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

Orthologous adh regions of the sorghum and maize genomes were sequenced and analyzed. Nine known or candidate genes, including adh1, were found in a 2 25-kilobase (kb) maize sequence. In a 78-kb space of sorghum, the nine homo logues of the maize genes were identified in a colinear order, plus five ad ditional 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 elem ents (MITEs), remnants of DNA transposons, 4 simple sequence repeats, and l ow-copy-number DNAs of unknown origin. In contrast, no LTR retroelements we re detected in the orthologous sorghum region. The unconserved sorghum DNA is composed of 20 putative MITEs, transposon-like elements, 5 simple sequen ce repeats, and low-copy-number DNAs of unknown origin. No MITEs were disco vered in the 166 kb of DNA occupied by the maize LTR retrotransposons. In b oth species, MITEs were found in the space between genes and inside introns , indicating specific insertion and/or retention for these elements. Two ad jacent sorghum genes, including one gene missing in maize, had colinear hom ologues an Arabidopsis chromosome IV, suggesting two rearrangements in the sorghum and three in the maize genome in comparison to a four-gene region o f Arabidopsis. Hence, multiple small rearrangements may be present even in largely colinear genomic regions. These studies revealed a much higher degr ee of diversity at a microstructural level than predicted by genetic mappin g studies for closely related grass species, as well as for comparisons of monocots and dicots.