BLAST-Based Categorization of HRCot, MRCot, and SLCot Clonesu
| BLASTcategories[i] | Subcategories[i] | HRCot | MRCot | St.Cot | Ref./Acc.[ii] | ||||||
| No. | % | No. | % | No. | % | ||||||
| No significant hit | 90 | 35.6 | 199 | 48.7 | 339 | 67.9 | |||||
| Chloroplast DNA | 0 | 0.0 | 41 | 10.0 | 5 | 1.0 | |||||
| Mitochondrial DNA | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | |||||
| rDNA | 18S-5.8S-26S rDNA | 22 | 8.7 | 35 | 8.6 | 9 | 1.8 | Many refs. | |||
| 5S rDNA | 2 | 0.8 | 0 | 0.0 | 0 | 0.0 | Many refs. | ||||
| Centromeric repent | Sorghum, pHind12 | 2 | 0.8 | 4 | 1.0 | 0 | 0.0 | Miller et al. 1998a | |||
| Sorghum, pHind22 | 0 | 0.0 | 1 | 0.2 | 0 | 0.0 | Miller et al. 1998a | ||||
| Sorghum, pSau3A9 | 4 | 1.6 | 1 | 0.2 | 0 | 0.0 | Jiang et al. 1996 | ||||
| Sorghum, pSau3A10 | 3 | 1.2 | 0 | 0.0 | 0 | 0.0 | Miller et al. 1998b | ||||
| Sorghum, CEN38 | 1 | 0.4 | 0 | 0.0 | 0 | 0.0 | Zwick et al. 2000 | ||||
| Retroelement[iii] | CACTA-type element/TNP-2 gene | 0 | 0.0 | 2 | 0.5 | 1 | 0.2 | He et al. 2000 | |||
| Sorghum Leviathan | 1 | 0.4 | 5 | 1.2 | 0 | 0.0 | U07815, U07816 | ||||
| Sorghum, Candystripe-1 | 2 | 0.8 | 0 | 0.0 | 0 | 0.0 | Chopra et al. 1999 | ||||
| Sorghum. Retrosor-2 | 1 | 0.4 | 1 | 0.2 | 3 | 0.6 | AF061282 | ||||
| Sorghum. Retrosor-6 | 34 | 13.4 | 7 | 1.7 | 0 | 0.0 | AF061282 | ||||
| Barley, cereba polyprotein pseudogene | 0 | 0.0 | 1 | 0.2 | 0 | 0.0 | Presting et al. 1998 | ||||
| Rice, gypsy-like integrase gene | 0 | 0.0 | 3 | 0.7 | 0 | 0.0 | AF244793 | ||||
| Maize, rev. tra./integr. pseudogene | 0 | 0.0 | 1 | 0.2 | 0 | 0.0 | AF030633 | ||||
| Sorghum, putative LTR | 1 | 0.4 | 0 | 0.0 | 0 | 0.0 | AF061282 | ||||
| MITE[iii] | Putative MITE in sugarcane ubi9 gene | 0 | 0.0 | 3 | 0.7 | 0 | 0.0 | AF093505 | |||
| Putative MITE in sorghum kafirin BAC | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | AF061282 | ||||
| Other dispersed repeat[iii] | PRBM-1-related repeat | 1 | 0.4 | 0 | 0.0 | 0 | 0.0 | Turcich et al. 1996 | |||
| Sorghurn HCSR-1 repeat | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | AF061282 | ||||
| Sorghum HCSR-7 repeat | 2 | 0.8 | 0 | 0.0 | 0 | 0.0 | AF061282 | ||||
| Johnsongrass XSR3 repeat[iv] | 0 | 0.0 | 1 | 0.2 | 0 | 0.0 | X54624 | ||||
| Johnsongrass XSR6 repeat[iv] | 1 | 0.4 | 0 | 0.0 | 0 | 0.0 | X54625 | ||||
| Sorghum, putative dispersed repeat | 1 | 0.4 | 2 | 0.5 | 0 | 0.0 | AF114171 | ||||
| Characterized gene | Rice, bZIP DNA-binding factor | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | U04295 | |||
| Rice, monosaccharide transporter 1 | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | AB052883 | ||||
| Barley, cp33Hv protein | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | AJ224325 | ||||
| Ice plant protein kinase | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | Z30331 | ||||
| Maize, peroxidase gene | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | AJ401276 | ||||
| Sorghum, NADPH-dependent reductase | 0 | 0.0 | 0 | 0.0 | 1 | 0.2 | AF010283 | ||||
| Rice, OsNAC4 gene | 0 | 0.0 | 1 | 0.2 | 0 | 0.0 | AR028183 | ||||
| Canola, FCA gene | 0 | 0.0 | 1 | 0.2 | 0 | 0.0 | AJ237848 | ||||
| Uncertain character[iii] | 4 | 1.6 | 7 | 1.7 | 3 | 0.6 | |||||
| Repetitive EST | 49 | 19.4 | 27 | 6.6 | 11 | 2.2 | |||||
| Ambiguous EST | 11 | 4.3 | 11 | 2.7 | 23 | 4.6 | |||||
| Unique EST | 21 | 8.3 | 55 | 13.4 | 96 | 19.2 | |||||
| Total | 253 | 100 | 409 | 100 | 499 | 100 | |||||
[i] Clones have been placed into 13 BLAST“categories” according to Figure 3. Some BLASTcategories have been further divided into “subcategories.” For each Cot library, the number (#) and percentage (%) of clones in aBLAST category/subcategory are given.
[ii] A literary reference (Ref.) or GenBank Accession number (Acc.) is given for the sequence or sequences in a subcategory.
[iii] Cot clones categorized as “Retroelements,” “MITEs,” and “Other dispersed repeats” collectively constitute “dispersed repeat sequences.”
[iv] Johnsongrass (Sorghum halepenese Pers.), an extremely aggressive weed, appears to be an interspecific hybrid descendant (autoallotetraploid) of S. bicolor and S. propinquum (Paterson et al. 1995).
[v] Genomic sequence of uncertain character.