C. elegans outside the Petri dish

eLife

Volumn 2015, Issue 4, 2015, Pages

  Frézal, Lise ^a   Félix, Marie Anne ^a  

^a ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; DEVELOPMENTAL STAGE; FOOD CHAIN; GENETIC VARIABILITY; HABITAT; HAPLOTYPE; LIFE CYCLE; LOCOMOTION; METAPOPULATION; NONHUMAN; PHYLOGENY; REPRODUCTION; VIRUS REPLICATION; ANIMAL; CAENORHABDITIS; CLASSIFICATION; ECOSYSTEM; FEMALE; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN; LIFE CYCLE STAGE; MALE; POPULATION DYNAMICS;

ANIMALIA; BACTERIA (MICROORGANISMS); CAENORHABDITIS ELEGANS; FUNGI; GASTROPODA; ISOPODA; MICROSPORIDIA; NEMATODA;

ANIMALS; CAENORHABDITIS; CAENORHABDITIS ELEGANS; ECOSYSTEM; FEMALE; HUMANS; LIFE CYCLE STAGES; MALE; PHYLOGENY; POPULATION DYNAMICS;

EID: 85016947636     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/elife.05849     Document Type: Article

References (93)

1. Abdul Kader N, Côté MG. 1996. Isolement, identification et caracté risation de souches qué bé coises du nématode Caenorhabditis elegans. Fundamental and Applied Nematology 19:381-389.
2. Andersen EC, Bloom JS, Gerke JP, Kruglyak L. 2014. A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology. PLOS Genetics 10:e1004156. doi: 10.1371/ journal.pgen.1004156.
3. Andersen EC, Gerke JP, Shapiro JA, Crissman JR, Ghosh R, Bloom JS, Fé Lix MA, Kruglyak L. 2012. Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nature Genetics 45:285-290. doi: 10.1038/ng.1050.
4. Ashe A, Bélicard T, Le Pen J, Sarkies P, Frézal L, Lehrbach NJ, Fé Lix MA, Miska EA. 2013. A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity. e Life 2:e00994. doi: 10.7554/e Life.00994.
5. Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TA, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER. 2014. Ubiquitin-mediated response to microsporidia and virus infection in C. elegans. PLOS Pathogens 10:e1004200. doi: 10.1371/journal.ppat. 1004200.
6. Baldi C, Cho S, Ellis RE. 2009. Mutations in two independent pathways are sufficient to create hermaphroditic nematodes. Science 326:1002-1005. doi: 10.1126/science.1176013.
7. Barrière A, Fé Lix MA. 2005a. High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations. Current Biology 15: 1176-1184. doi: 10.1016/j.cub.2005.06.022.
8. Barrière A, Fé Lix MA. 2005b. Natural variation and population genetics of C. elegans. In: The C. elegans Research Community editors. Wormbook. http://www. wormbook.org/. doi: 10.1895/wormbook.1.43.1.
9. Barrière A, Fé Lix MA. 2007. Temporal dynamics and linkage disequilibrium in natural C. elegans populations. Genetics 176:999-1011. doi: 10.1534/ genetics.106.067223.
10. Barrière A, Fé Lix MA. 2014. Isolation of C. elegans and related nematodes. In: The C. elegans Research Community editors. Wormbook. http://www. wormbook.org/. doi: 10.1895/wormbook.1.115.2.
11. Barrière A, Ruvinsky I. 2014. Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes. PLOS Genetics 10:e1004435. doi: 10.1371/ journal.pgen.1004435.
12. Bento G, Ogawa A, Sommer RJ. 2010. Co-option of the hormone-signalling module dafachronic acid-DAF-12 in nematode evolution. Nature 466:494-497. doi: 10. 1038/nature09164.
13. Carvalho S, Phillips PC, Teotónio H. 2014. Hermaphrodite life history and the maintenance of partial selfing in experimental populations of Caenorhabditis elegans. BMC Evolutionary Biology 14: 117. doi: 10.1186/1471-2148-14-117.
14. Caswell-Chen EP, Chen J, Lewis EE, Douhan GW, Nadler SA, Carey JR. 2005. Revising the standard wisdom of C. elegans natural history: ecology of longevity. Science of Aging Knowledge Environment 40:pe30.
15. Chang HC, Paek J, Kim DH. 2011. Natural polymorphisms in C. elegans HECW-1 E3 ligase affect pathogen avoidance behaviour. Nature 480:525-529. doi: 10.1038/nature10643.
