鳞翅目基因组IIB型内切酶位点的统计分析

IIB型限制内切酶能够识别并切割特异酶切位点两端特定距离的DNA,形成粘性末端的30 bp左右的等长DNA片段。利用其特性与限制性酶切位点关联测序技术(RAD)相结合发展出2b-RAD简化基因组测序技术,应用于遗传图谱构建、种群遗传结构分析、性状定位以及细菌分型等多种研究领域。构建2b-RAD测序文库之前,需要对基因组中的IIB型限制内切酶位点进行预测与统计分析,制定有效的测序文库构建方案。本文利用Python语言构建分析基因组中IIB型限制内切酶位点的流程,预测并统计6个鳞翅目代表物种基因组含有的8个商业化IIB型限制内切酶的酶切位点,比较了各个基因组与IIB型限制内切酶之间含有的酶切位点总量、重复序列数量以及酶切间隔长度的关系,为在昆虫基因组中进一步试行2b-RAD研究提供了参考。

Statistical analysis of the IIB restriction enzyme sites in lepidopteran genomes

IIB restriction enzymes can identify specific recognition sites and cleave DNA on both sides out of the recognition site, producing about 30 bp DNA fragments of equal length with sticky ends. Associating IIB restriction enzymes with restriction-site associated DNA sequencing (RAD), 2b-RAD was developed in genetic map construction, population genetic structure analysis, quantitative trait loci, bacterial typing, etc. Before 2b-RAD sequencing library construction, IIB restriction enzyme sites should be predicted and calculated to construct a valid sequencing library scheme. An analysis process of IIB restriction enzyme site in the genome based on Python was constructed in this article, which is performed to predict eight commercialized IIB restriction enzyme sites in six genomes of representative lepidopteran species. The counts of enzyme sites, amounts of repetitive sequences, and gap lengths between sites were compared between species and between enzymes, which provided a reference for the performance of 2b-RAD in entomology genomes.