Restriction enzyme optimization for RADseq with camel spiders (Arachnida: Solifugae)
Restriction enzyme optimization for RADseq with camel spiders (Arachnida: Solifugae)
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DOI：
10.1636/joa-s-20-040
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发表时间：
2021-02
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通讯作者：
C. E. Santibáñez-López;Keaka Farleigh;Paula E. Cushing;M. R. Graham
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作者：
C. E. Santibáñez-López;Keaka Farleigh;Paula E. Cushing;M. R. Graham
摘要。由于形态的保守和基因组资源的缺乏，人们对单尾纲蛛形纲的系统发育关系和进化模式知之甚少，而且在很大程度上尚未解决。在这项研究中，我们评估了限制性内切酶（RE）选择在双酶切限制性位点相关DNA测序（ddRADseq）中的作用，作为一种探索分离物的进化史及其对变化的沙漠景观和气候的响应的方法。我们通过计算机模拟对该方法进行了优化，探讨了不同酶组合对硅合成过程的影响。由于目前还没有独角兽的基因组数据，因此我们使用蜘蛛、蝎子、蜱虫、螨和剑蜥的基因组进行了模拟。在模拟的指导下，我们通过生成代表两个科和三个属的四个样本的数据，在Solifugae中开创了ddRADseq。我们的研究结果突出了模拟数据的实用性，并使我们相信ddRADseq将是研究分离物演化的理想方法。
Abstract. Phylogenetic relationships and evolutionary patterns within the arachnid order Solifugae are poorly understood and largely unresolved due to conserved morphology and scarce genomic resources. In this study, we evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) as a methodology for exploring the evolutionary history of solifuges and their responses to changing desert landscapes and climate. We optimized this method by using computer simulations to explore the effect of different enzyme combinations on the process in silico. Genome data are not yet available for Solifugae, so we performed the simulations using available spider, scorpion, tick, mite and xiphosuran genomes. Guided by the simulations, we then pioneered ddRADseq in Solifugae by generating data for four samples representing two families and three genera. Our results highlight the utility of simulated data and give us confidence that ddRADseq will be ideal for studying the evolution of solifuges.