PMC:4502367 / 31234-40442 JSONTXT

{"project":"2_test","denotations":[{"id":"25917918-25519841-43386577","span":{"begin":221,"end":225},"obj":"25519841"},{"id":"25917918-16093699-43386578","span":{"begin":412,"end":416},"obj":"16093699"},{"id":"25917918-24086727-43386579","span":{"begin":1709,"end":1713},"obj":"24086727"},{"id":"25917918-21695235-43386580","span":{"begin":4397,"end":4401},"obj":"21695235"},{"id":"25917918-15313550-43386581","span":{"begin":4564,"end":4568},"obj":"15313550"},{"id":"25917918-19014496-43386582","span":{"begin":4652,"end":4656},"obj":"19014496"},{"id":"25917918-21695235-43386583","span":{"begin":4744,"end":4748},"obj":"21695235"}],"text":"TEs in Z. tritici:\nOf 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).\nTable 2 Transposable element content in genomes of the Zymoseptoria species complex\nZ. tritici Z. pseudotritici Z. ardabiliae Z. brevis\nFamily No. DNA Amount (kb) % of Genome Family No. DNA Amount (kb) % of Genome Family No. DNA Amount (kb) % of Genome Family No. DNA Amount (kb) % of Genome\nClass I (retrotransposons)\nLTR RLC 12 1017 2.56 6 90 0.23 5 232 0.62 7 827 2.08\nRLG 14 2649 6.67 17 2906 7.50 16 1074 2.88 18 3616 9.09\nLINE RII 4 737 1.86 0 0 0.00 3 76 0.20 4 547 1.38\nRIL 2 747 1.88 0 0 0.00 1 32 0.09 0 0 0.00\nRIX 1 5 0.01 1 83 0.22 1 67 0.18 1 193 0.48\nDIRS RYN 1 23 0.06 0 0 0.00 0 0 0.00 0 0 0.00\nSINE RSX 1 1 0.00 0 0 0.00 0 0 0.00 0 0 0.00\nTRIM RLX-TRIM 4 35 0.09 0 0 0.00 0 0 0.00 1 4 0.01\nSub-total class I 39 5214 13.14 24 3080 7.94 26 1481 3.97 31 5186 13.04\nClass II (DNA transposons)\nTIR DTT 14 246 0.62 3 51 0.13 4 29 0.08 9 254 0.64\nDTA 7 150 0.38 1 35 0.09 1 4 0.01 5 175 0.44\nDTH 10 184 0.46 0 0 0.00 0 0 0.00 11 292 0.74\nDTM 7 145 0.36 1 44 0.11 0 0 0.00 4 213 0.54\nDTX 6 364 0.92 6 432 1.11 5 76 0.20 3 315 0.79\nUnknown DXX 2 40 0.10 0 0 0.00 0 0 0.00 0 0 0.00\nCrypton DYX 1 6 0.02 0 0 0.00 0 0 0.00 0 0 0.00\nHelitron DHH 4 470 1.18 7 357 0.92 1 39 0.10 5 391 0.98\nMaverick DMM 0 0 0.00 2 476 1.23 0 0 0.00 0 0 0.00\nMITE DTX-MITE 11 48 0.12 1 2 0.01 1 5 0.01 3 11 0.03\nSub-total class II 62 1653 4.17 21 1399 3.61 12 153 0.41 40 1652 4.15\nUncategorized repeats\nNoCat NoCat 10 516 1.30 60 1518 3.92 79 1303 3.49 93 2634 6.62\nTotal 111 7383 18.60 105 5997 15.47 117 2937 7.87 164 9472 23.87\nFigure 2 Transposable elements (TEs) characteristics along the 21 chromosomes of Zymoseptoria tritici. (A) Proportions of TEs in the chromosomes of Z. tritici. The red dashed lines show the mean values of TEs on core (1–13) and accessory chromosomes (14–21). (B) The distribution of five major TE classes across core and accessory chromosomes in Z. tritici show a more or less similar distribution and frequency on the two types of chromosomes. As already described by Goodwin et al. (2011), repetitive sequences are highly affected by the fungal-specific repeat inactivation mechanism known as repeat-induced point mutations (RIP) (Galagan and Selker 2004). Multiple alignments of several family copies analyzed by RIPCAL (Hane and Oliver 2008) showed an excess of CpA→TpA and TpG→TpA mutations. As hypothesized by Goodwin et al. (2011), these mutations should prevent TEs from expressing their own machinery. However, it appears that 98 predicted gene models overlap TE sequences with at least 50% of their length, including 75 genes models that are completely embedded in repetitive DNA. Of the 98 corresponding proteins, 33 harbor domains associated with TEs such as reverse-transcriptase, transposase, or integrase (Table 3). These domains belong to 22 distinct TE families, including 12 TIR, eight LTR, one LINE, and one uncategorized element. Comparison of these gene models with the reconstructed transcripts showed that 48% have RNA-seq support; this suggests that TE families (mainly class II DNA transposons) are still active in the Z. tritici genome despite the RIP machinery.