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 and͞or 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.The grasses belong to a family of monocotyledonous angiosperms that are well differentiated morphologically from the other angiosperm families and have a single (monophyletic) origin. Their genome sizes, however, may vary a great deal between species. Thus, rice has an estimated genome size of 430 megabases, which is Ϸ11ϫ smaller than barley, 6ϫ smaller than maize, and 2ϫ smaller than sorghum. These large differences in genome sizes, coupled with differences in the degree and the nature of their investigations, have obscured some common features of grass genomic design. Recent studies comparing high-density linkage maps with DNA markers revealed extensive synteny of chromosomal segments between related species (1-5). Valuable as it is, full genome recombinational mapping of DNA markers is not an efficient approach for detecting small rearrangements. Because the available high-resolution maps based on completed nucleotide sequence are largely restricted to individual genes and their proximal neighborhoods, we are left with two obvious questions that cannot be answered at a full-genome level of analysis. These questions are, will the colinearity observed at the 2-to 20-centimorgan level, the sensitivity level of standard recombinational mapping, be preserved or will it break down at a local level (5), and what will the pattern of gene distribution be, relative to the no...

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

“…The divergence within this family is higher than within any of the major families of maize. Many of the retroelements described previously and characterized in maize did not appear to be major components of the maize genome; such was the case for Hopscotch (White et al 1994), Stoner (Marillonnet andWessler 1998), Magellan, Reina, Fourf, Kake, Victim, andMilt (SanMiguel et al 1996;Tikhonov et al 1999). A repetitive sequence that represents 0.14% of the genome had a 95% probability of being found in our sample of 2157 sequences.…”

“…Additionally, clustered retrotransposon regions should be expected given the finding that retroelements preferentially insert into existing retroelements (San Miguel et al 1996;Suoniemi et al 1997). On the other hand, Tikhonov et al (1999), Chen et al (1998), and Llaca and Messing (1998) sequenced syntenic regions of rice, sorghum, and maize (Adh-1, Sh1-a2, zein genes) and demonstrated genome expansion by retrotransposon insertion into intergenic spaces. Based on the distribution of the most abundant repeats in BAC clones and on the correlation observed between the size of the BACs and the number of different repetitive elements, we conclude that repeats are, in general, randomly distributed in the genome.…”

“…For further identification of genic sequences, we compared the sequences with the DuPont EST database, which contained more than one million plant EST sequences at the time of the analysis. The cne1g library was compared with full-length DNA sequences of retroelements isolated from the Adh-1 region (SanMiguel et al 1996;Tikhonov et al 1999). The cne1g sequences were also compared with one another in a low stringency sequence assembly; sequences with >80% identity over 100 bp were classified as related.…”

Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum)

“…Large-insert libraries are useful for gene positional cloning strategies (Tanksley et al 1995), for genome structure analysis (Chen and Foolad 1997;Panstruga et al 1998;SanMiguel et al 2002), for genome organization comparisons between related species Tikhonov et al 1999;Dubcovsky et al 2001) and for map saturation with molecular markers and microsatellite discovery in targeted regions (Cregan et al 1999).…”

Genetic Mapping in Cotton

“…During the last couple of years, major emphasis of genomic research is on comparative analyses of closely related, homoeologous stretch of genomic sequence in plants i.e., maize, rice, and sorghum [21][22][23]. Cultivated upland cotton has a history of genetic bottlenecks in evolution that have significantly reduced the extent of genetic diversity of the cultivated cotton species, which compelled geneticists to use populations developed by hybridizing two different species for identifying high number of polymorphisms.…”