Forthman Michael, Gordon Eric R L, Kimball Rebecca T
California State Collection of Arthropods, Plant Pest Diagnostics Branch, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA.
Entomology and Nematology Department, University of Florida, 1881 Natural Area Drive, Gainesville, FL 32611, USA.
R Soc Open Sci. 2023 Jun 28;10(6):230307. doi: 10.1098/rsos.230307. eCollection 2023 Jun.
Target capture is widely used in phylogenomic, ecological and functional genomic studies. Bait sets that allow capture from a diversity of species can be advantageous, but high-sequence divergence from baits can limit yields. Currently, only four experimental comparisons of a critical target capture parameter, hybridization temperature, have been published. These have been in vertebrates, where bait divergences are typically low, and none include invertebrates where bait-target divergences may be higher. Most invertebrate capture studies use a fixed, high hybridization temperature to maximize the proportion of on-target data, but many report low locus recovery. Using leaf-footed bugs (Hemiptera: Coreoidea), we investigate the effect of hybridization temperature on capture success of ultraconserved elements targeted by (i) baits developed from divergent hemipteran genomes and (ii) baits developed from less divergent coreoid transcriptomes. Lower temperatures generally resulted in more contigs and improved recovery of targets despite a lower proportion of on-target reads, lower read depth and more putative paralogues. Hybridization temperatures had less of an effect when using transcriptome-derived baits, which is probably due to lower bait-target divergences and greater bait tiling density. Thus, accommodating low hybridization temperatures during target capture can provide a cost-effective, widely applicable solution to improve invertebrate locus recovery.
靶向捕获广泛应用于系统发育基因组学、生态学和功能基因组学研究。能够从多种物种中进行捕获的诱饵组可能具有优势，但诱饵的高序列差异会限制产量。目前，关于关键靶向捕获参数——杂交温度，仅发表了四项实验比较。这些研究均针对脊椎动物，其诱饵差异通常较低，且没有一项研究包括诱饵 - 靶标差异可能更高的无脊椎动物。大多数无脊椎动物捕获研究使用固定的高杂交温度来最大化靶向数据的比例，但许多研究报告基因座回收率较低。我们以缘蝽（半翅目：缘蝽科）为研究对象，调查了杂交温度对以下两类诱饵靶向的超保守元件捕获成功率的影响：（i）由分化的半翅目基因组开发的诱饵，以及（ii）由分化程度较低的缘蝽转录组开发的诱饵。尽管靶向 reads 的比例较低、读长深度较低且存在更多假定的旁系同源物，但较低的温度通常会产生更多的重叠群并提高靶标的回收率。使用转录组衍生的诱饵时，杂交温度的影响较小，这可能是由于诱饵 - 靶标差异较低且诱饵平铺密度较高。因此，在靶向捕获过程中采用较低的杂交温度可以提供一种经济高效、广泛适用的解决方案，以提高无脊椎动物基因座的回收率。
