109 | F-box; F_box_assoc |
| PbeSFBB.XXI-S67 | Chr 17 | 29412830 | 27470492-27471841 | F-box; F_box_assoc |
Pyrus betulifolia ASM784424v1 S genes Nucleotide
Pyrus betulifolia ASM784424v1 S genes Protein