16. Charron G, Leducq JB, Bertin C, Dubé AK, Landry CR. 2014. Exploring the northern limit of the distribution of Saccharomyces cerevisiae and Saccharomyces paradoxus in North America. FEMS Yeast Research 14: 281-288. doi: 10.1111/1567-1364.12100.
17. Chasnov JR, Chow KL. 2002. Why are there males in the hermaphroditic species Caenorhabditis elegans? Genetics 160:983-994.
18. Chasnov JR, So WK, Chan CM, Chow KL. 2007. The species, sex and stage specificity of a Caenorhabditis sex pheromone. Proceedings of the National Academy of Sciences of USA 104:6730-6735. doi: 10.1073/pnas. 0608050104.
19. Chelo IM, Carvalho S, Roque M, Proulx SR, Teotonio H. 2014. The genetic basis and experimental evolution of inbreeding depression in Caenorhabditis elegans. Heredity 112:248-254. doi: 10.1038/hdy.2013.100.
20. Conradt B, Xue D. 2005. The C. elegans Research Community editors. Wormbook. http://www. wormbook.org/. doi: 10.1895/wormbook.1.32.1.
21. Couillault C, Pujol N, Reboul J, Sabatier L, Guichou JF, Kohara Y, Ewbank JJ. 2004. TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM. Nature Immunology 5:488-494. doi: 10.1038/ ni1060.
22. Cutter AD. 2006. Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans. Genetics 172:171-184. doi: 10.1534/genetics.105.048207.
23. Cutter AD. 2008. Divergence times in Caenorhabditis and Drosophila, inferred from direct estimates of the neutral mutation rate. Molecular Biology and Evolution 25:778-786. doi: 10.1093/molbev/msn024.
24. Cutter AD, Dey A, Murray RL. 2009. Evolution of the Caenorhabditis elegans genome. Molecular Biology and Evolution 26:1199-1234. doi: 10.1093/molbev/msp048.
25. Dey A, Jeon Y, Wang GX, Cutter AD. 2012. Global population genetic structure of Caenorhabditis remanei reveals incipient speciation. Genetics 191:1257-1269. doi: 10.1534/genetics.112.140418.
26. Dey A, Chan CK, Thomas CG, Cutter AD. 2013. Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri. Proceedings of the National Academy of Sciences of the USA 110:11056-11060. doi: 10.1073/pnas. 1303057110.
27. Diezmann S, Dietrich FS. 2009. Saccharomyces cerevisiae: population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates. PLOS ONE 4:e5317. doi: 10.1371/journal. pone.0005317.
28. Dolgin ES, Charlesworth B, Baird SE, Cutter AD. 2007. Inbreeding and outbreeding depression in Caenorhabditis nematodes. Evolution 61:1339-1352. doi: 10.1111/j.1558-5646.2007.00118.x.
29. Dolgin ES, Fé Lix M-A, Cutter AD. 2008. Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae. Heredity 100:304-315. doi: 10.1038/sj.hdy.6801079.
30. Duveau F, Fé Lix MA. 2012. Role of pleiotropy in the evolution of a cryptic developmental variation in C. elegans. PLOS Biology 10:e1001230. doi: 10.1371/ journal.pbio.1001230.
31. Fay JC, Benavides JA. 2005. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLOS Genetics 1:66-71. doi: 10.1371/journal.pgen. 0010005.
32. Fé Lix MA. 2007. Cryptic quantitative evolution of the vulva intercellular signaling network in Caenorhabditis. Current Biology 17:103-114. doi: 10.1016/j.cub.2006. 12.024.
33. Fé Lix MA. 2008. RNA interference in nematodes and the chance that favored Sydney Brenner. Journal of Biology 7:34. doi: 10.1186/jbiol97.
34. Fé Lix MA, Ashe A, Piffaretti J, Wu G, Nuez I, Bé Licard T, Jiang Y, Zhao G, Franz CJ, Goldstein LD, et al. 2011. Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses. PLOS Biology 9:e1000586. doi: 10.1371/journal.pbio.1000586.
35. Fé Lix MA, Braendle C. 2010. The natural history of Caenorhabditis elegans. Current Biology 20: R965-R969. doi: 10.1016/j.cub.2010.09.050.
36. Fé Lix MA, Braendle C, Cutter AD. 2014. A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLOS ONE 9:e94723. doi: 10.1371/journal.pone.0094723.
