Table 2 Repetitive DNA composition of the Avena longiglumis genome.
From: Chromosome-level genome assembly of the diploid oat species Avena longiglumis
Repeat type | Super family | Family | Repeat sequences (bp) | Copy number | Repeat fraction | Genome fraction | |
|---|---|---|---|---|---|---|---|
Transposable elements | |||||||
Class I (Retrotransposons) | |||||||
LTR | Gypsy | 2,045,839,268 | 1,127,011 | 59.34% | 51.65% | ||
Copia | 1,035,647,971 | 575,382 | 30.04% | 26.15% | |||
Unknown LTR | 77,372,748 | 61,272 | 2.24% | 1.95% | |||
Other LTR | 213,586 | 628 | 0.01% | 0.01% | |||
Total LTR- Retrotransposons | 3,159,073,573 | 1,764,293 | 91.63% | 79.76% | |||
Non-LTR | LINE | L1 | 38,994,208 | 42,780 | 1.13% | 0.98% | |
Total Class I retrotransposons | 3,198,067,781 | 1,807,073 | 92.76% | 80.74% | |||
Class II (DNA transposons)-Subclass 1 | |||||||
Tc1_Mariner | 21,858,891 | 69,956 | 0.63% | 0.55% | |||
CACTA | 29,566,991 | 75,699 | 0.86% | 0.75% | |||
Mutator | 25,388,681 | 82,292 | 0.74% | 0.64% | |||
PIF_Harbinger | 9,194,639 | 31,402 | 0.27% | 0.23% | |||
hAT | 7,600,354 | 22,266 | 0.22% | 0.19% | |||
Class II (DNA transposons)-Subclass II | |||||||
Helitron | 43,779,456 | 117,248 | 1.27% | 1.11% | |||
Total Class II DNA transposons | 137,389,012 | 398,863 | 3.99% | 3.47% | |||
Total transposable elements | 3,335,456,793 | 2,205,936 | 96.75% | 84.21% | |||
Tandem and simple sequence repeats | 11,144,119 | 162,888 | 0.32% | 0.28% | |||
Other repeats | 100,883,895 | 369,975 | 2.93% | 2.55% | |||
Total repetitive DNAs | 3,447,484,807 | 2,728,799 | 100% | 87.04% | |||
