Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes

Colinearity of a large region from barley (Hordeum vulgare) chromosome 5H a nd rice (Oryza sativa) chromosome 3 has been demonstrated by mapping of sev eral common restriction fragment-length polymorphism clones on both regions . One of these clones, WG644,was hybridized to rice and barley bacterial ar tificial chromosome (BAC) libraries to select homologous clones. One BAC fr om each species with the largest overlapping segment was selected by finger printing and blot hybridization with three additional restriction fragment- length polymorphism clones. The complete barley BAC 635P2 and a SO-kb segme nt of the rice BAC 3615 were completely sequenced. A comparison of the rico and barley DNA sequences revealed the presence of four conserved regions, containing four predicted genes. The four genes are in the same orientation in rice, but the second gene is in inverted orientation in barley. The fou rth gene is duplicated in tandem in barley but not in rice. Comparison of t he homeologous barley and rice sequences assisted the gene identification p rocess and helped determine individual gene structures. General gene struct ure (exon number, size, and location) was largely conserved between rice an d barley and to a lesser extent with homologous genes in Arahidoysis. Colin earity; of these four genes is not conserved in Arabidopsis compared with t he two grass species. Extensive similarity was not found between the rice a nd barley sequences other than within the exons of the structural genes, an d short stretches of homology in the promoters and 3 ' untranslated regions . The larger distances between the first three genes in barley compared wit h rice are explained by the insertion of different transposable retroelemen ts.