Table 1

Annotation of TE superfamilies in flax WGS assembly determined using a filtered consolidated library produced with de-novo repeats from PILER, RepeatScout, LTR_finder and LTR_STRUC, and a library of TE from the viridiplantae division from Repbase
Class Order Superfamily No. of matches Elements percentage (%) Sequence occupied (bp) Sequence percentage of TEs (%) Sequence percentage of genome (%)
Retrotransposons LTR Copia 89951 38.31 29594882 40.08 9.30
Gypsy 72626 30.93 25123127 34.02 7.89
unclassified 2797 1.19 902298 1.22 0.28
DIRS DIRS 2 0.00 102 0.00 0.00
PLE Penelope 548 0.23 30214 0.04 0.01
LINE RTE 11 0.00 618 0.00 0.00
L1 27632 11.77 6684243 9.05 2.10
SINE unclassified 1 0.00 49 0.00 0.00
DNA transposons TIR Tc1-Mariner 191 0.08 38231 0.05 0.01
hAT 7935 3.38 1986522 2.69 0.62
Mutator 21124 9.00 6320424 8.56 1.99
P 2 0.00 96 0.00 0.00
Harbinger 1384 0.59 344876 0.47 0.11
En-Spm/CACTA 8330 3.55 2372592 3.21 0.75
Helitron Helitron 2154 0.92 434859 0.59 0.14
unclassified unclassified 95 0.04 8981 0.01 0.00
TOTALS 234783 100.00 73842114 100.00 23.06

González and Deyholos

Gonz├ílez and Deyholos BMC Genomics 2012 13:644   doi:10.1186/1471-2164-13-644

Open Data