Reiners Tobias Erik, Prochotta David, Schell Tilman, Greve Carola, Hamadou Alexander Ben, Gerheim Charlotte, Ortega Juan-Manuel, Nowak Carsten, Nebenführ Marcel, Janke Axel
Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.
LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Frankfurt Am Main, Germany.
BMC Biol. 2025 Sep 15;23(1):276. doi: 10.1186/s12915-025-02384-8.
The European hamster (Cricetus cricetus) was once a pest on European farmland, but its numbers have declined dramatically in recent decades, making it a critically endangered species throughout Europe and beyond. While it is strictly protected by EU law and several conservations, breeding and release programs have been initiated, and little is known about the level of genetic erosion and inbreeding on a European scale.
Here, we present a chromosome-level de novo genome of a female hamster and a first population genomic analysis from the western range of the species' distribution, using Illumina short reads (10 × coverage) from 34 individuals. The genome is 2.89 Gbp long, with 11 chromosome-level scaffolds and around 600 unplaced scaffolds and scaffolds N50 of 267 Mbp. The genome is above the average length of a mammalian genome and longer than that of other studied hamster species. Four distinct hamster populations with no admixture can be identified, indicating highly isolated populations with limited connectivity. Heterozygosity (Ho) is generally low (< 0.05%, comparable to polar bears) with some exceptions of populations with Ho near zero and a few with Ho as high as 0.2%.
Most dramatically, the genomes of individuals used as founders for conservation breeding programs show exceptionally long runs of homozygosity, questioning its long-term suitability. This study confirms earlier concerns about the dramatically decreasing genetic diversity of the European hamster and provides a basis for future conservation efforts, which require consideration of population genetic factors.
欧洲仓鼠（Cricetus cricetus）曾是欧洲农田中的害虫，但近几十年来其数量急剧下降，使其成为整个欧洲及其他地区的极度濒危物种。虽然它受到欧盟法律和多项保护措施的严格保护，并且已经启动了繁殖和放归计划，但在欧洲范围内，人们对其遗传侵蚀和近亲繁殖的程度知之甚少。
在此，我们展示了一只雌性仓鼠的染色体水平的从头基因组，并对该物种分布西部范围内的种群进行了首次基因组分析，使用了来自34个个体的Illumina短读长序列（10倍覆盖度）。该基因组长度为2.89 Gbp，有11个染色体水平的支架以及约600个未定位的支架，支架N50为267 Mbp。该基因组长度超过哺乳动物基因组的平均长度，且比其他已研究的仓鼠物种的基因组更长。可以识别出四个没有混合的不同仓鼠种群，表明这些种群高度隔离，连通性有限。杂合度（Ho）普遍较低（<0.05%，与北极熊相当），但有一些种群的Ho接近零，少数种群的Ho高达0.2%。
最引人注目的是，用于保护育种计划的奠基者个体的基因组显示出异常长的纯合子片段，这对其长期适用性提出了质疑。这项研究证实了早期对欧洲仓鼠遗传多样性急剧下降的担忧，并为未来的保护工作提供了基础，未来的保护工作需要考虑种群遗传因素。
