<i>Caenorhabditis briggsae</i> ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

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 <i>Caenorhabditis briggsae</i> is distributed world-wide and is a comparative model to <i>Caenorhabditis elegans</i> 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 <i>C. elegans</i> and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species <i>Caenorhabditis nigoni</i>, we conclude that long-term balancing selection has maintained substantial functional variation since the divergence from their outbreeding ancestor, likely in response to differences in the ecological niche. Overall, this massive strain resource enables future comparative genetics and genomics studies, including genome-wide association studies between <i>Caenorhabditis</i> species.

Authors

Institutions

Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2025-12-11
DOI
https://doi.org/10.64898/2025.12.08.693002
Citations
2
Primary Topic
Genetics, Aging, and Longevity in Model Organisms
Type
article
Field-Weighted Citation Impact
1.91
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

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

Asher D. Cutter, Stefan Zdraljevic, Clotilde Gimond, M. P. Devi et al.
2 citations
bioRxiv (Cold Spring Harbor Laboratory)
Genetics, Aging, and Longevity in Model Organisms
1.91
article

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

Asher D. Cutter, Stefan Zdraljevic, Clotilde Gimond, M. P. Devi, Lise Frézal, Aurélien Richaud, Viet Dai Dang, Zhongying Zhao, Michael E.G. Sauria, Daniel E. Cook, Annalise B. Paaby, Emily Koury, Gaotian Zhang, Matthew V. Rockman, Karthick Raja Arulprakasam, Robyn E. Tanny, Timothy A. Crombie, Amanda O. Shaver, Ayeh Khorshidian, Clayton M. Dilks, Varsha Singh, Nicolas D. Moya, Jung-Chen Hsu, Hagus Tarno, Erik C. Andersen, Nicole M. Roberto, Ryan McKeown, Charlie Gosse, Christian Braendle, Michael Ailion, Etta S. Schaye, Bowen Wang, John Wang, Tongshu Wen, L O'Connor, H Sharanya, Elkana Haryoso, Emha Ilhami Rais, Aatira Mehraj
article en
2 citations

Abstract

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 <i>Caenorhabditis briggsae</i> is distributed world-wide and is a comparative model to <i>Caenorhabditis elegans</i> 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 <i>C. elegans</i> and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species <i>Caenorhabditis nigoni</i>, we conclude that long-term balancing selection has maintained substantial functional variation since the divergence from their outbreeding ancestor, likely in response to differences in the ecological niche. Overall, this massive strain resource enables future comparative genetics and genomics studies, including genome-wide association studies between <i>Caenorhabditis</i> species.

bioRxiv (Cold Spring Harbor Laboratory)
Florida Institute of Technology (US), Northwestern University (US), Centre National de la Recherche Scientifique (FR), Georgia Institute of Technology (US), Hong Kong Baptist University (HK), Johns Hopkins University (US), Inserm (FR), University of Brawijaya (ID), University of Dundee (GB), University of Toronto (CA), University of Washington (US), Institut de Biologie Valrose (FR), Institut de Biologie de l'École Normale Supérieure (FR), Biodiversity Research Center, Academia Sinica (TW), New York Genome Center (US), Indian Institute of Science Bangalore (IN), Vietnam Academy of Science and Technology (VN)
Openalex Percentile: Top 12%
Genetics, Aging, and Longevity in Model Organisms
1.91
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.