37. Félix MA, Duveau F. 2012. Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae. BMC Biology 10:59. doi: 10.1186/1741-7007-10-59.
38. Fé Lix M-A, Jovelin R, Ferrari C, Han S, Cho YR, Andersen EC, Cutter AD, Braendle C. 2013. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest. BMC Evolutionary Biology 13:10. doi: 10. 1186/1471-2148-13-10.
39. Gimond C, Jovelin R, Han S, Ferrari C, Cutter AD, Braendle C. 2013. Outbreeding depression with low genetic variation in selfing Caenorhabditis nematodes. Evolution 67:3087-3101. doi: 10.1111/evo.12203.
40. Green JW, Stastna JJ, Orbidans HE, Harvey SC. 2014. Highly polygenic variation in environmental perception determines dauer larvae formation in growing populations of Caenorhabditis elegans. PLOS ONE 9: e112830. doi: 10.1371/journal.pone.0112830.
41. Grishok A. 2013. Biology and mechanisms of short RNAs in Caenorhabditis elegans. Advances in Genetics 83:1-69. doi: 10.1016/B978-0-12-407675-4.00001-8.
42. Guo Y, Lang S, Ellis RE. 2009. Independent recruitment of F box genes to regulate hermaphrodite development during nematode evolution. Current Biology 19:1853-1860. doi: 10.1016/j.cub.2009.09.042.
43. Haber M, Schüngel M, Putz A, Müller S, Hasert B, Schulenburg H. 2005. Evolutionary history of Caenorhabditis elegans inferred from microsatellites: evidence for spatial and temporal genetic differentiation and the occurrence of outbreeding. Molecular Biology and Evolution 22:160-173. doi: 10. 1093/molbev/msh264.
44. Hodgkin J, Doniach T. 1997. Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146:149-164.
45. Hodgkin J, Fé Lix MA, Clark LC, Stroud D, Gravato-Nobre MJ. 2013. Two Leucobacter strains exert complementary virulence on Caenorhabditis including death by worm-star formation. Current Biology 23: 2157-2161. doi: 10.1016/j.cub.2013.08.060.
46. Huang RE, Ren X, Qiu Y, Zhao Z. 2014. Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a nematode species used in comparative biology for C. elegans. PLOS ONE 9:e110957. doi: 10.1371/journal. pone.0110957.
47. Jansson HB, Jeyaprakash A, Zuckerman BM. 1985. Differential adhesion and infection of nematodes by the endoparasitic fungus Meria coniospora (Deuteromycetes). Applied and Environmental Microbiology 49:552-555.
48. Jovelin R, Ajie BC, Phillips PC. 2003. Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis. Molecular Ecology 12:1325-1337. doi: 10.1046/j.1365-294X.2003.01805.x.
49. Kiontke K. 1997. Description of Rhabditis (Caenorhabditis) drosophilae n. sp. and R. (C.) sonorae n. sp. (Nematoda: Rhabditida) from saguaro cactus rot in Arizona. Fundamental and Applied Nematology 20:305-315.
50. Kiontke K, Fé Lix MA, Ailion M, Rockman MV, Braendle C, Pénigault JB, Fitch DH. 2011. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evolutionary Biology 11:339. doi: 10.1186/1471-2148-11-339.
51. Kiontke K, Hironaka M, Sudhaus W. 2002. Description of Caenorhabditis japonica n. sp. (Nematoda: Rhabditida) associated with the burrower bug Parastrachia japonensis (Heteroptera: Cynidae) in Japan. Nematology 4:933-941. doi: 10.1163/ 156854102321122557.
52. Kiontke K, Sudhaus W. 2006. Ecology of Caenorhabditis species. In: The C. elegans Research Community editors. Wormbook. http://www. wormbook.org/. doi: 10.1895/wormbook.1.37.1.
53. Lee Q, Widden P. 1996. Folsomia candida, a 'fungivorous' collembolan, feeds preferentially on nematodes rather than soil fungi. Soil Biology & Biochemistry 28:689-690. doi: 10.1016/0038-0717(95) 00158-1.
54. Lee H, Choi MK, Lee D, Kim HS, Hwang H, Kim H, Park S, Paik YK, Lee J. 2011. Nictation, a dispersal behavior of the nematode Caenorhabditis elegans, is regulated by IL2 neurons. Nature Neuroscience 15:107-112. doi: 10.1038/nn.2975.
55. Liu Y, Samuel BS, Breen PC, Ruvkun G. 2014. Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature 508:406-410. doi: 10. 1038/nature13204.
