Evolution of DNA Sequence Nonhomologies among Maize Inbreds

Abstract

Allelic chromosomal regions totaling more than 2.8 Mb and located on maize (Zea mays) chromosomes 1L, 2S, 7L, and 9S have been sequenced and compared over distances of 100 to 350 kb between the two maize inbred lines Mo17 and B73. The alleles contain extended regions of nonhomology. On average, more than 50% of the compared sequence is noncolinear, mainly because of the insertion of large numbers of long terminal repeat (LTR)-retrotransposons. Only 27 LTR-retroelements are shared between alleles, whereas 62 are allele specific. The insertion of LTR-retrotransposons into the maize genome is statistically more recent for nonshared than shared ones. Most surprisingly, more than one-third of the genes (27/72) are absent in one of the inbreds at the loci examined. Such nonshared genes usually appear to be truncated and form clusters in which they are oriented in the same direction. However, the nonshared genome segments are gene-poor, relative to regions shared by both inbreds, with up to 12-fold difference in gene density. By contrast, miniature inverted terminal repeats (MITEs) occur at a similar frequency in the shared and nonshared fractions. Many times, MITES are present in an identical position in both LTRs of a retroelement, indicating that their insertion occurred before the replication of the retroelement in question. Maize ESTs and/or maize massively parallel signature sequencing tags were identified for the majority of the nonshared genes or homologs of them. In contrast with shared genes, which are usually conserved in gene order and location relative to rice (Oryza sativa), nonshared genes violate the maize colinearity with rice. Based on this, insertion by a yet unknown mechanism, rather than deletion events, seems to be the origin of the nonshared genes. The intergenic space between conserved genes is enlarged up to sixfold in maize compared with rice. Frequently, retroelement insertions create a different sequence environment adjacent to conserved genes.

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

“…The presence of genes and gene fragments in noncolinear locations is relatively frequent in the large genomes of the temperate grasses, which originated from massive amplifications of repetitive elements (39,(48)(49)(50). Some DNA transposons in wheat (e.g., CACTA) are able to move genes and gene fragments to noncolinear locations (51), as reported for rice 'Pack-MULEs' (52) and maize helitrons (53). However, this mechanism is associated with mobilization of small DNA fragments (<3 kb) (54) and is unlikely to explain the 290-kb insertion that originated VRN-D4.…”

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

“…Alternatively, O. nubilalis may show variation in IS content between haploid genomes. Since the O. nubilalis BAC library and real-time PCR template were derived from different sources, the discrepancy in IS copy number estimates may reflect actual differences in genome content analogous to that observed previously among Helitron elements within Z. maize inbred lines (Brunner et al 2005).…”

Improved maize reference genome with single-molecule technologies

“…Most of the maize Letter reSeArCH genome is derived from transposable elements 3, 21 , and careful study of a few regions has revealed a characteristic structure of sequentially nested retrotransposons 21,22 and the effect of deletions and recombina tion on retrotransposon evolution 23 . In the annotation of the original maize assembly, however, fewer than 1% of long terminal repeat (LTR) retrotransposon copies were intact 24 .…”