A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes

Abstract

The sequences of large insert clones containing genomic DNA that is orthologous to the maize adh1 region were obtained for sorghum, rice, and the adh1-homoeologous region of maize, a remnant of the tetraploid history of the Zea lineage. By using all four genomes, it was possible to describe the nature, timing, and lineages of most of the genic rearrangements that have differentiated this chromosome segment over the last 60 million years. The rice genome has been the most stable, sharing 11 orthologous genes with sorghum and exhibiting only one tandem duplication of a gene in this region. The lineage that gave rise to sorghum and maize acquired a two-gene insertion (containing the adh locus), whereas sorghum received two additional gene insertions after its divergence from a common ancestor with maize. The two homoeologous regions of maize have been particularly unstable, with complete or partial deletion of three genes from one segment and four genes from the other segment. As a result, the region now contains only one duplicated locus compared with the eight original loci that were present in each diploid progenitor. Deletion of these maize genes did not remove both copies of any locus. This study suggests that grass genomes are generally unstable in local genome organization and gene content, but that some lineages are much more unstable than others. Maize, probably because of its polyploid origin, has exhibited extensive gene loss so that it is now approaching a diploid state.

Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean

“…Furthermore, many paralogous genes generated by the recent WGD event have been retained within pairs (Supplemental Table S3). This observation contrasts with what has been found in studies of the maize (Zea mays) genome; the maize genome lost approximately half of its duplicated genes in nearly the same period of time (approximately 11.9 million years; Ilic et al, 2003;Lai et al, 2004;Messing et al, 2004). Several studies have suggested that the highly duplicated structure of the soybean genome reflects slow and incomplete diploidization in soybean (Schlueter et al, , 2007bShin et al, 2008).…”

Gene movement by Helitron transposons contributes to the haplotype variability of maize

“…maize genome to another. Hence, differences between allelic haplotypes do not appear to have the same basis as the differences between homeologous regions of the maize genome examined to date, which clearly originated by deletion (23)(24)(25). Since its paleotetraploid origin (26,27), maize has been undergoing extensive gene loss as it approaches a diploid state.…”

“…Since its paleotetraploid origin (26,27), maize has been undergoing extensive gene loss as it approaches a diploid state. In most cases, entire genes have been deleted, although partial gene deletions have been documented (23). The gene loss or fractionation of the duplicated regions has been extensive.…”

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

“…However, the major mechanism for DNA removal involves small deletions associated with illegitimate recombination (Devos et al, 2002), which has been shown to remove hundreds of megabases of LTR retrotransposon DNA in as little as 2 million years . This process acts across the entire genome (including in those genes lost in the fractionation process; Ilic et al, 2003), leaving highly degenerate legacies of earlier genome constituents that are peppered with small deletions and thus become unrecognizable within a few million years. Hence, any TEs observed in a grass genome must have been active in the last 5-10 million years, or much more recently, or they would no longer be detectable.…”