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International Citrus Genomics Consortium Sequences Sweet Orange, Mandarin Genomes

By Andrea Anderson

SAN DIEGO (GenomeWeb News) – At the annual Plant and Animal Genome conference here this weekend, members of the International Citrus Genomics Consortium announced that they have finished sequencing and assembling the diploid genome of the sweet orange and the haploid genome of the Clementine mandarin.

Genome sequencing has been a "longtime goal for those of us in the citrus community," Fred Gmitter, University of Florida citrus geneticist and International Citrus Genomics Consortium chair, said during a presentation at the citrus genomic workshop this weekend.

The International Citrus Genomics Consortium was established in Spain in 2003, he explained, with an eye toward developing genomic tools for citrus research as well as creating opportunities for those in the citrus research community to come together as part of a larger organization.

Along with genome sequencing itself, the team has been working on developing and bringing together related resources, such as a global EST database, physical and high density genetic linkage maps, and bioinformatics tools.

For the sweet orange sequencing project, which was spearheaded by researchers at the US Department of Energy's Joint Genome Institute, the University of Florida, the Georgia Institute of Technology, and 454 Life Sciences, the team used the Roche 454 GS FLX and FLX Titanium platforms to tackle the 320 million base genome of the Ridge Pineapple sweet orange, Citrus sinensis.

They then incorporated 1.2 times genome sequence generated by Sanger sequencing to get a total of nearly 31 times genome coverage.

In addition, the team used Roche 454 sequencing to generate transcriptome data for mature sweet orange leaves and for seedlings exposed to different conditions.

"Mapping the transcript sequence reads from the different conditions to the draft genome assembly will be critical for inferring the pattern of gene expression in sweet orange in response to these different stressors, which were selected due to their relevance to plant breeders seeking to address industry needs," Gmitter said in a statement.

Moreover, transcriptome data is being used to assist in gene prediction, gene modeling, and identification of alternative transcripts. For instance, Gmitter noted, transcriptome and other data suggests the sweet orange genome contains nearly 24,000 protein-coding loci and codes for more than 46,000 transcripts overall.

Meanwhile, researchers from Genoscope in France, JGI, the Institute of Genomic Applications in Italy, HudsonAlpha, and Spain's Lifesequencing used the Sanger approach to sequence the 296 million base genome of the Clementine mandarin to about 6.3 times coverage.

The current iteration of the Clementine genome, nicknamed "version 0.9," represents a preliminary annotation and assembly, Gmitter explained. Researchers hope to release a more fully annotated genome assembly sometime this summer.

Data from the sweet orange and mandarin genome projects are being made available to other members of the research community through the DOE JGI and Center for Integrative Genomes' public database Phytozome.net.