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Table 1 Characteristics of nuclear genome sequence in Dioscorea rotundata and other angiosperms

From: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

Feature Value
D. rotundata (v0.1) A. thaliana (TAIR10) B. distachyon (v3.1) O. sativa (v7_JGI 323)
Total length (Mbp) 594.23 119.67 271.16 374.47
GC (%) 35.83 36.06 46.40 43.57
Number of scaffolds (≥ 0 bp) 4723 7 10 14
Number of scaffolds (≥ 1000 bp) 4704 7 10 14
Largest scaffold (Mbp) 13.61 30.43 75.07 43.27
N50 (Mbp) 2.12 23.46 59.13 29.96
N75 (Mbp) 0.77 19.70 48.59 28.44
Number of Ns per 100 kb 282.45a 155.60 155.85 44.13
Ambiguous bases 1,413,029
Number of genes 26,198 27,416 34,310 42,189
Exons
 Number 158,059 141,044 154,104 178,353
 Average number per gene 6.03 5.14 4.49 4.25
 Total length (Mbp) 42.43 33.49 39.01 46.85
 Average size (bp) 268.43 237.46 253.15 262.70
 Average GC (%) 44.08 43.70 51.02 51.12
Introns
 Number 105,663 86,212 85,484 94,345
 Average number per gene 4.03 3.14 2.49 2.25
 Total length (Mbp) 83.12 17.87 47.70 53.34
 Average size (bp) 630.33 157.25 398.18 391.23
 Average GC (%) 32.37 32.45 38.29 37.20
Transposable elementsb
 % Total interspersed 46.07 13.32 37.39 44.40
 Total interspersed total length (Mbp) 274.51 15.94 101.39 166.27
 % Short interspersed nuclear elements (SINEs) 0.02 0.17 0.38 0.88
 SINEs total length (Mbp) 0.13 0.20 1.02 3.31
 % Long interspersed nuclear elements (LINEs) 2.43 1.07 2.91 1.29
 LINEs total length (Mbp) 14.46 1.29 7.90 4.83
 % Long terminal repeat (LTR) elements 22.82 6.35 19.31 21.09
 LTR elements total length (Mbp) 135.71 7.61 52.36 78.98
 % DNA elements 6.70 3.08 7.11 16.7
 DNA elements total length (Mbp) 39.83 3.69 19.27 62.82
 % Unclassified 14.20 2.64 7.68 4.36
 Unclassified total length (Mbp) 84.38 3.16 20.84 16.32
  1. aNumber of Ns per 100 kb using the D. rotundata broken scaffolds
  2. bTransposable elements were identified by masking the genomes using RepeatModeler and RepeatMasker, with the same parameters across all species
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