Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

作者：Nicolas D. Moya, Bowen Wang, Robyn E. Tanny, Michael E.G. Sauria, L O'Connor, Ayeh Khorshidian, Ryan McKeown, Charlie Gosse, Clayton M. Dilks, Timothy A. Crombie, Gaotian Zhang, Emha Ilhami Rais, Lise Frézal, Viet Dai Dang, Elkana Haryoso, M. P. Devi, Clotilde Gimond, Daniel E. Cook, Jung-Chen Hsu, Amanda O. Shaver, Stefan Zdraljevic, Aurélien Richaud, Tongshu Wen, Aatira Mehraj, H Sharanya, Karthick Raja Arulprakasam, Emily Koury, Nicole M. Roberto, Etta S. Schaye, Varsha Singh, Hagus Tarno, Michael Ailion, Annalise B. Paaby, Zhongying Zhao, Asher D. Cutter, John Wang, Matthew V. Rockman, Marie-Anne Felix, Christian Braendle, Erik C. Andersen · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2025 · DOI：10.64898/2025.12.08.693002 · 被引用次数：3 · 研究领域：Genetics, Aging, and Longevity in Model Organisms、Evolution and Genetic Dynamics、Nematode management and characterization studies

Comparative genomics provides a powerful framework to uncover the molecular and evolutionary mechanisms that shape genetic diversity within and across species, revealing how shared and lineage-specific processes influence their evolutionary trajectories through time. The nematode Caenorhabditis briggsae is distributed world-wide and is a comparative model to Caenorhabditis elegans in the biology of development, cellular mechanisms, neurobiology, genetic mappings of complex traits, and genome evolution. Following massive collection efforts by the nematode research community, we present the isolation of over 2,000 wild strains and analyses of genome sequences that catalog over six million single-nucleotide and insertion-deletion variants. This genome and strain resource provide a powerful means to interrogate the causal genetic bases of phenotypic variation for diverse traits. Additionally, we describe its global population structure and discover new and genetically distinct groups within this primarily self-fertilizing species, including groups of highly related strains that were sampled across different continents. We leverage expansive genetic variation to decipher the effects of linkage and selection on the distribution of genetic diversity across the genome and across geographic regions. Within the species, we find genomic regions with extremely high levels of genetic variation similar to hyper-divergent regions found in C. elegans and other species. These regions harbor n...