Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis

One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity of Bd in natural systems. The most common non-invasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully-selected regions of the Bd genome. We obtained robust...蛙壶菌（chytrid fungus，学名*Batrachochytrium dendrobatidis*，缩写Bd）是对野生动物极具破坏性的新发病原体之一，可感染全球范围内数百种两栖动物。通过纯培养Bd菌株获得的基因组数据，推动了我们对其系统发育、基因组结构以及致病机制的认知。然而，纯培养菌株的获取流程繁琐，全基因组测序的成本相对高昂，因此经遗传学特征鉴定的分离株数量相对有限。因此，我们对自然生态系统中Bd的遗传多样性仍知之甚少。从自然种群中采集Bd样本最常用的非侵入式方法为拭取两栖动物的皮肤样本。全球范围内已从两栖动物身上采集了数十万份拭子样本，但通过拭子获取的Bd DNA往往质量欠佳且/或浓度不足。本研究基于Fluidigm Access Array平台，开发了定制化的Bd基因分型检测方法，用于扩增Bd基因组中192个经过精心筛选的基因组区域。我们获得了稳定性极佳的……