| Analysis Name | Citrus clementina JGI v1.0 Assembly & Annotation |
| Sequencing technology | whole genome shotgun sequencing |
| Assembly method | Arachne |
| Release Date | 2012-12-20 |
Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol. 2014 Jul;32(7):656-62. doi: 10.1038/nbt.2906.
AbstractCultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
Assembly statistics
| Assembly Source: | JGI |
| Assembly Version: | v1 |
| Annotation Source: | JGI |
| Annotation Version: | v1.0 |
| Total Scaffold Length (bp): | 301,386,998 |
| Number of Scaffolds: | 1,398 |
| Min. Number of Scaffolds containing half of assembly (L50): | 4 |
| Shortest Scaffold from L50 set (N50): | 31,410,901 |
| Total Contig Length (bp): | 295,168,965 |
| Number of Contigs: | 8,692 |
| Min. Number of Contigs containing half of assembly (L50): | 712 |
| Shortest Contig from L50 set (N50): | 118,875 |
| Number of Protein-coding Transcripts: | 33,929 |
| Number of Protein-coding Genes: | 24,533 |
| Percentage of Eukaryote BUSCO Genes: | 96.7 |
| Percentage of Embroyphyte BUSCO Genes: | 94.6 |
The Citrus clementina JGI v1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Cclementina_182_v1.fa.gz |
The Citrus clementina JGI v1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Cclementina_182_v1.0.gene_exons.gff3.gz |
| CDS sequences (FASTA file) | Cclementina_182_v1.0.cds.fa.gz |
| Protein sequences (FASTA file) | Cclementina_182_v1.0.protein.fa.gz |
Functional annotation for the Citrus clementina JGI v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Citrus_clementina_JGI_v1.0.Pfam.tsv.gz |
Citrus S genes Nucleotide
Citrus S genes Protein