TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions

• Main Authors: Liang Sun, Yinbing Ge, J. Alan Sparks, Zachary T. Robinson, Xiaofei Cheng, Jiangqi Wen, Elison B. Blancaflor
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2019-07-01
• Series: Frontiers in Genetics
• Subjects: truncated T-DNA; next generation sequence; forward genetics; software; HLB3
• Online Access: https://www.frontiersin.org/article/10.3389/fgene.2019.00685/full

Transfer (T)-DNA insertions in mutants isolated from forward genetic screens are typically identified through thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), inverse PCR, or plasmid rescue. Despite the popularity and success of these methods, they have limited capabilities, particularly in situations in which the T-DNA is truncated. Here, we present a next generation sequencing (NGS)-based platform to facilitate the identification of complete and truncated T-DNA insertions. Our method enables the detection of the corresponding T-DNA insertion orientation and zygosity as well as insertion annotation. This method, called TDNAscan, was developed to be an open source software. We expect that TDNAscan will be a valuable addition to forward genetics toolkits because it provides a solution to the problem of causal gene identification, particularly genes disrupted by truncated T-DNA insertions. We present a case study in which TDNAscan was used to determine that the recessive Arabidopsis thaliana hypersensitive to latrunculin B (hlb3) mutant isolated in a forward genetic screen of T-DNA mutagenized plants encodes a class II FORMIN.