Citrus sinensis Genome


The Citrus sinensis v1.1 (Sweet orange) assembly and the following text comes from JGI Phytozome


Sweet orange (citrus, Citrus sinensis) represents the largest citrus cultivar group grown in the world, accounting for about 70% of the total. Brazil, Florida (USA), and China are the three largest sweet orange producers. Sweet orange is considered an introgression of a natural hybrid of mandarin and pummelo.
The goal of the Citrus Genome Project is to generate a draft sequence of the sweet orange genome using Next Generation (454) sequence generated by 454 Life Sciences (team headed by Chinnappa Kodira), University of Florida (team headed by Fred Gmitter) as well as Sanger sequence generated by JGI (team led by Daniel Rokhsar). EST sequence has been generated by JGI, University of Florida, and 454 Life Sciences. There is a separate deep Sanger sequencing project by the International Citrus Genome Consortium of a haploid derived from Clementine mandarin.
Assembly details 


Genome Size

This version (v.1) of the assembly is 319 Mb spread over 12,574 scaffolds. Half the genome is accounted for by 236 scaffolds 251 kb or longer.


The current gene set (orange1.1) integrates 3.8 million ESTs with homology and ab initio -based gene predictions (see below). 25,376 protein-coding loci have been predicted, each with a primary transcript. An additional 20,771 alternative transcripts have been predicted, generating a total of 46,147 transcripts. 16,318 primary transcripts have EST support over at least 50% of their length. Two-fifths of the primary transcripts (10,813) have EST support over 100% of their length.

Sequencing, Assembly, and Annotation

Whole genome sequencing strategy

Genomic sequence was generated using a whole genome shotgun approach with 2Gb sequence coming from GS FLX Titanium; 2.4 Gb from FLX Standard; 440 Mb from Sanger paired-end libraries; 2.0 Gb from 454 paired-end libraries

How was the assembly generated?

The 25.5 million 454 reads and 623k Sanger sequence reads were generated by a collaborative effort by 454 Life Sciences, University of Florida and JGI. The assembly was generated by Brian Desany at 454 Life Sciences using the Newbler assembler.

Reference Publication

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., Nature biotechnology. 2014 Jul; 32 7 656-62

Data sets 
The genome assembly, pseudomolecules, annotations and genome browser are available through the links below.
Bulk Datasets (via Phytozome) Genome browser
BLAST Pathways