Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes.
| Title: | Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes. |
|---|---|
| Authors: | Moya ND; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; Wang B; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; Tanny RE; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; Sauria MEG; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; O'Connor LM; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; Khorshidian A; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; McKeown R; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Gosse C; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.; Dilks CM; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Crombie TA; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.; Zhang G; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.; Rais E; Department of Pests and Disease, Faculty of Agriculture, University of Brawijaya, JL Veteran Malang, Malang, East Java 65145, Indonesia.; Frézal L; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.; Dang VD; Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.; Southern Institute of Ecology, Institute of Applied Material Science, Vietnam Academy of Science and Technology, Ho Chi Minh, Vietnam.; Haryoso E; Department of Pests and Disease, Faculty of Agriculture, University of Brawijaya, JL Veteran Malang, Malang, East Java 65145, Indonesia.; Devi MP; Department of Pests and Disease, Faculty of Agriculture, University of Brawijaya, JL Veteran Malang, Malang, East Java 65145, Indonesia.; Gimond C; Université Côte d'Azur, CNRS, Inserm, IBV, Nice, 06108, France.; Cook DE; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Hsu JC; Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.; Shaver AO; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; Zdraljevic S; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Richaud A; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.; Wen T; Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.; Mehraj A; Indian Institute of Science, Bengaluru, 2H88+R9, India.; Sharanya H; Indian Institute of Science, Bengaluru, 2H88+R9, India.; Arulprakasam KR; Indian Institute of Science, Bengaluru, 2H88+R9, India.; Koury EJ; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Roberto NM; Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.; Schaye ES; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.; Singh V; Indian Institute of Science, Bengaluru, 2H88+R9, India.; Division of Molecular Microbiology, School of Life Sciences, University of Dundee, F257+6M, UK.; Tarno H; Department of Pests and Disease, Faculty of Agriculture, University of Brawijaya, JL Veteran Malang, Malang, East Java 65145, Indonesia.; Ailion M; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.; Paaby AB; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.; Zhao Z; Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.; Cutter AD; Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S3B2, Canada.; Wang J; Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.; Rockman MV; Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY, 10003, USA.; Félix MA; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.; Braendle C; Université Côte d'Azur, CNRS, Inserm, IBV, Nice, 06108, France.; Andersen EC; Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA. |
| Source: | BioRxiv : the preprint server for biology [bioRxiv] 2025 Dec 14. Date of Electronic Publication: 2025 Dec 14. |
| Publication Type: | Journal Article; Preprint |
| Language: | English |
| Journal Info: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| 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 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 new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species Caenorhabditis nigoni, 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 Caenorhabditis species. |
