Eriobotrya japonica Genome v1.0 Assembly & Annotation

Analysis NameEriobotrya japonica Genome v1.0 Assembly & Annotation
MethodWTDBG, Falcon, Canu
SourceIllumina reads
Date performed2022-12-15


Wang, Y. A draft genome, resequencing, and metabolomes reveal the genetic background and molecular basis of the nutritional and medicinal properties of loquat (Eriobotrya japonica (Thunb.) Lindl). Hortic Res 8, 231 (2021).


Loquat (Eriobotrya japonica) is a popular fruit and medicinal plant. Here, a high-quality draft genome of the E. japonica ‘Big Five-pointed Star’ cultivar that covers ~98% (733.32 Mb) of the estimated genome size (749.25 Mb) and contains a total of 45,492 protein-coding genes is reported. Comparative genomic analysis suggests that the loquat genome has evolved a unique genetic mechanism of chromosome repair. Resequencing data from 52 loquat cultivars, including 16 white-fleshed and 36 yellow-fleshed variants, were analyzed, and the flower, leaf, and root metabolomes of ‘Big Five-pointed Star’ were determined using a UPLC-ESI-MS/M system. A genome-wide association study identified several candidate genes associated with flesh color in E. japonica, linking these phenotypes to sugar metabolism. A total of 577 metabolites, including 98 phenolic acids, 95 flavonoids, and 28 terpenoids, were found, and 191 metabolites, including 46 phenolic acids, 33 flavonoids, and 7 terpenoids, showed no differences in concentration among the leaves, roots, and flowers. Candidate genes related to the biosynthesis of various medicinal ingredients, such as phenolics, flavonoids, terpenoids, and polysaccharides, were identified. Some of these genes were confirmed to be members of expanding gene families, suggesting that the high concentrations of beneficial metabolites in loquat may be associated with the number of biosynthetic genes in this plant. In summary, this study provides fundamental molecular insights into the nutritional and medical properties of E. japonica.


Summary of genome components of common loquat


GS (Mb)

DGS (Mb)

DGS/GS (%)

RGS (Mb)

TEs (Mb)

PG No.

Eriobotrya japonica 749.3 733.0 97.8 516.1 514.9 45,450


Integrity estimation of initial assembled draft genome


Aligning dataset

Counting (%)

embryophyta_odb9 database 2,326 Complete BUSCOs (%) 2,170 (93.29%)


Complete and single-copy BUSCOs (%) 1,450 (62.34%)


Complete and duplicated BUSCOs (%) 689 (29.62%)


Fragmented BUSCOs (%) 31 (1.33%)


Missing BUSCOs (%) 156 (6.71%)

Homology of the Eriobotrya japonica 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

Eriobotrya japonica v1.0 proteins with NCBI nr homologs (EXCEL file) Eriobotrya-japonica_v1.0_vs_nr.xlsx.gz
Eriobotrya japonica v1.0 proteins with NCBI nr (FASTA file) Eriobotrya-japonica_v1.0_vs_nr_hit.fasta.gz
Eriobotrya japonica v1.0 proteins without NCBI nr (FASTA file) Eriobotrya-japonica_v1.0_vs_nr_noHit.fasta.gz
Eriobotrya japonica v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Eriobotrya-japonica_v1.0_vs_arabidopsis.xlsx.gz
Eriobotrya japonica v1.0 proteins with arabidopsis (Araport11) (FASTA file) Eriobotrya-japonica_v1.0_vs_arabidopsis_hit.fasta.gz
Eriobotrya japonica v1.0 proteins without arabidopsis (Araport11) (FASTA file) Eriobotrya-japonica_v1.0_vs_arabidopsis_noHit.fasta.gz
Eriobotrya japonica v1.0 proteins with SwissProt homologs (EXCEL file) Eriobotrya-japonica_v1.0_vs_swissprot.xlsx.gz
Eriobotrya japonica v1.0 proteins with SwissProt (FASTA file) Eriobotrya-japonica_v1.0_vs_swissprot_hit.fasta.gz
Eriobotrya japonica v1.0 proteins without SwissProt (FASTA file) Eriobotrya-japonica_v1.0_vs_swissprot_noHit.fasta.gz
Eriobotrya japonica v1.0 proteins with TrEMBL homologs (EXCEL file) Eriobotrya-japonica_v1.0_vs_trembl.xlsx.gz
Eriobotrya japonica v1.0 proteins with TrEMBL (FASTA file) Eriobotrya-japonica_v1.0_vs_trembl_hit.fasta.gz
Eriobotrya japonica v1.0 proteins without TrEMBL (FASTA file) Eriobotrya-japonica_v1.0_vs_trembl_noHit.fasta.gz



The Eriobotrya japonica Genome v1.0 assembly files are available in FASTA format.


Chromosomes (FASTA file) Ejaponica_v1.0.fasta.gz


Gene Predictions

The Eriobotrya japonica v1.0 genome gene prediction file are available in GFF3 and FASTA format.


Genes (GFF3 file) Ejaponica_v1.0.genes.gff3.gz
Protein sequences (FASTA file) Ejaponica_v1.0.pep.fasta.gz
CDS sequences (FASTA file) Ejaponica_v1.0.cds.fasta.gz
Transcript sequences(FASTA file) Ejaponica_v1.0.transcript.fasta.gz


Functional Analysis

Functional annotation for the Eriobotrya japonica Genome v1.0 are available for download below. The Eriobotrya japonica 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 Eriobotrya-japonica_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Eriobotrya-japonica_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Eriobotrya-japonica_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Eriobotrya-japonica_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 Eriobotrya japonica genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.


Fragaria x ananassa GDR RefTrans v1 Eriobotrya-japonica_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 Eriobotrya-japonica_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Eriobotrya-japonica_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Eriobotrya-japonica_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Eriobotrya-japonica_v1.0_rubus_GDR_reftransV2
Eriobotrya_japonica GDR RefTrans v1 Eriobotrya-japonica_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Eriobotrya-japonica_v1.0_pyrus_GDR_reftransV1