Colinearity and its exceptions in orthologous adh regions of maize and sorghum

Abstract

Orthologous adh regions of the sorghum and maize genomes were sequenced and analyzed. Nine known or candidate genes, including adh1, were found in a 225-kilobase (kb) maize sequence. In a 78-kb space of sorghum, the nine homologues of the maize genes were identified in a colinear order, plus five additional genes. The major fraction of DNA in maize, occupying 166 kb (74%), is represented by 22 long terminal repeat (LTR) retrotransposons. About 6% of the sequence belongs to 33 miniature inverted-repeat transposable elements (MITEs), remnants of DNA transposons, 4 simple sequence repeats, and low-copy-number DNAs of unknown origin. In contrast, no LTR retroelements were detected in the orthologous sorghum region. The unconserved sorghum DNA is composed of 20 putative MITEs, transposon-like elements, 5 simple sequence repeats, and low-copy-number DNAs of unknown origin. No MITEs were discovered in the 166 kb of DNA occupied by the maize LTR retrotransposons. In both species, MITEs were found in the space between genes and inside introns, indicating specific insertion and/or retention for these elements. Two adjacent sorghum genes, including one gene missing in maize, had colinear homologues on Arabidopsis chromosome IV, suggesting two rearrangements in the sorghum and three in the maize genome in comparison to a four-gene region of Arabidopsis. Hence, multiple small rearrangements may be present even in largely colinear genomic regions. These studies revealed a much higher degree of diversity at a microstructural level than predicted by genetic mapping studies for closely related grass species, as well as for comparisons of monocots and dicots.

Figure 1

Schematic representation of the structures of orthologous adh regions in maize and sorghum. The upper bar represents sorghum BAC 110K5. Putative genes are numbered by the order of their appearance on the contig, and the putative exons/introns are shown by boxes and connecting lines, respectively. The open triangles mark the end and the direction of transcription for the established cases. The red diamonds show the location and the size of MITEs and other transposon-like elements. The genes shown in blue are genes, lying among orthologous genes but missing from the maize contig. The stars reflect the location of simple repetitive DNAs. The composition of the maize region, derived from YAC 334B7, is shown below. Putative genes, exon/introns, and inserted small elements are marked as above. The purple triangles show the location, the size, and the orientation of transcription of the putative LINEs. The triangles show the location and sites of insertion of the retroelement blocks, and the numbers indicate the block sizes. The shaded regions connecting the maize and the sorghum contigs outline the regions of sequence homology between the two species. The lighter strips within correspond to stretches of interrupted homology, usually associated with insertion of small mobile elements. Both contigs are shown in scale.

Figure 2

dotplot homology comparisons for the colinear maize and sorghum regions. The location of the high- and middle-copy-number retroelement blocks is shown by the shaded and dotted boxes, respectively. The open boxes with the arrows show the putative maize genes identified on the contig. On the vertical line, the sorghum BAC is shown. The diagonals, reflecting homologous regions, coincide with the regions taken by genes. The sorghum genes 110K5.5, 110K5.8, and 110K5.9 missing from maize are shown by lighter arrows on the sorghum BAC.

Figure 3

A simplified schematic comparison between the contigs of maize (YAC 334B7), sorghum (BAC 110K5), and Arabidopsis (BAC T10M13). The arrows show the location and the orientation of the putative genes. The shaded regions outline the regions of colinearity between the three species.