Slimp Madeline, Williams Lindsay D, Hale Haley, Johnson Matthew G
Department of Biological Sciences Texas Tech University 2901 Main Street Lubbock Texas 79409 USA.
Appl Plant Sci. 2021 May 18;9(7). doi: 10.1002/aps3.11419. eCollection 2021 Jul.
The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested.
Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias.
We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)-typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics.
Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.
通用靶向测序标记（如为被子植物353探针集开发的标记）在种群中的成功应用，可能会减少或消除特定标记开发的需求，同时在种群水平分析中保留全基因序列的优势。然而，被子植物353标记在物种内是否提供足够的变异来计算种群统计学参数尚未得到验证。
利用得克萨斯州一项有50年历史的植物区系调查中的标本馆标本，我们使用被子植物353探针集对24个物种的95个样本进行了测序。我们的数据工作流程在物种内调用变异，并使用标准指标为群体遗传学分析准备数据。在我们的案例研究中，基因回收率仅在低浓度时受基因组文库浓度影响，且显示出有限的系统发育偏差。
我们识别出1000多个分离变异，92%的物种缺失数据为零，并证明被子植物353标记包含足够的变异来估计成对核苷酸多样性（π）——通常在0.002至0.010之间，大部分变异存在于侧翼非编码区。在经过过滤以减少连锁的一部分变异中，我们发现许多物种具有高杂合性，这表明在物种内进行更密集的采样应能估计基因流和种群动态。
被子植物353应能为保护遗传学研究带来益处，它能提供通用的可重复标记、低缺失数据和单倍型信息，同时允许纳入数十年前的标本馆标本。
