Table 1.
The ten most abundant repetitive sequence clusters detected in the Miscanthus genome
| Cluster ID | Cluster length (bp) | Estimated copy number in Miscanthus genome | Copy number in sorghum genome | Best match in GenBank nt | Best match in sorghum genome | Best match in Plant Repeat Database |
|---|---|---|---|---|---|---|
| 137362 | 3,866 | 8.82 × 103 | 2.15 × 103 | AC169373 Sorghum | Chromosome 2 | AF137608 Sorghum bicolor centromere-associated repetitive DNA element CEN38 |
| 136340 | 1,441 | 1.97 × 104 | 7.73 × 103 | No hits | Super contig 18 | AY129008 Zea mays CRM centromeric retrotranposon |
| 137115 | 2,512 | 1.02 × 104 | 1.90 × 103 | No hits | Super contig 20 | AY828019 Oryza sativa (japonica cultivar-group) clone CRR2_CH4-2 CRR2 retrotransposon |
| 136416 | 1,855 | 1.32 × 104 | 1.27 × 103 | No hits | Chromosome 10 | AY129008 Zea mays CRM centromeric retrotranposon |
| 137059 | 2,586 | 8.27 × 103 | 2.05 × 102 | No hits | Chromosome 2 | ZRSiTERTOOT00157 giepum_438D03-1 giepum_Z438D03-1 Z438D03 retrotransposon |
| 137200 | 3,655 | 5.61 × 103 | 3.68 × 102 | No hits | Chromosome 9 | SRSiTERTOOT00084 leviathan_98N8-1 leviathan_98N8-1 retrotransposon |
| 137015 | 2,882 | 6.83 × 103 | 7.5 × 101 | No hits | Chromosome 7 | AF078902.1 Sorghum bicolor centromere element pHind12 |
| 137326 | 3,527 | 5.56 × 103 | 3.30 × 102 | AF11417 Sorghum | Chromosome 2 | AZ922428 MRCot4C10 Sorghum bicolor MRCot Sorghum bicolor genomic similar to Sorghum bicolor centromere element pHind12 |
| 137201 | 3,647 | 5.28 × 103 | 2.16 × 102 | No hits | Chromosome 10 | ZRSiTERTOOT00156 giepum_333J11-1hdnm giepum_Z333J11-1hdnm Z333J11 retrotransposon |
| 135786 | 2,456 | 7.82 × 103 | 1.89 × 102 | No hits | Chromosome 4 | ORSiTERTOOT00275 osr10 retrotransposon |