Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am

Abstract

Sequencing of a contiguous 215-kb interval of Triticum monococcum showed the presence of five genes in the same order as in previously sequenced colinear barley and rice BACs. Gene 2 was in the same orientation in wheat and rice but inverted in barley. Gene density in this region was 1 gene per 43 kb and the ratio of physical to genetic distance was estimated to be 2,700 kb cM -1 . Twenty more-or-less intact retrotransposons were found in the intergenic regions, covering at least 70% of the sequenced region. The insertion times of 11 retrotransposons were less than 5 million years ago and were consistent with their nested structure. Five new families of retroelements and the first full-length elements for two additional retrotransposon families were discovered in this region. Significantly higher values of GC content were observed for Triticeae BACs compared with rice BACs. Relative enrichment or depletion of certain dinucleotides was observed in the comparison of introns, exons and retrotransposons. A higher proportion of transitions in CG and CNG sites that are targets for cytosine methylation was observed in retrotransposons (76%) than in introns (37%). These results showed that the wheat genome is a complex mixture of different sequence elements, but with general patterns of content and interspersion that are similar to those seen in maize and barley.

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

“…This result agreed with previous observations for T. tauschii (Moullet et al 1999) and other monocot species (Woo et al 1994;Zhang et al 1996;Tomkins et al 1999) that suggested a higher frequency of NotI restriction sites relative to dicot species. This result was also expected based on the higher GC content of the wheat genome (45.7%; SanMiguel et al 2002) and the GCGGCCGC recognition sequence of NotI.…”

“…3 Assignment of Langdon (LDN) BAC clones selected with the HMW-glutenin probe to the A or B genome using chromosome substitution lines Langdon 1D(1A) and Langdon 1D(1B). Genomic DNA and BAC clones were digested with the restriction enzyme TaqI requirement for chromosome walking in wheat because large regions of repetitive elements are present, even in gene-rich regions (SanMiguel et al 2002). The average insert size of this library (131 kb) was larger than the average insert size of previous published Triticeae BAC libraries (T. tauschii, 119 kb; T. monococcum, 115 kb; H. vulgare, 106 kb) and the proportion of clones with cpDNA or no inserts was reduced to very low levels (<2%).…”

“…The A and B genomes diverged approximately 2.5-4.5 million years ago (Huang et al 2002), providing a long period of time for divergence. Dating of 11 retrotransposon insertions in a 215-kb region of T. monococcum (SanMiguel et al 2002) showed that all of them were inserted during the last 4.5 million years and that more than half of them were inserted in the last 2.5 million years, after the divergence of the A and B genome diploid species. In addition, an active process of deletion of repetitive elements was detected in the intergenic regions, leading to an almost complete differentiation of the colinear intergenic regions from wheat and barley after 10-15 million years of divergence (SanMiguel et al 2002).…”

“…Dating of 11 retrotransposon insertions in a 215-kb region of T. monococcum (SanMiguel et al 2002) showed that all of them were inserted during the last 4.5 million years and that more than half of them were inserted in the last 2.5 million years, after the divergence of the A and B genome diploid species. In addition, an active process of deletion of repetitive elements was detected in the intergenic regions, leading to an almost complete differentiation of the colinear intergenic regions from wheat and barley after 10-15 million years of divergence (SanMiguel et al 2002). The divergence of the A-genome species, T. monococcum (A m ) and T. urartu (A), occurred more recently (approximately 0.5-1 million years; Huang et al 2002).…”

“…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).…”