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Rapid and efficient genome-wide characterization of Xanthomonas TAL effector genes.

Yu YH, Lu Y, He YQ, Huang S, Tang JL - Sci Rep (2015)

Bottom Line: Their specificity is determined by a tandem repeat domain.Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling.Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.

ABSTRACT
Xanthomonas TALE transcriptional activators act as virulence or avirulence factors by activating host disease susceptibility or resistance genes. Their specificity is determined by a tandem repeat domain. Some Xanthomonas pathogens contain 10-30 TALEs per strain. Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling. To facilitate TALE studies, we developed an efficient and rapid pipeline for genome-wide cloning of tal genes as many as possible from a strain. Here, we report the pipeline and its use to identify all 18 tal genes from a newly isolated strain of the rice pathogen Xathomonas oryzae. Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

No MeSH data available.


Related in: MedlinePlus

RFLP analysis of the tal genes in strain K74 and the correspondence between the banding pattern and the talXooK74 genes.The genomic DNA was digested with BamHI and a portion of 5′ sequence of talC was used as probe.
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f1: RFLP analysis of the tal genes in strain K74 and the correspondence between the banding pattern and the talXooK74 genes.The genomic DNA was digested with BamHI and a portion of 5′ sequence of talC was used as probe.

Mentions: Strain K74 is a spontaneous streptomycin-resistant mutant of Xoo strain 1074 collected from southern coastline region of China with strong virulence to a number of rice cultivars22 (Supplementary Table 1). To approximate the number of tal genes in the strain, we performed a RFLP analysis. Since typical tal genes contain two conserved BamHI restriction sites (Supplementary Fig. 1A), BamHI was used to digest the genomic DNA of strain K74 followed by agarose gel electrophoresis. After transferred to a membrane from the gel, the DNA fragments were hybridized with labeled 500 bp N-terminal fragment of the previously identified tal gene talC23 (Supplementary Fig. 1A). The hybridization result showed 10 clear, visible bands with sizes ranging from 2.8–4.5 kb. Of which, seven bands displayed similar hybridization signal intensity, while three exhibited significantly stronger signal intensity (Fig. 1), indicating more than one tal gene copy within each of the three bands. The RFLP result suggests that the genome of strain K74 may contain more than 13 tal gene copies.


Rapid and efficient genome-wide characterization of Xanthomonas TAL effector genes.

Yu YH, Lu Y, He YQ, Huang S, Tang JL - Sci Rep (2015)

RFLP analysis of the tal genes in strain K74 and the correspondence between the banding pattern and the talXooK74 genes.The genomic DNA was digested with BamHI and a portion of 5′ sequence of talC was used as probe.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4536657&req=5

f1: RFLP analysis of the tal genes in strain K74 and the correspondence between the banding pattern and the talXooK74 genes.The genomic DNA was digested with BamHI and a portion of 5′ sequence of talC was used as probe.
Mentions: Strain K74 is a spontaneous streptomycin-resistant mutant of Xoo strain 1074 collected from southern coastline region of China with strong virulence to a number of rice cultivars22 (Supplementary Table 1). To approximate the number of tal genes in the strain, we performed a RFLP analysis. Since typical tal genes contain two conserved BamHI restriction sites (Supplementary Fig. 1A), BamHI was used to digest the genomic DNA of strain K74 followed by agarose gel electrophoresis. After transferred to a membrane from the gel, the DNA fragments were hybridized with labeled 500 bp N-terminal fragment of the previously identified tal gene talC23 (Supplementary Fig. 1A). The hybridization result showed 10 clear, visible bands with sizes ranging from 2.8–4.5 kb. Of which, seven bands displayed similar hybridization signal intensity, while three exhibited significantly stronger signal intensity (Fig. 1), indicating more than one tal gene copy within each of the three bands. The RFLP result suggests that the genome of strain K74 may contain more than 13 tal gene copies.

Bottom Line: Their specificity is determined by a tandem repeat domain.Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling.Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.

ABSTRACT
Xanthomonas TALE transcriptional activators act as virulence or avirulence factors by activating host disease susceptibility or resistance genes. Their specificity is determined by a tandem repeat domain. Some Xanthomonas pathogens contain 10-30 TALEs per strain. Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling. To facilitate TALE studies, we developed an efficient and rapid pipeline for genome-wide cloning of tal genes as many as possible from a strain. Here, we report the pipeline and its use to identify all 18 tal genes from a newly isolated strain of the rice pathogen Xathomonas oryzae. Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

No MeSH data available.


Related in: MedlinePlus