| References: | Theor Popul Biol. 1975 Apr;7(2):256-76. (PMID: 1145509); BMC Biol. 2012 Jun 25;10:59. (PMID: 22731941); Curr Biol. 2022 Sep 26;32(18):R970-R983. (PMID: 36167050); Gigascience. 2015 Feb 25;4:7. (PMID: 25722852); Mol Ecol Resour. 2021 May;21(4):1359-1368. (PMID: 33453139); Heredity (Edinb). 2008 Mar;100(3):304-15. (PMID: 18073782); Bioinformatics. 2015 Oct 1;31(19):3210-2. (PMID: 26059717); Nat Protoc. 2024 Nov;19(11):3292-3320. (PMID: 39019974); Genetics. 2009 May;182(1):205-16. (PMID: 19237689); Am J Hum Genet. 2007 Sep;81(3):559-75. (PMID: 17701901); Genome Res. 2009 Sep;19(9):1655-64. (PMID: 19648217); Methods Mol Biol. 2006;351:13-29. (PMID: 16988423); Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168); Mob DNA. 2015 Jun 02;6:11. (PMID: 26045719); Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. (PMID: 26612867); Nat Genet. 2012 Jan 29;44(3):285-90. (PMID: 22286215); PLoS Biol. 2007 Jul;5(7):e167. (PMID: 17608563); Mol Ecol. 2012 Mar;21(6):1345-59. (PMID: 22320847); BMC Evol Biol. 2011 Nov 21;11:339. (PMID: 22103856); Mol Ecol. 2003 May;12(5):1325-37. (PMID: 12694294); Nucleic Acids Res. 2025 Jan 6;53(D1):D609-D617. (PMID: 39552041); BMC Genomics. 2023 Aug 25;24(1):486. (PMID: 37626289); Genetics. 2006 Oct;174(2):901-13. (PMID: 16951062); Genetics. 2012 Jan;190(1):5-22. (PMID: 22219506); Genome Biol. 2004;5(2):R12. (PMID: 14759262); OMICS. 2012 May;16(5):284-7. (PMID: 22455463); Bioinformatics. 2014 May 1;30(9):1236-40. (PMID: 24451626); Mol Biol Evol. 2019 Feb 1;36(2):239-251. (PMID: 30445510); Genetics. 2002 May;161(1):99-107. (PMID: 12019226); Science. 2010 Oct 15;330(6002):372-6. (PMID: 20947766); Genome Res. 2015 May;25(5):667-78. (PMID: 25783854); Imeta. 2022 Aug 01;1(3):e43. (PMID: 38868715); Nat Methods. 2021 Apr;18(4):366-368. (PMID: 33828273); Bioinformatics. 2018 Mar 1;34(5):867-868. (PMID: 29096012); Nat Biotechnol. 2019 May;37(5):540-546. (PMID: 30936562); BMC Bioinformatics. 2008 Jan 14;9:18. (PMID: 18194517); Genome Res. 2017 May;27(5):722-736. (PMID: 28298431); Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700); G3 (Bethesda). 2020 Apr 9;10(4):1361-1374. (PMID: 32071071); Nucleic Acids Res. 2024 Jan 5;52(D1):D850-D858. (PMID: 37855690); PLoS Genet. 2006 Dec;2(12):e190. (PMID: 17194218); PeerJ. 2016 Oct 18;4:e2584. (PMID: 27781170); Trends Genet. 2025 Apr;41(4):303-314. (PMID: 39706705); Nat Methods. 2021 Feb;18(2):170-175. (PMID: 33526886); Nat Ecol Evol. 2019 Oct;3(10):1455-1463. (PMID: 31548647); Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419. (PMID: 33125078); IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):645-56. (PMID: 24091398); Genetics. 2016 Sep;204(1):371-83. (PMID: 27449056); Nat Ecol Evol. 2021 Jun;5(6):794-807. (PMID: 33820969); Nat Genet. 2006 Aug;38(8):904-9. (PMID: 16862161); BMC Evol Biol. 2013 Jan 12;13:10. (PMID: 23311925); Genetics. 2008 Apr;178(4):2093-104. (PMID: 18430935); Nucleic Acids Res. 2011 Jan;39(Database issue):D70-4. (PMID: 21036865); Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278); Genetics. 1989 Nov;123(3):585-95. (PMID: 2513255); New Phytol. 2019 Nov;224(3):1080-1094. (PMID: 31336389); Bioinformatics. 2015 Jun 15;31(12):2032-4. (PMID: 25697820); Genetics. 1997 Jul;146(3):1185-95. (PMID: 9215919); Mol Ecol. 2016 Feb;25(3):723-40. (PMID: 26523848); Nat Biotechnol. 2019 Aug;37(8):852-857. (PMID: 31341288); Nat Rev Genet. 2013 Apr;14(4):262-74. (PMID: 23478346); Genetics. 2006 Aug;173(4):2021-31. (PMID: 16783011); Nat Genet. 2011 Aug 28;43(10):956-63. (PMID: 21874002) |
| Grant Information: | F32 AI181342 United States AI NIAID NIH HHS; R01 ES029930 United States ES NIEHS NIH HHS; R35 GM141906 United States GM NIGMS NIH HHS; R50 ES037948 United States ES NIEHS NIH HHS |
| Entry Date(s): | Date Created: 20251222 Date Completed: 20251231 Latest Revision: 20260101 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC12715550 |
| DOI: | 10.64898/2025.12.08.693002 |
| PMID: | 41427407 |
| Database: | MEDLINE |
Journal Article; Preprint