Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
Chunxian Chen , Young A Choi , Allan D. Burrage , Jaya R. Soneji , Madhugiri N. Rao , Shu Huang , Fred G. Gmitter Jr.
Three freely available computer programs have been used to align two assemblies of citrus unigenes into five Arabidopsis and twelve rice chromosome sequences. One assembly, Citrus sinensis UniGene Build #5 at the NCBI, contains 8786 sweet orange unigenes (Designated Cs5). Another assembly, C28 of HarvEST-Citrus EST database developed by Tim Close at UC Riverside, contains 49355 unigenes from all Citrus and the related species (Designated HC28). Five Arabidopsis chromosome sequences, as well as all contigs and gaps of 12 rice chromosomes (about 93% done), were downloaded from the NCBI. A general Java program, AssembleChrSeq, was developed to build 12 rice chromosome sequences by assembling the contigs and the assumed gaps among the contigs (using "N" as a gap base). The gaps can be optionally excluded or included in the make-up of chromosome sequences by the program. A total of 3952 hits were found from Cs5 and 13693 hits from HC28 on 5 Arabidopsis chromosomes by one alignment program, in which the E value was set to 1.0E-7. Another Java program, AlignmentView, to determine/classify the unique hits and to compare/display the aligning information on each chromosome in a graphic view, is being developed. These physical alignment results of citrus unigenes on known Arabidopsis and rice chromosomes can not only provide an overall comparative view on and understanding of the entire citrus genome, but also a useful guide to facilitate and hasten the citrus mapping process.