Matthews Alix E, Boves Than J, Percy Katie L, Schelsky Wendy M, Wijeratne Asela J
College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR 72401, USA.
Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA.
Life (Basel). 2023 Oct 14;13(10):2054. doi: 10.3390/life13102054.
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: ) from four individual Prothonotary Warblers (Parulidae: ). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.
微观共生体是生物群落中的关键环节。然而，由于其体积小且高质量DNA产量极低，在高通量测序（HTS）研究中带来了技术挑战，阻碍了我们在微观进化和宏观进化尺度上对宿主 - 共生体共同进化的理解。克服这些障碍的一种方法是将来自同一亚种群（即个体宿主）的多个个体汇集在一起并进行联合测序（Pool-Seq），但这样个体层面的信息就会受损。为了同时解决这两个问题（即DNA产量低和个体层面信息丢失），我们实施了一种策略性的Pool-Seq方法，以评估测序性能的差异，并在个体水平和亚种群水平上对微观羽螨的遗传多样性（单核苷酸多态性（SNP））进行分类。为此，我们从四只黄喉地莺（森莺科：）个体身上收集了带有螨虫（长缘螨科：）的羽毛。从这四个宿主（即四个螨虫亚种群）中的每一个，我们对由不同数量螨虫（1只螨虫、5只螨虫和20只螨虫）组成的三个提取池进行了全基因组测序。我们发现，与仅包含单个螨虫的样本相比，包含多个螨虫池的样本有更多的测序读数比对到羽螨参考基因组上。螨虫亚种群主要通过其相关的个体宿主（而非池大小）在遗传上形成结构，并且一个亚种群内的所有池共享大多数SNP。总之，这些结果表明观察到的模式是由亚种群水平上发生的进化过程驱动的，而不是由于池大小产生的技术信号。总的来说，尽管微观共生体在HTS研究中带来了挑战，但这项工作凸显了个体水平和亚种群水平测序对于我们在多个进化尺度上理解宿主 - 共生体共同进化的价值。
