From: The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
 | BAC3 | BAC12 | BAC15 | BAC17 | BAC19 | BAC20 | BAC21 | BAC31 | BAC37 | BAC40 | ALL |
---|---|---|---|---|---|---|---|---|---|---|---|
No. dicot-like genes | 0 | 2 | 2 | 2 | 1 | 1 | 2 | 1 | 0 | 7 | 18 |
Dicot-like gene content | 0 | 3.0% | 4.7% | 4.5% | 3.7% | 2.5% | 2.8% | 1.5% | - | 6.5% | 2.6% |
No. monocot-like genes | 0 | 2 | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 8 | 18 |
Monocot-like genes content | 0 | 20% | 3.9% | 3.7% | 11.3% | 2.5% | 1.9% | 1.5% | - | 5.8% | 4.2% |
TRANSPOSONS | 72 | 46 | 31 | 73 | 47 | 51 | 64 | 79 | 81 | 55 | 599 |
DNA transposons | 23 | 11 | 11 | 19 | 19 | 15 | 28 | 22 | 24 | 18 | 190 |
ERVs | 4 | 2 | 2 | 6 | 1 | 1 | 2 | 3 | 0 | 6 | 27 |
Non-LTR retroelement | 7 | 13 | 6 | 18 | 12 | 16 | 7 | 28 | 18 | 7 | 132 |
LTR retrotransposons | 38 | 20 | 12 | 30 | 15 | 19 | 27 | 26 | 39 | 24 | 250 |
Gypsy-like | 26 | 7 | 9 | 17 | 6 | 14 | 15 | 13 | 26 | 10 | 143 |
Named elements* | 4 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 14 |
Copia-like | 17 | 3 | 3 | 13 | 6 | 4 | 12 | 10 | 11 | 13 | 92 |
Named elements* | 1 | 0 | 1 | 2 | 1 | 1 | 0 | 2 | 2 | 0 | 10 |
INTEGRATED VIRUSES | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 3 |
OTHER REPBASE | 0 | 0 | 0 | 1 | 0 | 2 | 2 | 1 | 1 | 1 | 8 |
SIMPLE REPEATS | 16 | 10 | 4 | 9 | 12 | 2 | 22 | 18 | 41 | 18 | 152 |
TOTAL NO. REPBASE HITS | 88 | 56 | 36 | 83 | 59 | 55 | 88 | 99 | 123 | 75 | 762 |
Similar to Repbase or RM | 18% | 12% | 12% | 15% | 17% | 19% | 12% | 17% | 15% | 9% | 17% |
Tandem repeats/minisats** | 13 | 11 | 10 | 14 | 23 | 14 | 22 | 45 | 21 | 41 | 214 |
Direct rpts/potential LTRs** | 40 | 12 | 10 | 10 | 4 | 6 | 12 | 24 | 27 | 16 | 161 |
Putative ORF elements** | 11 | 5 | 3 | 8 | 5 | 6 | 8 | 3 | 14 | 7 | 70 |
NO. ADD'L REP. ELEMENTS | 64 | 28 | 23 | 32 | 32 | 26 | 42 | 72 | 62 | 64 | 445 |
New Repetitive Content | 72% | 54% | 50% | 59% | 34% | 75% | 44% | 93% | 59% | 38% | 63% |
Repetitive content*** at 75% threshold (similarity) | 81% | 83% | 80% | 82% | 70% | 86% | 76% | 85% | 75% | 82% | 80% |
Repetitive content*** at 99% threshold (identity) | 25% | 21% | 22% | 24% | 15% | 35% | 19% | 30% | 15% | 29% | 24% |