TABLE 1.
Characteristics of SSR primer sequences produced and used to study X. fastidiosa isolatesa
| Primer | Forward sequence | Reverse sequence | Type of repeat motif | No. of alleles | Amplicon size (bp) | ORF definition | Locus location in genome |
|---|---|---|---|---|---|---|---|
| OSSR-2 | TTGCTTCACCATTAGCCTTATC | GGCCGTACAGGACCGATC | (ATG)9 | 4 | 264 | Conserved hypothetical protein | 9403-9430 |
| OSSR-9 | TAGGAATCGTGTTCAAACTG | TTACTATCGGCAGCAGAC | (TTTCCGT)13 | 16 | 362 | Exopolyphosphatase | 24428-24519 |
| OSSR-12 | ACAGTCTGTGTCCGCAATTTG | CAGGCGCAGATAGCATTGATC | (AGAGGGTAT)9 | 7 | 360 | Conserved hypothetical protein | 71017-71098 |
| OSSR-14 | GGCGTAACGGAGGAAACG | ATGAACACCCGTACCTGG | (TGATCCATCCCTGTG)11 | 16 | 370 | copB | 35279-35444 |
| OSSR-16 | GCAAATAGCATGTACGAC | GTGTTGTGTATGTGTTGG | (CTGCTA)12 | 13 | 275 | NADH-ubiquinone oxidoreductase NQO12 subunit | 10784-11856 |
| OSSR-17 | AGTACAGCGAACAGGCATTG | AGCAACCAGGACGGGAAC | (TGCCTG)10 | 23 | 257 | Cell cycle protein | 25656-25716 |
| OSSR-19 | GCTGTGAACTTCCATCAATCC | GCAAGTAGGGGTAAATGTGAC | (CAGGATCA)10 | 11 | 274 | Adenylosuccinate lyase | 33208-33288 |
| OSSR-20 | ATCTGTGCGGCGGTTCTG | CACTTGCGGCGTAGATACTTC | (AGGATGCTA)20 | 14 | 154 | Competence-related protein | 1512703-1512883 |
| CSSR-4 | AACCCAATTCTTTTAATATGTG | TTGCAGCATTAGATATTTGAG | (TGCC)7 | 4 | 231 | Peptidyl-prolyl cis-trans isomerase | 1143270-1143298 |
| CSSR-6 | CGCACTGTCATCCATTTAATC | GCTGCTTCATCTAGACGTG | (GCTGTA)7 | 11 | 279 | Hypothetical protein | 98393-98435 |
| CSSR-7 | CACAGCGAACAGGCATTG | AGCAACCAAGACGGGAAC | (CTGTGC)14 | 14 | 279 | Alkaline phosphatase | 628252-628336 |
| CSSR-10 | GCAACCACAAAGCCGCAG | AGCACCTCTTAGCATCACTGG | (CAATGA)10 | 13 | 202 | tRNA/rRNA methylase | 1882243-1882303 |
| CSSR-12 | TAAGTCCATCACCGAGAAG | AAACGGATTTAGGAACACTC | (GAAGGCGTA)27 | 8 | 491 | Conserved hypothetical protein | 1220096-1220339 |
| CSSR-13 | CAATGTCACTCAGGTCAG | TTCTGGAATACATCAAATGC | (TGTTGGGG)10 | 14 | 305 | Hypothetical protein | 2639987-2640067 |
| CSSR-16 | CGATCAACCCATTCACTG | GCTCCTATTTGCATGATATTG | (GTGGTGGCA)6 | 5 | 199 | PilY1 | 30060-30114 |
| CSSR-17 | AGAAGTATTCGCTACGCTACG | GGTGATGATTCAGTTGGTGTTG | (CTGATGTG)9 | 13 | 199 | Hydroxyacylglutathione hydrolase | 2050614-2050686 |
| CSSR-18 | GTGCTTCCAGAAGTTGTG | GACTGTTCTCTTCGTTCAG | (GCCAA)12 | 9 | 304 | Hypothetical protein | 408996-409056 |
