TEs in Z. pseudotritici, Z. ardabiliae, and Z. brevis:
To improve the repeat annotation of Z. pseudotritici, Z. ardabiliae, and Z. brevis, we generated improved assemblies of Illumina-sequenced genomes of the isolates: ST04IR55 of Z. pseudotritici, ST11IR611 of Z. ardabiliae, and Zb163 of Z. brevis. The assembly sizes were 38.8 Mb, 37.3 Mb, and 39.8 Mb, respectively, compared to the 39.7 Mb genome assembly of Z. tritici.
The three genomes reflect different extents of repeat invasion: repetitive DNA comprises 7.9% of the Z. ardabiliae genome, 15.5% of the Z. pseudotritici genome, and 23.9% of the Z. brevis genome, including a total of 117, 105, and 164 repeat families identified in the genomes, respectively (Table 2). As a result of the fragmented assemblies, the number of uncategorized repeat families in the Z. pseudotritici, Z. ardabiliae, and Z. brevis genomes represent more than 50% of all the families and between 25% and 44% of the repetitive fraction. In contrast, the number of uncategorized families in the Z. tritici genome represents only 9% of the families and 7% of the repetitive fraction. Nevertheless, it was possible to classify some TE families of Z. pseudotritici, Z. ardabiliae, and Z. brevis and to record general patterns of TE distribution among the three genomes. As in the Z. tritici genome, class I TEs that are mainly represented by LTR-Gypsy elements are most abundant and account for 51–55% of the total repetitive fraction (Table 2). LINE elements are hardly represented in the Z. pseudotritici, Z. ardabiliae, and Z. brevis assemblies; however, this may be an artifact of the fragmented assemblies. In Z. pseudotritici and Z. brevis, class II TEs are mainly composed of TIRs that represent approximately 20% of the repetitive fraction similar to class II TEs in Z. tritici. Helitron elements were also identified in Z. pseudotritici, Z. ardabiliae, and Z. brevis; however, they accounted for only 1–6% of the repetitive fraction compared to 6.4% in Z. tritici. Maverick elements (Pritham et al. 2007) were only identified in Z. pseudotritici and were the third most represented TE family in the genome (Table 2). The unique presence and distribution of Maverick elements in Z. pseudotritici could result from a recent invasion of the genome followed by massive waves of transposition of these elements.