Rapid and Quantitative Detection of Leifsonia xyli subsp. xyli in Sugarcane Stalk Juice Using a Real-Time Fluorescent (TaqMan) PCR Assay

Table 1

Primers and probe information for Leifsonia xyli subsp. xyli (Lxx).

Primer/probe	Sense	Sequence (5′-3′)	Gene target	Amplicon size (bp)	Reference
Pat1-F1	Forward	TTGTTTAGTTTTCGTTGGCG	Pat1	942	In this study
Pat1-R1	Reverse	CTATGCTGGAGCCACAG
CxxITSf#5	Forward	TCAACGCAGAGATTGTCCA	ITS	305	Fegan et al., 1998 [19]
CxxITSr#5	Reverse	GTACGGGCGGTACCTTTTC
Pat1-F2	Forward	GGAATACTCGCTATGTGTTG	Pat1	597	In this study
Pat1-R2	Reverse	CCAATACTATGCCGTAGAAAG
Pat1-QF	Forward	GGTTCCATTGCTTACCGATT	Pat1	106	Wang et al., 2015 [23]
Pat1-QR	Reverse	CAAGTTTCGACAGGAACAGC
Pat1-QP	Probe	FAM-CCACGGCTACGTCAATTCGGG-TAMRA

FAM, 6-carboxy-fluorescein reporter dye; TAMRA, 6-carboxytetramethylrhodamine fluorescent quencher.
Primers and probe targeted at Pat1 gene of Leifsonia xyli subsp. xyli (strain CTCB07, GenBank acc. number NC_006087) were designed by authors of this study and Wang et al. [23]. CxxITSf#5/CxxITSr#5 targeted at 16S-23S rRNA internal transcribed spacer (ITS) regions reported by Fegan et al. [19].