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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