Downloads: Orange Genome Annotation Project

The genome data are free for scientific use when it has been published (with cite information when this happen). Re-distribution and re-package of these data was not allowed without permission. These data may contain errors, please feedback us when you find errors by email to Dr. Qiang Xu at xuqiang@mail.hzau.edu.cn. And we keep continuous update on the genome version.

Genome of Sweet orange (Citrus sinensis)

    swo_v3: a Dihaploid of sweet orange cultivar 'Valencia' based on PacBio, version3
    swo_v4: a Dihaploid of sweet orange cultivar 'Valencia' based on Nanopore Ultra long, version4
    HXC: a diploid sweet orange cultivar 'Valencia'
    TCPS: a high acid orange from Hunan Province in South China
    BTC: a low acid orange cutivar 'BintTangCheng' from South China
    UKXC: a local variety from South China
    NHE: a cutivar of navel orange
    NW: a late mature mutant of navel orange

Assemblies in FASTA format

swo_v3.tar.gz (Pseudomolecule Sequences)
swo_v4.tar.gz (Pseudomolecule Sequences)
BTC.chromosome.fa.gz (Pseudomolecule Sequences)
UKXC.chromosome.fa.gz (Pseudomolecule Sequences)
NHE.chromosome.fa.gz (Pseudomolecule Sequences)
TCPS.chromosome.fasta.gz (Pseudomolecule Sequences)
NW.chromosome.fasta.gz (Pseudomolecule Sequences)
HXC.chromosome.fa.gz (Pseudomolecule Sequences)

Genome of Trifoliate orange (Poncirus trifoliata) Status: high quality, version1

Cite:Yue Huang#, Yuantao Xu# et al. Genome of a citrus rootstock and global DNA demethylation caused by heterografting. Horticulture Research, 2021, doi: https://doi.org/10.1038/s41438-021-00505-2

Assemblies in FASTA format

ZK.chromosome.fa.tar.gz (Pseudomolecule Sequences)

Annotation files

ZK.gene.model.gff3.tar.gz (Gene annotation in GFF3 format)
ZK.gene.fa.tar.gz (Nucleotide sequences of all genes)
ZK.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
ZK.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
ZK.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of hongkong kumquat (Fortunella hindsii) Status: draft, version1

Cite:Chenqiao Zhu#, Xiongjie Zheng#, Yue Huang# et al. Genome sequencing and CRISPR/Cas9 gene editing of an early flowering mini citrus (Fortunella hindsii). Plant Biotechnology Journal , 2019, doi: 10.1111/pbi.13132

Assemblies in FASTA format

GJ.contig.fa.tar.gz (Contig sequences)

Annotation files

GJ.gene.model.gff3.tar.gz (Gene annotation in GFF3 format for contig sequence)
GJ.gene.fa.tar.gz (Nucleotide sequences of all genes)
GJ.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
GJ.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
GJ.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of wild mandarin (Citrus reticulata 'Mangshan') Status: draft, version1

Cite:Lun Wang# et al. Genome of wild mandarin and domestication history of mandarin. Molecular Plant, 2018, doi:https://doi.org/10.1016/j.molp.2018.06.001

Assemblies in FASTA format

MSYJ.fa.tar.gz (Pseudomolecule Sequences)

Annotation files

MSYJ.gene.models.gff3.tar.gz (Gene annotation in GFF3 format)
MSYJ.gene.fa.tar.gz (Nucleotide sequences of all genes)
MSYJ.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
MSYJ.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
MSYJ.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of Pummelo (Citrus grandis) Status: high quality, version1

Cite:Xia Wang#, Yuantao Xu#, Siqi Zhang#, Li Cao# et al. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nature Genetics, 2017, doi:10.1038/ng.3839

Assemblies in FASTA format

HWB.chromosome.fa.tar.gz (Pseudomolecule Sequences)
HWB.scaffold.fa.tar.gz (Superscaffold Sequences)

Annotation files

HWB.gene.models.gff3.tar.gz (Gene annotation in GFF3 format)
HWB.gene.fa.tar.gz (Nucleotide sequences of all genes)
HWB.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
HWB.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
HWB.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of Papeda (Citrus ichangensis) Status: draft, version1

Assemblies in FASTA format

XJC.scaffold.fa.tar.gz (Superscaffold Sequences)

Annotation files

XJC.gene.models.gff3.tar.gz (Gene annotation in GFF3 format)
XJC.gene.fa.tar.gz (Nucleotide sequences of all genes)
XJC.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
XJC.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
XJC.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of Citron (Citrus medica) Status: draft, version1

Assemblies in FASTA format

XZ.scaffold.fa.tar.gz (Superscaffold Sequences)

Annotation files

XZ.gene.models.gff3.tar.gz (Gene annotation in GFF3 format)
XZ.gene.fa.tar.gz (Nucleotide sequences of all genes)
XZ.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
XZ.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
XZ.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of Chinese Box Orange, a primitive citrus (Atlantia buxifolia) Status: draft, version1

Assemblies in FASTA format

HKC.scaffold.fa.tar.gz (Superscaffold Sequences)

Annotation files

HKC.gene.models.gff3.tar.gz (Gene annotation in GFF3 format)
HKC.gene.fa.tar.gz (Nucleotide sequences of all genes)
HKC.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
HKC.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
HKC.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome of Sweet Orange (Citrus sinensis) Status: draft, version2

Cite:Qiang Xu#, Ling-Ling Chen#, Xiaoan Ruan#, Di-Jun Chen, Andan Zhu, et al. The draft genome of sweet orange (Citrus sinensis). Nat Genet. 2013 45(1):59-66.

Assemblies in FASTA format

csi.chromosome.fa.tar.gz (Pseudomolecule Sequences)
csi.chromosome.masked.fa.tar.gz (Pseudomolecule Sequences, RepeatMasked)
csi.scaffold.fa.tar.gz (Superscaffold Sequences)
csi.scaffold.masked.fa.tar.gz (Superscaffold Sequences, RepeatMasked)

Genome Annotation of Citrus sinensis

csi.gene.models.gff3.tar.gz (Gene annotation in GFF3 format)
csi.gene.fa.tar.gz (Nucleotide sequences of all genes)
csi.CDS.fa.tar.gz (Nucleotide sequences of coding sequences, i.e. no introns and no UTRs)
csi.cDNA.fa.tar.gz (Nucleotide sequences of all transcript sequences, UTRs+CDS)
csi.exon.fa.tar.gz (Nucleotide sequences of all exon sequences)
csi.intron.fa.tar.gz (Nucleotide sequences of all intron sequences)
csi.peptide.fa.tar.gz (Amino acid sequences corresponding to all gene coding sequences)

Genome Resequencing Data

mandarin1.tar.bz2 (Mandarin1 Resequencing Data)
mandarin2.tar.bz2 (Mandarin2 Resequencing Data)
mandarin3.tar.bz2 (Mandarin3 Resequencing Data)
pummelo1.tar.bz2 (Pummelo1 Resequencing Data)
pummelo2.tar.bz2 (Pummelo2 Resequencing Data)
pummelo3.tar.bz2 (Pummelo3 Resequencing Data)

These data may contain errors, we keep continuous update on the genome version in future. We request that you notify us if use our data for genomic analysis so that we can provide you the most recently annotated yet not-open version. If any problem on the usage of these data, please contact Dr. Qiang Xu at xuqiang@mail.hzau.edu.cn and Huang Yue at yilunhuangyue@webmail.hzau.edu.cn.

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