Genes
The MLST for Xylella fastidiosa scheme uses internal fragments of the following seven house-keeping genes:
| Gene | Gene Function | Biochemical Function | Temecula (PD0001) Gene Position | M12 (ALS0299) Gene Position | 9a5c (CVC0018) Gene Postion |
|---|---|---|---|---|---|
| leuA | 2-isopropylmalate synthase | amino acid biosynthesis | PD1047 | Xfasm_1205 | XF1818 |
| petC | ubiquinol cytochrome C oxidoreductase, cystochrome C1 subunit | electron transport | PD1775 | Xfasm_1943 | XF0910 |
| malF | ABC transporter sugar permease | transport of carbohydrates | PD1465 | Xfasm12_1606 | XF2447 |
| cysG | siroheme synthase | biosynthesis of heme, porphyrin | PD1840 | Xfasm12_2018 | XF0832 |
| holC | DNA polymerase III holoenzyme, chi subunit | replication | PD0104 | Xfasm12_0112 | XF0136 |
| nuoL | NADH-ubiquinone oxidoreductase, NQO12 subunit | aerobic respiration | PD0259 | Xfasm12_0280 | XF0316 |
| gltT | glutamate symport protein | transport of amino acids | PD1516 | Xfasm12_1656 | XF0656 |
PCR Primers
The following primers are used for both PCR and sequencing:
| Gene | Primer Sequences | Amplicona Length (bp) |
|---|---|---|
| leuA | for - 5' GGTGC ACGCC AAATC GAATG 3' rev - 5' GTATC GTTGT GGCGT ACACT G 3' | 708 |
| petC | for - 5' GCTGC CATTC GTTGA AGTAC CT 3' rev - 5' GCACG TCCTC CCAAT AAGCC T 3' | 533 |
| malF | for - 5' TTGC TGGT CCTG CGGT GTTG 3' rev - 5' GACAGCAGAAGCACGTCCCAGAT 3' | 730 |
| cysG | for - 5' GCCGA AGCAG TGCTG GAA G 3' rev - 5' GCCGA AGCAG TGCTG GAA G 3' | 600b |
| holC | for - 5' ATGGC ACGCG CCGAC TTCT 3' rev - 5' ATGTC GTGTT TGTTC ATGTG CAGG 3' | 379 |
| nuoL | for - 5' TAGCG ACTTA CGGTT ACTGG GC 3' rev - 5' ACCAC CGATC CACAA CGCAT 3' | 557c |
| gltT | for - 5' TCATG ATCCA AATCA CTCGC TT 3' rev - 5' ACTGG ACGCT GCCTC GTA AA CC 3' | 654 |
| a Amplicon length with primers removed. | ||
| b A 6bp indel appears in some isolates. | ||
| c A 30bp indel appears in some isolates. | ||