56. Maguire SM, Clark CM, Nunnari J, Pirri JK, Alkema MJ. 2011. The C. elegans touch response facilitates escape from predacious fungi. Current Biology 21:1326-1330. doi: 10.1016/j.cub.2011.06.063.
57. Maupas E. 1900. Modes et formes de reproduction des nématodes. Archives de Zoologie Expé rimentale et Géné rale 8:463-624.
58. Maydan JS, Flibotte S, Edgley ML, Lau J, Selzer RR, Richmond TA, Pofahl NJ, Thomas JH, Moerman DG. 2007. Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Research 17:337-347. doi: 10. 1101/gr.5690307.
59. McGrath PT, Rockman MV, Zimmer M, Jang H, Macosko EZ, Kruglyak L, Bargmann CI. 2009. Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors. Neuron 61: 692-699. doi: 10.1016/j.neuron.2009.02.012.
60. McGrath PT, Xu Y, Ailion M, Garrison JL, Butcher RA, Bargmann CI. 2011. Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes. Nature 477:321-325. doi: 10.1038/nature10378.
61. Morran LT, Parmenter MD, Phillips PC. 2009. Mutation load and rapid adaptation favour outcrossing over selffertilization. Nature 462:350-352. doi: 10.1038/ nature08496.
62. Nigon V. 1949. Modalité s de la reproduction et dé terminisme du sexe chez quelques nématodes libres. Annales Des Sciences Naturelles, Zoologie 11:1-132.
63. Nigon V, Guerrier P, Monin H. 1960. L'architecture polaire de l'oeuf et les mouvements des constituants cellulaires au cours des premières é tapes du dé veloppement chez quelques Nématodes. Bulletin Biologique De La France Et De La Belgique 93:131-202.
64. Okumura E, Ishikawa Y, Tanaka R, Yoshiga T. 2013a. Propagation of Caenorhabditis japonica in the nest of its carrier insect, Parastrachia japonensis. Zoological Science 30:174-177. doi: 10.2108/zsj.30.174.
65. Okumura E, Tanaka R, Yoshiga T. 2013b. Speciesspecific recognition of the carrier insect by dauer larvae of the nematode Caenorhabditis japonica. Journal of Experimental Biology 216:568-572. doi: 10.1242/jeb. 073593.
66. Palopoli MF, Rockman MV, Tin Maung A, Ramsay C, Curwen S, Aduna A, Laurita J, Kruglyak L. 2008. Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans. Nature 454:1019-1022. doi: 10.1038/nature07171.
67. Pénigault JB, Fé Lix MA. 2011. Evolution of a system sensitive to stochastic noise: P3.p cell fate in Caenorhabditis. Developmental Biology 357:419-427. doi: 10.1016/j.ydbio.2011.05.675.
68. Petersen C, Dirksen P, Prahl S, Strathmann EA, Schulenburg H. 2014. The prevalence of Caenorhabditis elegans across 1.5 years in selected North German locations: the importance of substrate type, abiotic parameters, and Caenorhabditis competitors. BMC Ecology 14:4. doi: 10.1186/1472-6785-14-4.
69. Pradel E, Zhang Y, Pujol N, Matsuyama T, Bargmann CI, Ewbank JJ. 2007. Detection and avoidance of a natural product from the pathogenic bacterium Serratia marcescens by Caenorhabditis elegans. Proceedings of the National Academy of Sciences of USA 104:2295-2300. doi: 10.1073/pnas.0610281104.
70. Riche S, Zouak M, Argoul F, Arneodo A, Pecreaux J, Delattre M. 2013. Evolutionary comparisons reveal a positional switch for spindle pole oscillations in Caenorhabditis embryos. Journal of Cell Biology 201: 653-662. doi: 10.1083/jcb.201210110.
71. Rockman MV, Kruglyak L. 2009. Recombinational landscape and population genomics of Caenorhabditis elegans. PLOS Genetics 5:e1000419. doi: 10.1371/ journal.pgen.1000419.
72. Rockman MV, Skrovanek SS, Kruglyak L. 2010. Selection at linked sites shapes heritable phenotypic variation in C. elegans. Science 330:372-376. doi: 10. 1126/science.1194208.
73. Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L. 2009. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458:342-345. doi: 10.1038/nature07670.
