Prunus humilis Genome v1.0 Assembly & Annotation

Analysis NamePrunus humilis Genome v1.0 Assembly & Annotation
MethodCANU (1.8)
SourceIllumina, Pacbio and HiC reads, Prunus humilis
Date performed2022-07-11

Yi Wang, Jun Xie, Hongna Zhang, Weidong Li, Zhanjun Wang, Huayang Li, Qian Tong, Gaixia Qiao, Yujuan Liu, Ying Tian, Yongzan Wei, Ping Li, Rong Wang, Weiping Chen, Zhengchang Liang, Meilong Xu. The genome of Prunus humilis provides new insights to drought adaption and population diversity. DNA Research. 2022 Jun 25;29(4):dsac021. doi: 10.1093/dnares/dsac021. (GDR | Journal)

Prunus humilis (2n =2x = 16) is dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, Pacbio and HiC sequencing technologies. This genome was 254.38Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor with Prunus mume and Prunus armeniaca at ∼ 29.03 Mya. Gene expansion analysis implied that the expansion of WAX-related and LEA genes might be associated with high drought tolerance of P. humilis and LTR maybe one of the driver factors for the drought adaption by increase the copy number of LEAs. Population diversity analysis among 20 P. humilis accessions found that the genetic diversity of P. humilis populations was limited, only 1.40% base pairs were different with each other, more wild resources need to be collected and utilized in the breeding and improvement. This study provides new insights to the drought adaption and population diversity of P. humilis, that could be used as a potential model plant for horticultural research.


Homology of the Prunus humilis Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 


Protein Homologs

Prunus humilis v1.0 proteins with NCBI nr homologs (EXCEL file) prunus_humilis_v1.0_vs_nr.xlsx.gz
Prunus humilis v1.0 proteins with NCBI nr (FASTA file) prunus_humilis_v1.0_vs_nr_hit.fasta.gz
Prunus humilis v1.0 proteins without NCBI nr (FASTA file) prunus_humilis_v1.0_vs_nr_noHit.fasta.gz
Prunus humilis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) prunus_humilis_v1.0_vs_arabidopsis.xlsx.gz
Prunus humilis v1.0 proteins with arabidopsis (Araport11) (FASTA file) prunus_humilis_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus humilis v1.0 proteins without arabidopsis (Araport11) (FASTA file) prunus_humilis_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus humilis v1.0 proteins with SwissProt homologs (EXCEL file) prunus_humilis_v1.0_vs_swissprot.xlsx.gz
Prunus humilis v1.0 proteins with SwissProt (FASTA file) prunus_humilis_v1.0_vs_swissprot_hit.fasta.gz
Prunus humilis v1.0 proteins without SwissProt (FASTA file) prunus_humilis_v1.0_vs_swissprot_noHit.fasta.gz
Prunus humilis v1.0 proteins with TrEMBL homologs (EXCEL file) prunus_humilis_v1.0_vs_trembl.xlsx.gz
Prunus humilis v1.0 proteins with TrEMBL (FASTA file) prunus_humilis_v1.0_vs_trembl_hit.fasta.gz
Prunus humilis v1.0 proteins without TrEMBL (FASTA file) prunus_humilis_v1.0_vs_trembl_noHit.fasta.gz



The Prunus humilis Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) prunus_humilis_v1.0.fasta.gz
Repeats (GFF3 file) prunus_humilis_v1.0.repeats.gff3.gz


Gene Predictions

The Prunus humilis v1.0 genome gene prediction file is available in GFF3 format.


Genes (GFF3 file) prunus_humilis_v1.0.genes.gff3.gz
Protein sequences  (FASTA file) prunus_humilis_v1.0.proteins.fasta.gz
RNA sequences  (FASTA file) prunus_humilis_v1.0.transcripts.fasta.gz
Gene sequences  (FASTA file) prunus_humilis_v1.0.genes.fasta.gz


Functional Analysis

Functional annotation for the Prunus humilis Genome v1.0 are available for download below. The Prunus humilis Genome v1.0 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 prunus_humilis_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan prunus_humilis_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs prunus_humilis_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways prunus_humilis_v1.0_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 Prunus humilis genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.


Fragaria x ananassa GDR RefTrans v1 prunus_humilis_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 prunus_humilis_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 prunus_humilis_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 prunus_humilis_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 prunus_humilis_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 prunus_humilis_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 prunus_humilis_v1.0_pyrus_GDR_reftransV1