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Fig. 4 | BMC Genomics

Fig. 4

From: Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

Fig. 4

Analysis of the ToxA effector region of Ptr isolates and other Pleosporales species. a A large-scale nucleotide sequence alignment of ToxA-flanking regions (length ≥ 2000 bp) is plotted for (top to bottom) Pa. nodorum (Sn15), P. tritici-repentis BFP (NCBI accession DS231618), M4 (Ch6), 86-124 (C169 reversed and C85), and B. sorokiniana (Bs). The GC content from 0 to 100% is plotted in a 1 kb window for M4 and SN15 to show AT-rich regions. Large regions of mesosynteny flank the central co-linear region containing ToxA. Alignments in the same orientation are red, and reverse complemented alignments are blue. * SN15 scaffold order: 30, 19, 68 (reversed), 51, 46 (reversed), 73 (reversed), 8 (reversed). ** Bs scaffold order: 80, 51, 45, 37, 224, 278, 44, 136, 86, 29, 215, 117. b Mid-scale nucleotide sequence alignment of ToxA-flanking regions between Pa. nodorum (SN15), Ptr isolates (BFP, M4, 86-124, SD20, DW5 and AR CrossB10) and B. sorokiniana (Bs). A large deletion in Ptr races 4, 5 and the new race is represented by a blue dotted line. The LTC sequence breakpoints locations in BFP and M4 (represented by the letter B in blue) are displayed. Conserved blocks of co-linear sequence containing ToxA are represented by black boxes. The relative position of the ToxA locus is shown in green. c Nucleotide multiple sequence alignment of the highly conserved 14 kb co-linear region containing the ToxA locus in seven P. tritici-repentis isolates (BFP (DS231618: 1,433,261–1,435,189, 1,442,208–1,453,406), 11,137 (C11: 5087–64,267), 239 (C28: 89,064–102,896), 134 (C27: 89,083–102,915), M4 (C1B: 1,555,340–1,569,173), 5213 (C15: 50,499–64,331), 86-124 (C169: c0–8.619, C85: c84711–89800), two Pa. nodorum isolates Sn4 (C2085: 2559–3207, C1970: 1–3780, C1503: 1–7085, C2213: 793–2502) and Sn15 (scaf68: 3025–6288, scaf51: 4470–14,377) and B. sorokiniania (Bs) (C278: 1–13,886). Blue shading and white spaces show alignment identity and absence respectively. Two variable regions are shown upstream of the ToxA locus (yellow) and neighbouring SNOG16572 transposase element (red). d Neighbour joining tree of (c). DNA branch distances show a race 1 clade of the Australian isolates (blue)

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