Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Analysis Of A 1.2x Whole Genome Sequence Of Citrus sinensis

Mikeal L. Roose¹ , Randall P. Niedz² , Fredrick G. Gmitter³ , Timothy J. Close¹ , Abhaya M. Dandekar⁴ , Jan-Fang Cheng⁵ , Daniel S. Rokhsar⁵

¹  Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

²  US Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA

³  Citrus Research and Extension Center, University of Florida, Lake Alfred, FL 33850, USA

⁴  Department of Plant Sciences, University of California, Davis, CA 95616, USA

⁵  U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA

The Joint Genome Institute produced a low coverage (ca 1.2X) whole-genome shotgun sequence of Citrus sinensis (sweet orange) by sequencing ends of about 126,000 fosmid clones containing 40 kb inserts and 257,000 plasmid clones containing 8 kb inserts. Total sequence coverage was about 473 Mb of q20 sequence. A preliminary analysis of this sequence will be described including contigs, linkage to public EST sequence, repeat content, and automated annotation. Problems in assembling sequences from the heterozygous sweet orange were analyzed by comparison of “blind” and “haplotype-known” assemblies of BAC clones from six regions, where each clone was assigned to a haplotype based on SSR alleles. Alignment of contigs to Arabidopsis sequence will be used to illustrate synteny. Prospects for merging linkage maps, BAC physical maps, and the sequence contigs will be discussed.