Next-Gen Sequencing of the Sweet Orange Genome: Challenges and Outcomes

The International Citrus Genome Consortium (ICGC) has organized a collaborative effort, currently underway, to sequence the genome of a haploid line derived from ‘Clementine’ mandarin, using primarily Sanger technology.  In parallel to and as an additional contribution to the ICGC efforts, the genome of heterozygous sweet orange (2n=2x=18; ~380Mb), the most economically important citrus cultivar group represented by the ‘Ridge Pineapple’ genome, is being sequenced jointly by Roche/454 and the University of Florida-ICBR Genome Sequencing Center using 454 technology.  Currently, a combination of whole genome shotgun sequencing (WGS) and paired end sequencing of several large insert libraries using FLX and Titanium platforms, has produced nearly 30X sequence coverage; another 1.2X WGS Sanger coverage produced from ‘Ridge Pineapple’ previously by USDOE-Joint Genome Institute was also included in the cumulative reads.  Several rounds of assembly followed using the Newbler assembly platform, finally resulting in an assembly that is amenable to gene modeling and prediction, to be followed by annotation.  The current status of the project in July 2010, including progress in assembly, gene prediction and annotation, will be presented.  Additionally, the underlying motivation for the Florida citrus industry’s decision to partially support both of these genome sequencing projects will be discussed, as that will highlight the first priority applications of the information to benefit citrus growers in their battle against serious diseases which threaten their continued existence.