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Table 3 Comparison of gene content between grapevine whole-genome and segmentally duplicated regions

From: Analysis of high-identity segmental duplications in the grapevine genome

chr total genes full dup genes chr gene density full dup gene density ratio of densities
chr1 1,399 72 6.07 2.63 0.43
chr2 976 93 5.20 3.07 0.59
chr3 1,104 143 5.71 3.70 0.65
chr4 1,363 95 5.71 2.88 0.50
chr5 1,435 138 5.74 3.74 0.65
chr6 1,289 66 5.99 2.30 0.38
chr7 1,357 59 6.45 2.53 0.39
chr8 1,488 67 6.65 3.30 0.50
chr9 1,136 166 4.94 2.91 0.59
chr10 842 100 4.64 2.93 0.63
chr11 1,082 57 5.46 2.64 0.48
chr12 1,263 175 5.56 4.02 0.72
chr13 1,281 150 5.25 3.27 0.62
chr14 1,625 153 5.37 3.38 0.63
chr15 957 122 4.71 2.72 0.58
chr16 1,048 140 4.75 2.53 0.53
chr17 1,006 54 5.87 2.20 0.37
chr18 1,796 143 6.12 3.14 0.51
chr19 1,200 192 5.00 3.30 0.66
Tot_nonrandom 23,647 2,185 5.55 3.06 0.55
chr1_random 7 1 1.23 0.73 0.60
chr3_random 28 7 2.29 2.35 1.03
chr4_random 5 - 6.56 - -
chr5_random 10 - 2.37 - -
chr7_random 73 8 5.04 5.71 1.13
chr9_random 4 2 0.82 1.46 1.78
chr10_random 52 12 6.59 3.95 0.60
chr11_random 11 - 3.89 - -
chr12_random 36 6 2.30 1.49 0.65
chr13_random 156 47 4.77 4.35 0.91
chr16_random 28 26 3.78 3.87 1.02
chr17_random 15 3 1.81 2.38 1.32
chr18_random 211 44 4.08 3.22 0.79
Tot_random 636 156 3.77 3.35 0.89
Tot_placed 24,283 2,341 5.48 3.08 0.56
chrUn 2,063 248 4.78 2.79 0.58
Tot_whole 26,346 2,589 5.42 3.05 0.56
  1. Number of total genes (total genes), number of fully duplicated genes (full dup genes), chromosome gene density (chr gene density), density of fully duplicated genes in duplicated regions (full dup gene density), and ratio between full dup gene density and chr gene density (ratio of densities) are shown for each chromosome, all nonrandom chromosomes, all random chromosomes, all nonrandom and random chromosomes, and for the whole genome. Gene density is calculated as the average number of genes present in 100 kb of genomic sequence.