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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

Repeat numbers and RVDs of the 18 TalXooK74 effectors.The last half repeat is counted as one repeat.
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f3: Repeat numbers and RVDs of the 18 TalXooK74 effectors.The last half repeat is counted as one repeat.

Mentions: According to the sizes of the tal-BamHI fragments, the tal genes of Xoo strain K74 and their corresponding protein products were denoted as talXooK74-1 to talXooK74-18 (Fig. 1) and TalXooK74-1 to TalXooK74-18 (Fig. 3), respectively. The number of repeat units in the TALEs varies from 12.5 to 26.5 (Fig. 3) and the majority of the repeat units encode 34 amino acids. Similar to all known TALEs, the last unit in the tandem repeat motifs of all 18 TalXooK74 effectors is only a half repeat (Supplementary Table 6).


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

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

Repeat numbers and RVDs of the 18 TalXooK74 effectors.The last half repeat is counted as one repeat.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Repeat numbers and RVDs of the 18 TalXooK74 effectors.The last half repeat is counted as one repeat.
Mentions: According to the sizes of the tal-BamHI fragments, the tal genes of Xoo strain K74 and their corresponding protein products were denoted as talXooK74-1 to talXooK74-18 (Fig. 1) and TalXooK74-1 to TalXooK74-18 (Fig. 3), respectively. The number of repeat units in the TALEs varies from 12.5 to 26.5 (Fig. 3) and the majority of the repeat units encode 34 amino acids. Similar to all known TALEs, the last unit in the tandem repeat motifs of all 18 TalXooK74 effectors is only a half repeat (Supplementary Table 6).

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