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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.