Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat

Abstract

Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.

Figure 1.—

Detailed annotation, BIN map positions, and sequence composition of 10 sequenced BAC clones of wheat chromosome 3B. (A) Detailed annotations of the 10 sequenced BAC clones. Main TEs, other repeats, and gene sequence information (GSI) are represented with distinct features and motifs (detailed in the “features and motifs” key). g, genes; pg, putative genes; gr, gene relics; and psg, pseudogenes. For nested insertions of TEs, the newly inserted TE is presented above the split one. Complete reconstruction of split TEs was done and the different parts are linked with a line to visualize the entire element. Some BAC clones are represented by several unordered contigs (TA3B63E4, TA3B63C11, TA3B63N2). EMBL BAC clone references and annotation files are given in materials and methods. Detailed coding sequence and TE descriptions are supplied in supplemental Text 1 and supplemental Text 2. Arrows indicate novel TEs identified in this study and described in supplemental Text 2 and supplemental Table 5. (B) BIN map position of nine of the BAC clones. The wheat chromosome 3B bins are according to Qi et al. (2003). Details of the genotyping results are given in supplemental Table 6. (C) Proportions of the main sequence classes and types. See “features and motifs” in A for an explanation of colors. Details are given in supplemental Table 2.

Figure 2.—

Changes of the coefficient of variation of proportions (in percentages) of the main transposable element superfamilies calculated over all possible BAC clone combinations and simulated over a size varying from 1 to 12 BAC clones for the wheat B genome and 1 to 18 for the wheat A genome (combination size). For each number of considered BAC clones (x-axis), sequence proportions (in percentages) were calculated for all possible BAC clone combinations, and the coefficient of variation between these proportions was calculated (y-axis).

Figure 3.—

Distribution of insertion dates estimated for LTR retrotransposons in the B and A-genome sequences of wheat (divergence and MYA). (A) All dated LTR retrotransposons combined at the three main superfamily levels (Athila, Gypsy, and Copia). (B) The most abundant retrotransposon families, showing five or more dated copies in at least one of the A or B wheat genomes. Mean insertion dates calculated for retrotransposons are represented by vertical bars. For the A-genome sequences, blue indicates retrotransposons detected from the diploid and red from the polyploid genomic sequences. The genomic sequences of the B genome (red) were obtained from the polyploid wheat. Copies of a given retrotransposon superfamily or family showing identical mean insertion dates are presented by adjacent vertical bars that are joined with a lower horizontal gray bar. The number within parentheses corresponds to the total number of considered retrotransposon copies. Gray triangles indicate retrotransposon insertions that have been traced using PCR in a collection of genotypes of T. aestivum and T. turgidum. The interval period of the allotetraploidization event (0.5–0.6 MYA, divergence 0.013–0.016) is highlighted in gray. “Uniformity test” refers to Kolmogorov–Smirnov (Férignac 1962) tests determining probabilities (P-value) that the distribution of insertion dates of retrotransposons deviates from uniformity (thus confirming a burst of higher proliferation): “All” refers to the last 3 million years (0.078 divergence); “Recent” refers to the most recent periods, estimated when dividing the LTR–retrotransposon insertions by the median (indicated by gray circles). Tests were done on families that show five copies or more. “Comparison of distribution” indicates the same Kolmogorov–Smirnov tests determining probabilities that distributions of insertion dates for the last 3 million years (0.078 divergence) are different in the retrotransposon superfamilies and families as well as the in B and A genomes of wheat.

Figure 4.—

PCR-based tracing of series of retrotransposons, inserted at different dates in wheat chromosome 3B across a collection of wheat tetraploid (T. turgidum) and hexaploid (T. aestivum) genotypes. Averages and intervals (means ±SE) of retrotransposon insertion dates are presented. The interval of the allotetraploidization event (0.5–0.6 MYA), calculated according to gene sequence divergence (Huang et al. 2002; Dvorak et al. 2006; Chalupska et al. 2008), is in gray. Retrotransposons for which insertion dates were estimated on the basis of divergence of their LTR prior to the tetraploidization event were generally detected in almost all genotypes, whereas those posterior to the tetraploidization event were detected in only some genotypes. Gels show PCR-based detection of insertion of RLC_Alixa_TA3B95C9-1 (into DTC_Caspar_TA3B95C9-1) in all tested genotypes, except one and insertion of RLG_Nathalia_TA3B63E4-1 (into DTC_Vincent_TA3B63E4-2) in some genotypes. Primer sequences, details of insertion dates (averages and intervals), and PCR-based detection in different wheat genotypes are given in supplemental Table 1 and supplemental Table 7. AABBDD (hexaploid wheat accessions): -1—T. aestivum cv. Renan; -2—T. aestivum cv. Chinese Spring; -3—T. aestivum spelta, Erge 27216; -4—T. aestivum spelta, Erge 2776; -5—T. aestivum spelta, Erge 2771; -6—T. aestivum spelta Rouquin, Erge 6329; -7—T. aestivum macha 1793, Erge 27240; -8—T. aestivum compactum rufulum 71V, Erge 26786; -9—T. aestivum compactum crebicum 72V, Erge 26787; -10—T. aestivum compactum clavatum 73V, Erge 26788; -11—T. aestivum compactum icterinum 74V, Erge 26789; -12—T. aestivum compactum erinaceum 75V, Erge 26790; -13—T. aestivum sphaerococcum tumidum perciv globosum, Erge 27016; -14—T. aestivum cv. Soisson. AABB (T. turgidum, tetraploid wheat accessions): -15—T. turgidum durum cv. Langdon; -16—T. turgidum durum; -17—T. turgidum dicoccum, -18—T. turgidum dicoccoides; -19—T. turgidum polinicum; -20—T. turgidum turgidum.

Figure 5.—

Proliferation periods and rates of the main retrotransposon superfamilies in the wheat B and A genomes. Expressed as probability density functions, where the area under each curve was calculated on the basis of the estimated insertion dates of retrotransposons (in Figure 3) and their corresponding standard errors, using Gaussian kernel density estimation (Silverman 1986). The curves have been scaled with respect to the number of observations, so that the sum of their areas (given for each retrotransposon superfamily in the key) equals the probability of 1 and comparisons between genomes and retrotransposon superfamilies can be performed. When calculated standard errors were very low, a minimum value of 80,000 years (corresponding to 0.002 divergence) was used. The shaded field is due to uncertainty in very recent insertion date estimations.