| CSSR-19 | TGCTGTGATTGGAGTTTTGC | TCAAACGAATCTGTCCATCAAG | (TGGTGAG)7 | 3 | 354 | Site-specific DNA-methyltransferase | 1717597-1717646 |
| CSSR-20 | GGTATCGCCTTTGGTTCTGG | GACAACCGACATCCTCATGG | (GTAGCA)8 | 15 | 247 | Phosphoglycolate phosphatase | 1155075-1155523 |
| ASSR-9 | GGTTGTCGGGCTCATTCC | TTGTCACAGCATCACTATTCTC | (CAAGTAC)11 | 16 | 259 | 50S ribosomal protein L13 | 35632-35709 |
| ASSR-11 | AGAGGCAACGCAGGAACAG | GTGAGTTATATCGGTGCAGCAG | (ACGCATC)10 | 9 | 260 | 50S ribosomal protein L20 | 10087-10157 |
| ASSR-12 | TGCTCATTGTGGCGAAGG | CGCAACGTGCATTCATCG | (GATTCAG)14 | 6 | 300 | Fructose-bisphosphate aldolase | 76999-77097 |
| ASSR-14 | TTGACTCAAGGAATAAAAC | GAAAAGAGTGTCAATACG | (CTGCGTGC)11 | 13 | 410 | Hypothetical protein | 61336-61424 |
| ASSR-16 | TTAATCAACAACGCTTATCC | TCGCAGTAGCCAGTATAC | (GCTCCGGTTCTA)26 | 12 | 497 | 1,4-β-Cellobiosidase | 803-1115 |
| ASSR-19 | CGCCGACTGTCTATGTGAC | TTCCTAGCAATGGCAATGTTG | (ACAACG)10 | 4 | 332 | Conserved hypothetical protion | 10957-11017 |
| ASSR-20 | TTACTATCGGCAGCAGACG | TGAAGCAATGGTGGATTTAGG | (ACAGAAA)10 | 16 | 302 | Exopolyphosphatase | 17324-17394 |
| GSSR-4 | GCGTTACTGGCGACAAAC | GCTCGTTCCTGACCTGTG | (ATCC)7 | 15 | 289 | Conserved hypothetical protein | 1729643-1729671 |
| GSSR-6 | TGTTCTCTTCGTTCAGCCAAGC | CGCAGCAGAGCAGCAGTG | (CTTGT)12 | 8 | 265 | None coding | 1941750-1941810 |
| GSSR-7 | ATCATGTCGTGTCGTTTC | CAATAAAGCACCGAATTAGC | (GGCAAC)24 | 17 | 385 | None coding | 19306-19850 |
| GSSR-12 | TTACGCTGATTGGCTGCATTG | GTCAAACACTGCCTATAGAGCG | (TATCTGT)20 | 10 | 471 | None coding | 52417-52557 |
| GSSR-14 | TTGATGTGCTTTTGCGGTAAG | GACAGGTCCTCTCATTGCG | (TCCCGTA)24 | 14 | 402 | None coding | 404211-404379 |
| GSSR-15 | CCGCAGAGTCCGTTGTAAC | AGCCGACGCACGGTATATC | (AGCCTGC)17 | 10 | 404 | Conserved hypothetical protein | 2229645-2229764 |
| GSSR-19 | GCCGATGCAGAACAAGAAC | TCAACTTCGCCACACCTG | (GAAAACAAG)19 | 13 | 388 | Phosphomannomutase | 153189-153360 |
| GSSR-20 | TGGATGGATAGATGATTCAGCC | CGATCAGTGGAGGATGTCTTG | (GAACCACTA)7 | 4 | 354 | None coding | 2203868-2203931 |
a
The O, C, A, and G prefixes in the primer names refer to the X. fastidiosa genome (oleander, citrus, almond, and grape strains, respectively) from which they were designed. The open reading frame (ORF) definition refers to the gene the SSR locus is in or close to.