PMC:4502367 / 31253-33296 JSONTXT

{"project":"2_test","denotations":[{"id":"25917918-25519841-43386577","span":{"begin":202,"end":206},"obj":"25519841"},{"id":"25917918-16093699-43386578","span":{"begin":393,"end":397},"obj":"16093699"},{"id":"25917918-24086727-43386579","span":{"begin":1690,"end":1694},"obj":"24086727"}],"text":"Of the 39.7-Mb genome assembly of Z. tritici IPO323, 7.4 Mb (18.6%) (Table 2) were found to be repetitive DNA, in agreement with the recently reported repeat content of IPO323 (\u003e17%) in Dhillon et al. (2014). Repeats were classified into TE families based on features such as terminal repeats, protein domains, and homology with known TE available in the Repbase Update database (Jurka et al. 2005). The fact that the assembled genome of Z. tritici consists of complete chromosomes allowed a high-quality repeat annotation with only few uncategorized families. TEs of class I (retrotransposons) are the most abundant in the IPO323 genome and represent 13.1% of the total genome size (5.2 Mb), whereas TEs of class II (DNA transposons) represent 4.2% (1.6 Mb) (Table 2). The remaining repetitive sequences represent 0.5 Mb and could not be associated with classified TEs. From the 111 consensus sequences obtained by our procedure (see Materials and Methods), we identified 101 families of TEs. The majority of these families belong to the class II (62 families), mainly represented by TIRs (44 families), MITEs (11 families), and Helitron (4 families). Although present in a lower number (32 families), class I elements represent 71% of the repetitive fraction of the genome. The most abundant group of class I elements is the LTR elements from the Gypsy superfamily (14 families), followed by those of the Copia superfamily (12 families) and LINEs (7 families) (Table 2). Interestingly, we also identified one family of a complete tyrosine-recombinase retrotransposon that belongs to the Ngaro superfamily and that otherwise has been described to be absent in Ascomycota (Muszewska et al. 2013). Distinguishing core and accessory chromosomes of Z. tritici, we find that repetitive DNA represents 16.6% of the core chromosomes and 33.6% of the accessory chromosomes (Figure 2A). However, the relative distribution of the major TE families on core and accessory chromosomes does not differ significantly (Wilcoxon test, P = 0.3692) (Figure 2B)."}