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Ebert MS, Bargmann CI. Evolution remodels olfactory and mating-receptive behaviors in the transition from female to hermaphrodite reproduction. Curr Biol 2024; 34:969-979.e4. [PMID: 38340714 DOI: 10.1016/j.cub.2024.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Male/hermaphrodite species have arisen multiple times from a male/female ancestral state in nematodes, providing a model to study behavioral adaptations to different reproductive strategies. Here, we examined the mating behaviors of male/female (gonochoristic) Caenorhabditis species in comparison with male/hermaphrodite (androdiecious) close relatives. We find that females from two species in the Elegans group chemotax to volatile odor from males, but hermaphrodites do not. Females, but not hermaphrodites, also display known mating-receptive behaviors such as sedation when male reproductive structures contact the vulva. Focusing on the male/female species C. nigoni, we show that female chemotaxis to males is limited to adult females approaching adult or near-adult males and relies upon the AWA neuron-specific transcription factor ODR-7, as does male chemotaxis to female odor as previously shown in C. elegans. However, female receptivity during mating contact is odr-7 independent. All C. nigoni female behaviors are suppressed by mating and all are absent in young hermaphrodites from the sister species C. briggsae. However, latent receptivity during mating contact can be uncovered in mutant or aged C. briggsae hermaphrodites that lack self-sperm. These results reveal two mechanistically distinct components of the shift from female to hermaphrodite behavior: the loss of female-specific odr-7-dependent chemotaxis and a sperm-dependent state of reduced receptivity to mating contact. Hermaphrodites from a second androdioecious species, C. tropicalis, recover all female behaviors upon aging, including chemotaxis to males. Regaining mating receptivity after sperm depletion could maximize hermaphrodite fitness across their lifespan.
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Affiliation(s)
- Margaret S Ebert
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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2
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Widen SA, Bes IC, Koreshova A, Pliota P, Krogull D, Burga A. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Science 2023; 380:eade0705. [PMID: 37384706 DOI: 10.1126/science.ade0705] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.
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Affiliation(s)
- Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Israel Campo Bes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
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Sun S, Kanzaki N, Dayi M, Maeda Y, Yoshida A, Tanaka R, Kikuchi T. The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus. BMC Genomics 2022; 23:765. [PMID: 36418933 PMCID: PMC9682657 DOI: 10.1186/s12864-022-09011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. RESULTS In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. CONCLUSIONS The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species.
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Affiliation(s)
- Simo Sun
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Natsumi Kanzaki
- grid.417935.d0000 0000 9150 188XKansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855 Japan
| | - Mehmet Dayi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.412121.50000 0001 1710 3792Forestry Vocational School, Duzce University, 81620 Duzce, Türkiye
| | - Yasunobu Maeda
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Akemi Yoshida
- grid.410849.00000 0001 0657 3887Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Ryusei Tanaka
- grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Taisei Kikuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
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Sloat SA, Noble LM, Paaby AB, Bernstein M, Chang A, Kaur T, Yuen J, Tintori SC, Jackson JL, Martel A, Salome Correa JA, Stevens L, Kiontke K, Blaxter M, Rockman MV. Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests. Ecol Evol 2022; 12:e9124. [PMID: 35898425 PMCID: PMC9309040 DOI: 10.1002/ece3.9124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe-rich patches of rotten material. Here, we use field experiments and large-scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis species in two of the world's best-studied lowland tropical field sites: Barro Colorado Island in Panamá and La Selva in Sarapiquí, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. We formally describe two species and place them within the Caenorhabditis phylogeny. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis individuals were able to colonize baits accessible only through phoresy and preferentially colonized baits that were in direct contact with the ground. We estimate the number of colonization events per patch to be low.
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Affiliation(s)
- Solomon A. Sloat
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Luke M. Noble
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Annalise B. Paaby
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Max Bernstein
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Audrey Chang
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Taniya Kaur
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Yuen
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Renaissance School of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Sophia C. Tintori
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jacqueline L. Jackson
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Arielle Martel
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jose A. Salome Correa
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | | | - Karin Kiontke
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger InstituteHinxtonUK
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
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Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJ, Baugh LR, Andersen EC. Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics. Genome Biol Evol 2022; 14:6554914. [PMID: 35348662 PMCID: PMC9011032 DOI: 10.1093/gbe/evac042] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.
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Affiliation(s)
- Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Nicolas D. Moya
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Robyn E. Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sophia B. Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Huimin Na
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Albertha J.M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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Andersen EC, Rockman MV. Natural genetic variation as a tool for discovery in Caenorhabditis nematodes. Genetics 2022; 220:iyab156. [PMID: 35134197 PMCID: PMC8733454 DOI: 10.1093/genetics/iyab156] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/11/2021] [Indexed: 11/12/2022] Open
Abstract
Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated the power of quantitative genetic approaches to reveal the evolutionary, ecological, and genetic factors that shape traits. These studies complement the use of the laboratory-adapted strain N2 and enable additional discoveries not possible using only one genetic background. In this chapter, we describe how to perform quantitative genetic studies in Caenorhabditis, with an emphasis on C. elegans. These approaches use correlations between genotype and phenotype across populations of genetically diverse individuals to discover the genetic causes of phenotypic variation. We present methods that use linkage, near-isogenic lines, association, and bulk-segregant mapping, and we describe the advantages and disadvantages of each approach. The power of C. elegans quantitative genetic mapping is best shown in the ability to connect phenotypic differences to specific genes and variants. We will present methods to narrow genomic regions to candidate genes and then tests to identify the gene or variant involved in a quantitative trait. The same features that make C. elegans a preeminent experimental model animal contribute to its exceptional value as a tool to understand natural phenotypic variation.
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Affiliation(s)
- Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
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