\nTable 3 Gene models with protein domains associated with transposable elements\nProtein ID Length (aa) Domain Name Domain Description Interpro or Pfam Accession No. Overlapping Repeat Family RNA-seq Support\nZt09_chr_1_00001 143 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 —\nZt09_chr_1_00017 272 DDE_Tnp_4 DDE superfamily endonuclease PF13359 DTH_element5_ZTIPO323 —\nZt09_chr_1_01076 477 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 Yes\nZt09_chr_2_00093 477 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 —\nZt09_chr_2_00258 409 DDE_Tnp_1_7 Transposase IS4 PF13843 DTX_element1_ZPST04IR55 Yes\nZt09_chr_2_00383 648 DDE_1 DDE superfamily endonuclease PF03184 DTT_element1_ZTIPO323 Yes\nZt09_chr_2_00481 532 Chromo Chromo (CHRromatin Organization MOdifier) domain PF00385 RLG_element5_ZPST04IR55 —\nZt09_chr_2_00619 272 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element3_ZTIPO323 —\nZt09_chr_2_00906 219 DDE_1 DDE superfamily endonuclease PF03184 DTT_element5_ZTIPO323 Yes\nZt09_chr_2_00907 269 DDE_1 DDE superfamily endonuclease PF03184 DTT_element5_ZTIPO323 Yes\nZt09_chr_3_00204 734 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element2_ZTIPO323 Yes\nZt09_chr_3_00229 349 DDE_3 DDE superfamily endonuclease PF13358 DTT_element14_ZTIPO323 Yes\nZt09_chr_4_00051 195 DDE_3 DDE superfamily endonuclease PF13358 DTT_element4_ZB163 —\nZt09_chr_4_00288 371 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element3_ZTIPO323 Yes\nZt09_chr_5_00137 477 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 Yes\nZt09_chr_7_00478 338 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element6_ZTIPO323 Yes\nZt09_chr_7_00479 108 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element6_ZTIPO323 Yes\nZt09_chr_9_00003 1506 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 —\nZt09_chr_9_00154 621 DDE_1 DDE superfamily endonuclease PF03184 DTT_element1_ZTIPO323 Yes\nZt09_chr_9_00557 1061 rve Integrase core domain PF00665 RLC_element7_ZTIPO323 Yes\nZt09_chr_9_00615 458 DDE_Tnp_1_7 Transposase IS4 PF13843 DTX_element1_ZAST11IR611 Yes\nZt09_chr_10_00001 218 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element7_ZTIPO323 —\nZt09_chr_11_00364 162 Chromo Chromo (CHRromatin Organization MOdifier) domain PF00385 RLG_element7_ZPST04IR55 —\nZt09_chr_13_00054 869 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 Yes\nZt09_chr_13_00057 150 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element2_ZTIPO323 —\nZt09_chr_13_00271 480 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element1_ZTIPO323 Yes\nZt09_chr_17_00004 876 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 —\nZt09_chr_17_00088 523 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 —\nZt09_chr_18_00008 750 RNaseH-like_dom Ribonuclease H-like domain IPR012337 NoCat_element60_ZAST11IR611 —\nZt09_chr_19_00003 169 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element5_ZTIPO323 —\nZt09_chr_19_00040 947 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element9_ZTIPO323 —\nZt09_chr_19_00041 107 UBN2_3 gag-polypeptide of LTR copia-type PF14244 RLC_element9_ZTIPO323 —\nZt09_chr_21_00003 1609 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RLG_element9_ZTIPO323 —"}