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Table 3 Genetic variants and their effects on genes in melon cultivars DHL92 and C-836

From: Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome

 

DHL921

C-8362

 

Whole genome

R-genes region

Whole genome

R-genes region

 

CM3.5

Improved

CM3.5a

Improvedb

CM3.5

Improved

CM3.5a

CM3.6.1b

Changes/kb

1

0.5

4.1

0.25

12.2

12

8.9

9.5

Variants

365,012

193,146

3,085

180

4,482,184

4,455,971

6,761

7,219

SNPs

        

       Homo

18,606

15,867

2,106

21

3,463,344

3,488,405

5,311

5,631

       Hetero

77,841

63,846

261

112

424,469

416,645

522

685

Insertions

        

       Homo

90,809

45,563

254

31

244,983

242,498

390

415

       Hetero

1,992

2,115

12

2

11,240

12,037

16

23

Deletions

        

       Homo

172,138

62,162

429

7

323,714

271,219

510

442

       Hetero

3,570

3,576

23

7

14,380

15,136

12

23

Effects in genes

        

       Missense

1,469

-c

125d

2d

62,321

-c

393d

520d

       Nonsense

54

-c

4d

0d

1,461

-c

2d

6d

       Silent

934

-c

97d

5d

62,200

-c

210d

249d

       Exons

4,317

-c

232d

7d

131,515

-c

625d

800d

       Introns

50,688

-c

118d

12d

526,990

-c

309d

496d

       Splice sites

700

-c

5d

0d

8,809

-c

8d

15d

  1. 1DHL92 Illumina PE reads mapped either to the melon reference assembly (CM3.5) or to the improved sequence.
  2. 2C-836 Illumina PE reads mapped either to the melon reference assembly (CM3.5) or to the improved sequence.
  3. aRegion comprising MELO3C004258 to MELO3C004324 genes (CM3.5, scaffold0003: 5,478,521 - 6,236,414).
  4. bRegion comprising MELO3C004258 to MELO3C004324 genes (improved scaffold0003: 5,478,926 - 6,186,068).
  5. cGene annotation not available.
  6. dOnly TIR-NBS-LRR and CC-NBS-LRR genes are considered.
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BMC Genomics

ISSN: 1471-2164

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