SNP discovery via 454 transcriptome sequencing.
SNP discovery via 454 transcriptome sequencing.
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通过454转录组测序发现SNP。
DOI：
10.1111/j.1365-313x.2007.03193.x
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发表时间：
2007-09
期刊：
影响因子：
7.2
通讯作者：
Schnable, Patrick S
中科院分区：
文献类型：
--
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
454生命科学公司商业化的大规模平行焦磷酸测序技术被用于对通过激光捕获显微切割（LCM）从两个玉米自交系中分离出的茎尖分生组织的转录组进行测序。一个使用POLYBAYES多态性检测系统的计算流程被应用于454表达序列标签（ESTs），并用于检测两个自交系之间的单核苷酸多态性（SNPs）。分别使用来自B73和Mo17自交系的260000和280000个454 ESTs通过计算确定了假定的SNPs。在9980个独特的B73基因组锚定序列（MAGIs）中检测到超过36000个假定的SNPs。严格的后处理将这个数量减少到>7000个假定的SNPs。这些假定的SNPs的一个样本中超过85%（94/110）通过桑格测序成功验证。基于这个验证率，这个初步实验保守地在>2400个玉米基因中确定了>4900个有效的SNPs。这些结果表明，基于454的转录组测序是一种用于高通量获取基因相关SNPs的极佳方法。
A massively parallel pyro-sequencing technology commercialized by 454 Life Sciences Corporation was used to sequence the transcriptomes of shoot apical meristems isolated from two inbred lines of maize using laser capture microdissection (LCM). A computational pipeline that uses the POLYBAYES polymorphism detection system was adapted for 454 ESTs and used to detect SNPs (single nucleotide polymorphisms) between the two inbred lines. Putative SNPs were computationally identified using 260 000 and 280 000 454 ESTs from the B73 and Mo17 inbred lines, respectively. Over 36 000 putative SNPs were detected within 9980 unique B73 genomic anchor sequences (MAGIs). Stringent post-processing reduced this number to > 7000 putative SNPs. Over 85% (94/110) of a sample of these putative SNPs were successfully validated by Sanger sequencing. Based on this validation rate, this pilot experiment conservatively identified > 4900 valid SNPs within > 2400 maize genes. These results demonstrate that 454-based transcriptome sequencing is an excellent method for the high-throughput acquisition of gene-associated SNPs.