de Visser Manon Chantal, France James, McCartney-Melstad Evan, Bucciarelli Gary M, Theodoropoulos Anagnostis, Shaffer Howard Bradley, Wielstra Ben
Faculty of Science, Institute of Biology Leiden Leiden University Leiden the Netherlands.
Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands.
Ecol Evol. 2025 Aug 12;15(8):e71835. doi: 10.1002/ece3.71835. eCollection 2025 Aug.
Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome-wide data. We present NewtCap: a sequence capture bait set that targets . 7 k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as "salamandrids"). We test the efficacy of NewtCap, originally designed for the Eurasian newts, in 30 species, belonging to 17 different genera that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; (1) phylogenomics, by reconstructing the phylogeny of Salamandridae, (2) phylogeography, by sequencing the four closely related species comprising the genus , (3) hybrid zone analysis, by genotyping two species and different classes of interspecific hybrids, and (4) conservation genetics, by comparing samples from several wild populations and one captive-bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.
蝾螈拥有庞大而复杂的基因组，这阻碍了全基因组测序。然而，简化代表性测序为获取全基因组数据提供了一种可行的替代方法。我们展示了NewtCap：一种序列捕获诱饵集，它靶向所有真蝾螈和火蜥蜴（蝾螈科，也称为“蝾螈”）基因组中的7000多个编码区域。我们在属于17个不同属的30个物种中测试了最初为欧亚火蜥蜴设计的NewtCap的功效，这些物种涵盖了所有主要的蝾螈科谱系。我们还在另外两个蝾螈科中测试了NewtCap。我们发现NewtCap在所有蝾螈科谱系中表现良好（但在钝口螈科和隐鳃鲵科中表现不佳）。正如预期的那样，与该属的遗传差异量与捕获效率和映射成功率呈负相关。然而，这并不妨碍我们的下游分析。我们展示了NewtCap在以下方面的潜力：（1）系统发育基因组学，通过重建蝾螈科的系统发育；（2）系统地理学，通过对组成该属的四个近缘物种进行测序；（3）杂交带分析，通过对两个物种和不同类别的种间杂种进行基因分型；（4）保护遗传学，通过比较来自几个野生种群和一个圈养繁殖种群的样本。总体而言，NewtCap有潜力推动直接、可重复且经济实惠的基因组研究，解决蝾螈科的基础和应用研究问题。
