Skip to main content

Advertisement

Table 1 Nicotiana genome assembly metrics

From: The impact of genome evolution on the allotetraploid Nicotiana rustica – an intriguing story of enhanced alkaloid production

  N. rustica N. undulata N. paniculata N. knightiana
Coverage 90x 122x 100x 82x
Contigs 863,445 240,808 289,247 368,273
Scaffolds 246,567 117,559 181,973 160,417
Average scaffold length 18,053 16,284.2 12,038.2 14,331.7
Longest scaffold 709,624 435,587 551,851 749,769
N50 length 84,603 61,881 52,808 82,722
E-size 106,321.7 76,855.5 68,024.3 103,550.5
Assembly length 4,451,279,893 1,914,350,984 2,190,627,570 2,299,051,887
Undefined bases 458,861,024 (10.31%) 15,815,547 (0.83%) 2,994,201 (0.14%) 47,367,942 (2.06%)
Genome size (KMER) [Gb] 4.99 2.18 3.26 3.12
Genome size (KEW) [Gb] 5.181 2.362 2.88 3.09
Genome coverage (KMER) 0.892 0.878 0.672 0.737
Genome coverage (KEW) 0.8591 0.81 0.761 0.744
genes and regulatory sequences 956,876,918 (24%) 469,801,265 (25%) 487,609,360 (22%) 513,178,366 (23%)
DNA transposons 107,092,333 (3%) 56,581,894 (3%) 55,826,622 (3%) 55,840,784 (2%)
LTR elements 1,747,332,959 (44%) 820,008,945 (43%) 981,515,044 (45%) 1,014,595,360 (45%)
Retrotransposons 532,753,114 (13%) 243,526,350 (13%) 303,566,434 (14%) 304,961,922 (14%)
Non-LTR retroelements (SINES, LINES) 30,145,844 (1%) 15,712,962 (1%) 15,526,693 (1%) 15,258,713 (1%)
Others (Satellites, unknown, low complexity) 618,217,701 (15%) 292,904,021 (15%) 343,589,216 (16%) 347,848,800 (15%)