Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains

Abstract

Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number.

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

“…In a recent study of rice, we showed a possible connection between the copy numbers of TEs and the methylation levels of flanking CCGG sites, where a negative correlation was seen in different rice strains for a MITE family termed mPing (Baruch and Kashkush, 2012). The nature of the connection between the methylation of TE insertion sites and TE copy number could be explained by a difference in the genomic context of the initial insertion of an element.…”

“…Past studies on phylogenetic relationships between members of the Triticum-Aegilops group employed nuclear (Mori et al, 1995;Sasanuma et al, 1996;Wang et al, 2000a;Huang et al, 2002;Kudryavtsev et al, 2004;Sallares and Brown, 2004) or organellar (Wang et al, 2000b;Haider and Nabulsi, 2008) DNA markers to cluster divergent species. At the same time, molecular markers have been developed to study wheat phylogeny resulting from polymorphism in transposable element (TE) insertions (Queen et al, 2004;Kalendar et al, 2011;Baruch and Kashkush, 2012), including miniature inverted-repeat transposable elements (MITEs; .…”

Early Embryogenesis-Specific Expression of the Rice Transposon Ping Enhances Amplification of the MITE mPing

“…These samples were loaded onto an agarose gel, separated by electrophoresis, blotted onto a nylon membrane, and probed with the Ping fragment. The mPing copy number was determined by real-time quantitative PCR as described previously [45] with little modification. Quantitative PCR was performed using the LightCycler 480 system (Roche).…”

Genome-wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes

“…The quantification of genomic repetitive units by comparative qPCR has been performed in several species (Baruch and Kashkush, 2012; Yaakov et al , 2013; Marcon et al , 2015). The genomes of E. grandis (1C = 630 Mb) and E. urophylla (1C = 640 Mb) are of similar size and diverged < 20 Mya (Myburg et al , 2014), making them a good congeneric pair for comparative analyses of EgEVE_1 distribution in the two genomes.…”