Skip to main content

Table 1 Isolate source, race and genome de novo assembly statistics

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

  M4a BFPb 134 239 5213 11137 86-124 AR CrossB10 DW5 DW7c SD20c
Sequencing Platform PacBio Sanger, Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina
 PE Read length (bp) N/A N/A 100 100 100 100 150 150 100 75 75
Genome accessiond NQIK00000000 N/A MVBF00000000 MVBH00000000 MVBI00000000 MVBG00000000 NRDI00000000 NQWZ00000000 MUXC00000000 N/A N/A
Isolate information
 Collection site Western Australia South Dakota, USA Queensland, Australia Victoria, Australia Queensland, Australia Western Australia Canada Arkansas, USA North Dakota, USA North Dakota, USA South Dakota, USA
 Collection year 2009 1994e 2001 2003 1987 2001 1989 2002 1998 1998 1998f
 Race 1 1 1 1 1 1 2 Newk 5 5 4
 Effectors AC AC AC AC AC AC A C B B b
Optical map
 % Mapped 98 90 N/A N/A N/A N/A N/A N/A N/A N/A N/A
Contig assembly statistics
 Total length (Mb) 40.9 38.0 34.0 34.4 34.1 33.9 34.4 33.8 33.4 32.9 34.1
 Number 50 48 3579 3309 3318 2645 3223 2867 3964 3533 7322
 N50 (Mb) 2.930 1.900 0.064 0.065 0.066 0.074 0.060 0.058 0.045 0.028 0.014
 L50 6 6 150 148 150 130 168 171 208 348 661
 Mean (Kb) 802 778 9.5 10.4 10.3 12.8 10.3 11.3 8.4 9.3 4.6
 Max (Mb) 5.60 6.70 0.29 0.53 0.53 0.38 0.26 0.34 0.22 0.12 0.08
 GC % 50.73 50.89 50.86 50.84 50.85 50.87 51.35 50.90 50.90 50.89 50.79
 % Repeath 7.96 5.87 2.64 2.62 2.58 2.33 2.65 2.71 2.36 1.88 1.97
 RNA-Seqi 33.55 21.92g 22.34 21.00 23.00 21.22 19.87 19.92 24.44 20.63g 16.10g
 % RNA-Seqj 85.1 79.4–81.4 81.1 81.2 82.2 80.9 76.0 76.2 81.9 74.2–78.5 58.2–60.0
  1. aPacBio contiguous sequence, bThe BFP genome was downloaded from DDBJ/ENA/GenBank. Gene predictions were made on the scaffolds sourced from GenBank, cRaw reads were downloaded from NCBI SRA and assembled for gene predictions. dNew Genbank WGS submissions (NA = Not Applicable), eIsolate was subcultured from Pt-1C [12] fSD20 collection [13]. gAverage read alignment across six isolates. hPercentage of genome masked for RepBase (“Fungi”) repeats [38]. iNumber of concordant aligned RNA-Seq paired reads (millions). jPercentage RNA-read concordant alignment, kisolate does not meet race 1–8 classification
\