Aegle marmelos cv. AEG genome v1.0 | Citrus Genome Database

Overview


Analysis Name	Aegle marmelos cv. AEG genome v1.0
Method	PacBio, Nanopore (Assembly with SMARTdenovo, miniasm)
Source	Huazhong Agriculture University
Date performed	2024-01-22

About the assembly

For this genome, please cite Huang et al, Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. This data was originally downloaded from the Citrus Pan-genome to Breeding Database. This data is also on NCBI under BioProject PRJNA782429 and the assembly accession number is GCA_030449875.1. The listed BioSample isolate designation is AEG.

Assembly metrics

Assembly size	276 Mb
Number of scaffolds	143
N50	16,833,768 bp
Predicted transcripts	45,573
Annotated genes	28,519
Assembly BUSCO score (embryophyta_odb10)	98.6%
Annotation BUSCO score (embryophyta_odb10)	97.2%

Assembly

The Aegle marmelos cv. AEG genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

aem_AEG_v1.0.fasta.gz

Gene Predictions

The Aegle marmelos cv. AEG v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences (FASTA file)	aem_AEG_v1.0.proteins.fasta.gz
Gene sequences (FASTA file)	aem_AEG_v1.0.genes.fasta.gz
CDS (FASTA file)	aem_AEG_v1.0.cds.fasta.gz
Genes (GFF3 file)	aem_AEG_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Aegle marmelos AEG genome v1.0 are available for download below. The Aegle marmelos AEG 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).

Downloads

GO assignments from InterProScan	Aem_AEG_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan	Aem_AEG_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Aem_AEG_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Aem_AEG_v1.0_KEGG-pathways.xlsx.gz

Homology

Homology of the Aegle marmelos AEG 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^-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format.

Protein Homologs

Aegle marmelos AEG v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	aem_AEG_v1.0_vs_arabidopsis.xlsx.gz
Aegle marmelos AEG v1.0 proteins with arabidopsis (Araport11) (FASTA file)	aem_AEG_v1.0_vs_arabidopsis_hit.fasta.gz
Aegle marmelos AEG v1.0 proteins without arabidopsis (Araport11) (FASTA file)	aem_AEG_v1.0_vs_arabidopsis_noHit.fasta.gz
Aegle marmelos AEG v1.0 proteins with SwissProt homologs (EXCEL file)	aem_AEG_v1.0_vs_swissprot.xlsx.gz
Aegle marmelos AEG v1.0 proteins with SwissProt (FASTA file)	aem_AEG_v1.0_vs_swissprot_hit.fasta.gz
Aegle marmelos AEG v1.0 proteins without SwissProt (FASTA file)	aem_AEG_v1.0_vs_swissprot_noHit.fasta.gz
Aegle marmelos AEG v1.0 proteins with TrEMBL homologs (EXCEL file)	aem_AEG_v1.0_vs_trembl.xlsx.gz
Aegle marmelos AEG v1.0 proteins with TrEMBL (FASTA file)	aem_AEG_v1.0_vs_trembl_hit.fasta.gz
Aegle marmelos AEG v1.0 proteins without TrEMBL (FASTA file)	aem_AEG_v1.0_vs_trembl_noHit.fasta.gz