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Table 2 Chromosomal locations of duplications and their distribution among strains

From: Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum

Duplication

Chromosome

Start (gene)

Start (position)

Stop (gene)

Stop (position)

Length, bp (estimated)

Strain

1A

1

DDB0216544

597,838

DDB0202121

630,646

32,808

NP81, HU32

1B

1

DDB0190413

3,180,718

DDB0190424

3,207,169

26,451

Ax2(all)

1C

1

DDB0190683

3,902,919

DDB0190710

3,958,366

55,447

KAx3(U)

1D

1

DDB0190972

4,651,366

end

4,923,596

272,230

Ax2(I)

2A

2

end

1

DDB0216807

200,951

200,950

NP81

2B

2

DDB0217042

1,829,463

DDB0167938

3,760,461

1,930,998

Ax2(Wee)

2C

2

DDB0168867

1,848,568

DDB0217158

3,002,504

1,153,936

Ax2-214

2D

2

DDB0168894

1,898,568

DDB0231868

3,020,328

1,121,760

Ax2(M)

2E

2

DDB0185119

2,249,563

DDB0217157

3,002,134

752,571

Ax3/Ax4(all), NC4A2(both), JH10, DH1, HU32, NP81

2F

2

DDB0203552

6,131,391

DDB0217791

6,752,329

620,938

Ax2-206

2G

2

DDB0169405

6,623,914

DDB0217791

6,752,329

128,415

JH10

2H

2

DDB0217974

7,981,227

end

8,470,628

489,401

NC4(L), NC4(Kn)

2I

2

DDB0203385

8,080,299

DDB0217992

8,181,086

100,787

DH1, Ax3(D)

3A

3

DDB0206361

2,898,815

DDB0206368

2,915,972

17,157

NP81, HU32

3B

3

DDB0206089

3,595,775

DDB0206091

3,599,648

3,873

all non-NC4, some NC4s, X22

4A

4

DDB0186951

4,413,680

DDB0186970

4,474,299

60,619

NC28.2

4B

4

DDB0218826

4,572,845

end

5,450,249

877,404

NC4(B)

5A

5

DDB0219507

3,476,579

DDB0188678

3,531,501

54,922

DH1, Ax3(C), Ax3(D), Ax4(F), XP99, HU32, NP81

6A

6

DDB0183998

578,375

DDB0184007

595,296

16,921

NP81, HU32

6B

6

DDB0184069

763,797

DDB0184181

1,066,872

303,075

XP99

6C

6

DDB0219696

767,768

DDB0219699

787,282

19,514

NP81, HU32

6D

6

DDB0191606

838,926

DDB0184104

858,379

19,453

NP81, HU32

6E

6

DDB0184203

1,144,841

end

3,602,379

2,457,538

Ax2-206

6F

6

DDB0184511

1,919,891

DDB0219875

3,055,147

1,135,256

Ax2-206

6G

6

DDB0191998

3,022,031

DDB0219875

3,055,147

33,116

NP81, HU32

6H

6

DDB0192115

3,311,430

end

3,602,379

290,949

NC4(Wi)

6I

6

DDB0192193

3,468,862

end

3,602,379

133,517

NC4(S)

  1. Breakpoints were estimated by eye, and their map locations determined by aligning the probe sequence with the dictyBase assembly version 2.5. The duplication in the sequenced strain is given as the breakpoints and size revealed by the sequence itself. As noted in the text there appears to be variation in this duplication among the different strains that inherited it. The putative duplications in Ax2-214 and Ax2(M) are atypical in that the average log2 ratio across their lengths is considerably lower than 0.5. The larger duplication of chromosome 6 sequence in Ax2-206 may be similar in this respect. We do not understand why these features differ from the more typical duplications we observe.
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Genome Biology

ISSN: 1474-760X

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