Data from: Cross-platform compatibility of de novo-aligned SNPs in a non-model butterfly genus

High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation. We then used a de novo approach to bioinformatic locus assembly and SNP discovery for subsequent phylogenetic analyses. We found a high rate of locus recovery despite differences in library preparation and sequencing platforms, as well as overall high levels of data compatibility after data processing and filtering. These results provide the first application of NGS methods for phylogenetic reconstruction in Speyeria, and support the use and long-term viability of SNP genotyping applications in non-model systems.用于全基因组标记基因分型的高通量测序技术，正快速被应用于保护生物学与生物多样性研究中的非模式生物（non-model organisms）系统发育分析领域。然而，单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因分型的可重复性，以及不同方法生成的数据集间标记重叠程度与兼容性，尚未在非模式生物系统中得到验证。本研究采用双酶切限制性位点关联DNA测序技术，在两种不同的Illumina测序平台上，通过两种文库制备方案变体，对来自贝凤蝶属（Speyeria）的22份共通标本完成了测序。随后采用从头组装（de novo）的生物信息学策略完成位点组装与SNP发掘，用于后续的系统发育分析。研究结果表明，尽管文库制备方案与测序平台存在差异，但位点回收率仍维持在较高水平；且经数据处理与过滤后，数据集整体展现出高度的数据兼容性。本研究成果实现了下一代测序（Next Generation Sequencing，NGS）技术在贝凤蝶属（Speyeria）系统发育重建中的首次应用，并证实了SNP基因分型技术在非模式生物系统中的应用价值与长期可行性。