Genome-Wide Analysis ofStowaway-Like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification    

Abstract

The diversity and evolution of wheat (Triticum-Aegilops group) genomes is determined, in part, by the activity of transposable elements that constitute a large fraction of the genome (up to 90%). In this study, we retrieved sequences from publicly available wheat databases, including a 454-pyrosequencing database, and analyzed 18,217 insertions of 18 Stowaway-like miniature inverted-repeat transposable element (MITE) families previously characterized in wheat that together account for approximately 1.3 Mb of sequence. All 18 families showed high conservation in length, sequence, and target site preference. Furthermore, approximately 55% of the elements were inserted in transcribed regions, into or near known wheat genes. Notably, we observed significant correlation between the mean length of the MITEs and their copy number. In addition, the genomic composition of nine MITE families was studied by real-time quantitative polymerase chain reaction analysis in 40 accessions of Triticum spp. and Aegilops spp., including diploids, tetraploids, and hexaploids. The quantitative polymerase chain reaction data showed massive and significant intraspecific and interspecific variation as well as genome-specific proliferation and nonadditive quantities in the polyploids. We also observed significant differences in the methylation status of the insertion sites among MITE families. Our data thus suggest a possible role for MITEs in generating genome diversification and in the establishment of nascent polyploid species in wheat.Wheat (Triticum-Aegilops group) likely originated from a common ancestor some 4 million years ago and has since undergone multiple polyploidization events. As such, this organism has been the subject of substantial research into genomic evolution and diversification. Beginning with three ancestral diploid species, two major allopolyploidization events subsequently occurred, resulting in the appearance of tetraploid (pasta) wheat (Triticum turgidum ssp. durum; 2n = 4x = 28; genome AABB) around 0.5 million years ago and hexaploid (bread) wheat (Triticum aestivum; 2n = 6x = 42; genome AABBDD) around 10,000 years ago (Feldman and Levy, 2005). Bread wheat harbors three distinct, yet related, genomes, namely the A u genome originating from Triticum urartu, the B (or S) genome originating from a section of Sitopsis species, most probably Aegilops speltoides or Aegilops searsii, and the D genome originating from Aegilops tauschii (Petersen et al., 2006). The availability of several diploid ancestors of wheat and their polyploid species as research models allows for the tracking of those evolutionary changes that enabled diversification of the different genomes as well as their differentiation within the polyploid species. Past studies on phylogenetic relationships between members of the Triticum-Aegilops group employed nuclear (Mori et al

Asymmetric Epigenetic Modification and Elimination of rDNA Sequences by Polyploidization in Wheat

“…Twenty microsatellite sequences in 15 populations of Triticum dicoccoides from Israel and Turkey showed that different distribution patterns of simple sequence repeat alleles (Fahima et al, 2002). The sequences of Stowawaylike transposable element families displayed high conservation, genomic diversification, and significant differences in the methylation status of the insertion sites in diploid, tetraploid, and hexaploid wheat (Yaakov et al, 2013). These reports suggest that evolution of repetitive sequences can be affected by both the genomic and environmental context.…”

Comparative analysis of Stowaway‐like miniature inverted repeat transposable elements in wheat group 7 chromosomes: Abundance, composition, and evolution

“…Computational identification of MITEs was carried out following the method described previously (Yaakov et al, 2013a) with some small modifications. A MITE Analysis Kit (Yang & Hall, 2003) was used to search the MITEs and the flanking sequences with the identified MITEs in TREP 10 as the query and the survey sequences of group 7 chromosomes as the database, respectively.…”

“…This biological feature makes the wheat genomic study a huge challenge, but it also appears to be a good model for chromosome interaction and polyploidization study (Berkman et al, 2011;Nie et al, 2012). Furthermore, it was found that the repetitive sequences occupied $80% of the whole genome, which offer a useful platform for the study of the effect of "genomic stress" on the activity of repetitive elements, especially transposable elements (TEs) (Cantu et al, 2010;Middleton et al, 2013;Yaakov et al, 2013a).…”

“…Among the TEs, miniature inverted repeat transposable elements (MITEs) are the most ubiquitous in eukaryotic genomes, a cluster of non-autonomous DNA transposons with a set of significant characteristics: very high copy numbers (>90 000 in rice), structural homogeneity, and very short in length (Yang et al, 2009;Yaakov et al, 2013a). There are usually two classes of MITEs: the Stowaway-like and Touristlike (Bureau & Wessler, 1994a, 1994b.…”

“…Yaakov et al (2012) identified some MITEs from wheat and assessed the utility of MITEs for marker development. They further systematically identified the Stowaway-like MITEs in the wheat genome using 454 survey sequences (Yaakov et al, 2013a), which provided comprehensive information about the abundance, composition, and diversity of MITEs. However, not all of the identified MITEs could be located in certain chromosomes because of the absence of complete wheat genome sequences, which are important determinants of their function on the evolution of homoeologous chromosomes during polyploidization.…”