DOI: 10.5281/zenodo.17014036
title: Data from: Haplotype-resolved genome of Citrus × sinensis 'Pera Rio', Brazil's most widely cultivated sweet orange

description: README – Citrus × sinensis ‘Pera IAC’ (Pera-Rio) Genome Resources

This dataset contains the haplotype-resolved genome assemblies, organellar genomes, and comprehensive annotations of Citrus × sinensis ‘Pera IAC’ (Pera-Rio), Brazil’s most widely cultivated sweet orange and a key cultivar in the global orange juice industry.

The assemblies were generated using PacBio Revio HiFi long reads and Arima Hi-C scaffolding, producing chromosome-scale haplotypes representing the parental progenitors (C. maxima and C. reticulata).

The Zenodo record includes:





Genome assemblies: hapA and hapB nuclear assemblies, plastid genome (ptDNA), and mitochondrial genome (mtDNA).




Annotation files:





Structural annotation (GFF3) of predicted genes, CDSs, transcripts, and proteins.




Functional annotation (GO, KEGG, Pfam, CAZy, TFs, resistance gene catalogs).




Transposable element (TE) annotation and classification (GFF3 and FASTA) generated with EDTA-GUI in AnnoTEP mode.






Gene family classification: duplication categories (WGD, tandem, proximal, transposed, dispersed), retrocopies, and small-scale duplicates.


Validation metrics and summary tables: BUSCO, LAI, Inspector, Merqury, and assembly statistics.


Raw sequencing reads (PacBio HiFi and Illumina Hi-C) are not included here due to size and are deposited in the NCBI SRA under BioProject PRJNA1301450.

All files are provided in community-standard formats (FASTA, GFF3, and etc) to maximize reusability and interoperability. This curated dataset complements ongoing citrus pangenome initiatives and supports allele-aware analyses, comparative genomics, and breeding for disease resistance and fruit quality.

 

Files Description (see the README.txt):

Genome Assemblies





Csinensis_perario.fasta.gzPrimary haplotype-phased nuclear genome assembly in FASTA format.




Csinensis_perario-Softmasked.fasta.gzNuclear genome assembly with repetitive regions soft-masked (lowercase letters). Useful for gene prediction and downstream analyses.




mtDNA.fasta.gzComplete mitochondrial genome sequence.




ptDNA.fasta.gzComplete plastid (chloroplast) genome sequence.



Annotation Files





Cs-Annotation-HQ.gff3.gzHigh-quality gene annotation in GFF3 format.




Cs-Annotation-HQ.prot.gzPredicted protein sequences from annotated genes (FASTA).




Cs-Annotation-HQ.CDS.gzCoding sequences (CDS) in nucleotide FASTA format.




Cs-Annotation-HQ.cDNA.gzTranscript (cDNA) sequences in nucleotide FASTA format.




Cs-Annotation-HQ.gene.gzGene-level annotation summary in tabular format.




Cs-Annotation.tRNA.gff3.gz / Cs-Annotation.tRNA.gff3Transfer RNA (tRNA) annotation.




Cs-Annotation.rRNA.gff3Ribosomal RNA (rRNA) annotation.




Cs-NoAnnotation.gff3Regions of the genome lacking annotation (intergenic/unassigned).



Organelle Annotation





Pera_mtDNA.gbkGenBank-format annotated mitochondrial genome.




Pera_ptDNA.gbkGenBank-format annotated plastid genome.




mtDNA.tbl / ptDNA.tblAnnotation tables for mitochondrial and plastid genomes.



Repeats and Transposable Elements





Csinensis.fa.mod.cat.gzConcatenated repeat-masked genome file produced by EDTA/RepeatMasker.




Csinensis.fa.mod.filtered.cat.gzFiltered repeat-masked genome.




Csinensis.fa.mod.filtered.align.gzAlignment file containing filtered repeat annotations.




Csinensis.fa.mod.EDTA.TEanno.gff3.gzTransposable element annotation in GFF3 format.




Csinensis.fa.mod.EDTA.TEanno.sum.gzSummary of TE annotation results.




Csinensis.fa.mod.EDTA.intact.raw.gff3.gzPutative intact/full-length TE annotations.




Csinensis.fa.mod.EDTA.TElib.fa.gzCustom transposable element library (FASTA).




Csinensis.fa.mod.LAI.gzLTR Assembly Index (LAI) statistics for assembly quality assessment.




TEs-report-lite.tbl / TEs-report-complete.tblTabular reports summarizing TE annotation.



Functional Annotation and Biosynthetic Clusters





Cs-plantiSMASH-v1.zipPredicted secondary metabolite biosynthetic gene clusters identified by antiSMASH/plantiSMASH.



Structural Features





Cs-Telomers.telo.infoTelomeric repeat locations.




Cs-centromers.infoCentromere locations.




Cs-Idiogram.pngIdiogram image of C. sinensis ‘Pera Rio’ chromosomes.



Assembly and Anbnotation Statistics





hp1-stats.txt / hp2-stats.txtAssembly statistics (e.g., N50, contig counts, genome size) for haplotype 1 and haplotype 2 assemblies.