Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes

Abstract

Colinearity of a large region from barley (Hordeum vulgare) chromosome 5H and rice (Oryza sativa) chromosome 3 has been demonstrated by mapping of several common restriction fragment-length polymorphism clones on both regions. One of these clones, WG644, was hybridized to rice and barley bacterial artificial chromosome (BAC) libraries to select homologous clones. One BAC from each species with the largest overlapping segment was selected by fingerprinting and blot hybridization with three additional restriction fragment-length polymorphism clones. The complete barley BAC 635P2 and a 50-kb segment of the rice BAC 36I5 were completely sequenced. A comparison of the rice 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 fourth gene is duplicated in tandem in barley but not in rice. Comparison of the homeologous barley and rice sequences assisted the gene identification process and helped determine individual gene structures. General gene structure (exon number, size, and location) was largely conserved between rice and barley and to a lesser extent with homologous genes in Arabidopsis. Colinearity of these four genes is not conserved in Arabidopsis compared with the two grass species. Extensive similarity was not found between the rice and barley sequences other than within the exons of the structural genes, and short stretches of homology in the promoters and 3' untranslated regions. The larger distances between the first three genes in barley compared with rice are explained by the insertion of different transposable retroelements.

Figure 1

Sequence comparison of barley BAC 635P2 with the first 50 kb of rice BAC 36I5 using the program Dotter (word 25, similarity 80). The location of genes and large transposable elements in rice (vertical) and barley (horizontal) are indicated by arrows and boxes, respectively. A more detailed annotation is presented in Figure 2.

Figure 2

Organization of repetitive and conserved sequences in barley BAC 635P2 and the first 50 kb of rice BAC36I5. Genes are represented by arrows, transposable elements by boxes, and MITEs by triangles. Ta and Tb, Copia-like retrotransposon; Tc, non-LTR retroelement; Td, terminal-inverted repeat element; Te and Tf, nested BARE-1 retrotransposons; Tg, MuDR-like element; Th, Copia-like retrotransposon; Ti, nonautonomous Mutator element. SSRs with eight or more repeats are indicated by an asterisk.

Figure 3

Structure of the genes found in the regions conserved between rice BAC 36I5 and barley BAC 635P2 and the closest Arabidopsis homologues (Table I). Exons (boxes) and introns (lines) are proportional to their length. Exons of identical length in the three species are indicated in black and those of identical length in rice and barley in black with white diagonal lines.