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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

A flow chart diagram illustrating the steps in the pipeline and in conventional methods.
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f5: A flow chart diagram illustrating the steps in the pipeline and in conventional methods.

Mentions: Here, we report a simple and convenient method for genome-wide identification of Xanthomonas tal genes. To meet the challenges of highly conserved tal gene structures and their large tandem repeat segments, divers strategies have been used to determine accurately the DNA sequences of the repeat region; however, most of the strategies rely on the use of transposon-based or random DNA shearing sequencing technologies1920, which are cumbersome and expensive. The pipeline described in this paper aimed to overcome these drawbacks with simple experiments and approaches. Most experiments involved in the pipeline are standard routine experiments in many laboratories. The method is efficient, rapid, and economical. In our laboratory, a well-trained technician can complete the pipeline to identify tal genes genome-widely from one or two Xoo strains in less than one month. A flow chart diagram illustrating the steps in the pipeline is shown in Fig. 5.


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

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

A flow chart diagram illustrating the steps in the pipeline and in conventional methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: A flow chart diagram illustrating the steps in the pipeline and in conventional methods.
Mentions: Here, we report a simple and convenient method for genome-wide identification of Xanthomonas tal genes. To meet the challenges of highly conserved tal gene structures and their large tandem repeat segments, divers strategies have been used to determine accurately the DNA sequences of the repeat region; however, most of the strategies rely on the use of transposon-based or random DNA shearing sequencing technologies1920, which are cumbersome and expensive. The pipeline described in this paper aimed to overcome these drawbacks with simple experiments and approaches. Most experiments involved in the pipeline are standard routine experiments in many laboratories. The method is efficient, rapid, and economical. In our laboratory, a well-trained technician can complete the pipeline to identify tal genes genome-widely from one or two Xoo strains in less than one month. A flow chart diagram illustrating the steps in the pipeline is shown in Fig. 5.

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