74. Seidel HS, Ailion M, Li J, van Oudenaarden A, Rockman MV, Kruglyak L. 2011. A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. PLOS Biology 9: e1001115. doi: 10.1371/journal.pbio.1001115.
75. Seidel HS, Rockman MV, Kruglyak L. 2008. Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 319:589-594. doi: 10. 1126/science.1151107.
76. Sivasundar A, Hey J. 2005. Sampling from natural populations with RNAI reveals high outcrossing and population structure in Caenorhabditis elegans. Current Biology 15:1598-1602. doi: 10.1016/j.cub.2005.08.034.
77. Sudhaus W. 2011. Phylogenetic systematisation and catalogue of paraphyletic 'Rhabditidae' (Secernentea, Nematoda). Journal of Nematode Morphology and Systematics 14:113-178.
78. Sudhaus W, Kiontke K. 1996. Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda). Journal of Zoological Systematics and Evolutionary Research 34:217-233. doi: 10.1111/j.1439-0469.1996.tb00827.x.
79. Sudhaus W, Kühne R. 1989. Nematodes associated with Psychodidae: description of Rhabditis berolina sp. n. and redescription of R. dubia Bovien, 1937 (Nematoda: Rhabditidae), with biological and ecological notes, and a phylogenetic discussion. Nematologica 35:305-320. doi: 10.1163/ 002825989X00412.
80. Teotonio H, Carvalho S, Manoel D, Roque M, Chelo IM. 2012. Evolution of outcrossing in experimental populations of Caenorhabditis elegans. PLOS ONE 7: e35811. doi: 10.1371/journal.pone.0035811.
81. Teotonio H, Manoel D, Phillips PC. 2006. Genetic variation for outcrossing among Caenorhabditis elegans isolates. Evolution 60:1300-1305. doi: 10.1111/ j.0014-3820.2006.tb01207.x.
82. The C. elegans research community. 2005/2014. Wormbook: the online review of C. elegans biology. http://www.wormbook.org.
83. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018. doi: 10.1126/science.282.5396.2012.
84. Thomas CG, Li R, Smith HE, Woodruff GC, Oliver B, Haag ES. 2012. Simplification and desexualization of gene expression in self-fertile nematodes. Current Biology 22:2167-2172. doi: 10.1016/j.cub.2012.09.038.
85. Thomas CG, Woodruff GC, Haag ES. 2012. Causes and consequences of the evolution of reproductive mode in Caenorhabditis nematodes. Trends in Genetics 28: 213-220. doi: 10.1016/j.tig.2012.02.007.
86. Thomas JH. 2006. Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Research 16:1017-1030. doi: 10.1101/ gr.5089806.
87. Thompson O, Edgley M, Strasbourger P, Flibotte S, Ewing B, Adair R, Au V, Chaudhry I, Fernando L, Hutter H, et al. 2013. The million mutation project: a new approach to genetics in Caenorhabditis elegans. Genome Research 23:1749-1762. doi: 10.1101/gr. 157651.113.
88. Tijsterman M, Okihara KL, Thijssen K, Plasterl RH. 2002. PPW-1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C. elegans. Genome Research 12:1535-1540. doi: 10. 1016/S0960-9822(02)01110-7.
89. Troemel ER, Fé Lix M-A, Whiteman NK, Barrière A, Ausubel FM. 2008. Microsporidia are natural intracellular parasites of the nematode C. elegans. PLOS Biology 6:e309. doi: 10.1371/journal.pbio. 0060309.
90. Verster AJ, Ramani AK, McKay SJ, Fraser AG. 2014. Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function. PLOS Genetics 10:e1004077. doi: 10.1371/journal.pgen.1004077.
91. Wang GX, Ren S, Ren Y, Ai H, Cutter AD. 2010. Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5. Molecular Ecology 19:5022-5029. doi: 10.1111/j.1365-294X. 2010.04862.x.
92. Wang X, Chamberlin H. 2002. Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-28 ovo gene. Genes & Development 16:2345-2348. doi: 10.1101/gad. 996302.
93. Woodruff GC, Eke O, Baird SE, Fé Lix M-A, Haag ES. 2010. Fertile interspecies hybrids in Caenorhabditis nematodes and their implications for the evolution of hermaphroditism. Genetics 186:997-1012. doi: 10. 1534/genetics.110.120550.