ARS | Publication request: A SYNTENIC STUDY BETWEEN COTTON AND ARABIDOPSIS USING INTEGRATED PHYSICAL MAPS AND CONSERVED ORTHOLOG MARKERS

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: December 15, 2004
Publication Date: January 15, 2005
Citation: Xu, Z., Kohel, R.J., Dong, J., Zhang, H., Stelly, D.M., Covaleda, L., Koo, P., Yu, J. 2005. A syntenic study between cotton and Arabidopsis using integrated physical maps and conserved ortholog markers [abstract]. Plant and Animal Genome XIII Conference. p. 135.

Technical Abstract: Arabidopsis genome is well studied and its genomic information widely used to understand other plant genomes. Cotton and Arabidopsis have very close evolutionary relation based on previous reports. The objective of this research was to investigate the level of genome-wide synteny between cotton and Arabidopsis by use of both cotton integrated contig maps and Conserved Orthologs Set (COS) sequences developed at Cornell. Fifty-two large contigs (two contigs/cotton chromosome) were chosen from 5,466-contig (100,000 BAC clones) map. Sequences of 1,152 BAC-ends were generated from all 576 clones. A- and D- subgenomes of 576 clones were separated by use of subgenome-specific probes and synteny between A-Arabidopsis and D-Arabidopsis was compared. In total, 1,685 fiber ESTs, 163 disease resistance ESTs, 300 SSR markers, and 36 repetitive elements were located in the 52 contigs. While the results indicated a low level of synteny between cotton and Arabidopsis when the direct sequences were blasted against Arabidopsis whole genome sequence by Blastn, but they indicated a high level of synteny between the two species when EST sequences were used to blast Arabidopsis database by tBlastx. When COS sequences were used to blast cotton ESTs, there was a very high level of synteny between cotton and Arabidopsis, with most of them being single or low-copy in cotton. Comparative genomic analyses between cotton and Arabidopsis could facilitate cross-utilization of genetic resources and tools of both species and could shed light on evolutionary events associated with the divergence of their seemingly disparate genomes.