Survey of genome size in 28 hydrothermal vent species covering 10 families

Genome

Volumn 52, Issue 6, 2009, Pages 524-536

  Bonnivard, Eric ^a   Catrice, Olivier ^b   Ravaux, Juliette ^a   Brown, Spencer C ^b   Higuet, Dominique ^a  

^a Université Paris VI ^*  (France)

^b CNRS   (France)

Author keywords

Decapods; DNA content; Flow cytometry; Genome size; Hydrothermal vents

Indexed keywords

PLANT DNA;

ANIMAL; ARTICLE; CLASSIFICATION; DECAPODA (CRUSTACEA); FLOW CYTOMETRY; GENOME; MOLECULAR EVOLUTION; PHYSIOLOGY; PLANT CHROMOSOME;

ANIMALS; CHROMOSOMES, PLANT; DECAPODA (CRUSTACEA); DNA, PLANT; EVOLUTION, MOLECULAR; FLOW CYTOMETRY; GENOME;

BRACHYURA; DECAPODA (CRUSTACEA); GALATHEIDAE; MIROCARIS FORTUNATA; MUNIDOPSIS; NECORA PUBER; PHYLLODOCIDA; VENEROIDA; XANTHO PILIPES;

EID: 67650315660     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G09-027     Document Type: Article

References (60)

1. Bachmann, K., and Rheinsmith, E.L. 1973. Nuclear DNA amounts in pacific Crustacea. Chromosoma, 43: 225-236. doi:10.1007/BF00294271. PMID:4747576.
2. Badaracco, G., Baratelli, L., Ginelli, E., Meneveri, R., Plevani, P., Valsasnini, P., and Barigozzi, C. 1987. Variations in repetitive DNA and heterochromatin in the genus Artemia. Chromosoma, 95: 71-75. doi:10.1007/BF00293844.
3. Beermann, S. 1977. The diminution of heterochromatic chromosomal segments in Cyclops (Crustacea, Copepoda). Chromosoma, 60: 297-344. doi:10.1007/BF00292858. PMID:870296.
4. Bennetzen, J.L., Ma, J., and Devos, K.M. 2005. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. (Lond.), 95: 127-132. doi:10.1093/aob/mci008. PMID:15596462.
5. Bouchet, P., and Rocroi, J. 2005. Classification and nomenclator of gastropod families. Malacologia, 47: 1-397.
6. Conner, W., Hinegardner, R., and Bachmann, K. 1972. Nuclear DNA amounts in polychaete annelids. Experientia, 28: 1502-1504. doi:10.1007/ BF01957880.
7. Deiana, A.M., Cau, A., Coluccia, E., Cannas, R., Milia, A., Salvadori, S., and Libertini, A. 1999. Genome size and AT-DNA content in thirteen species of Decapoda. In Crustaceans and the biodiversity crisis. Edited by F.R. Schram and J.C. Von Vaupel Klein. Leiden, the Netherlands. pp. 981-985.
8. Desbruyères, D., and Segonzac, M. (Editors). 1997. Handbook of deep-sea hydrothermal vent fauna. Denisia 18. IFREMER, Brest, France.
9. Dixon, D., Dixon, L., Pascoe, P., and Wilson, J. 2001. Chromosomal and nuclear characteristics of deep-sea hydrothermal-vent organisms: correlates of increased growth rate. Mar. Biol. (Berl.), 139: 251-255. doi:10.1007/s002270100564.
10. Dolezel, J., Bartos, J., Voglmayr, H., and Greilhuber, J. 2003. Nuclear DNA content and genome size of trout and human. Cytometry A, 51: 127-129. doi:10.1002/cyto.a.10013. PMID: 12541287.
11. Dziak, R.P., and Johnson, H.P. 2002. Hydrothermal systems. Stirring the oceanic incubator. Science, 296: 1406-1407. doi:10. 1126/science.1072075. PMID:12029115.
12. Ebina, H., and Levin, H.L. 2007. Stress management: how cells take control of their transposons. Mol. Cell, 27: 180-181. doi:10.1016/j.molcel.2007.07.004. PMID:17643368.
13. Escribano, R., McLaren, I.A., and Breteler, K. 1992. Innate and acquired variation of nuclear DNA contents of marine copepods. Genome, 35: 602-610. doi:10.1139/g92-090.
14. Galbraith, D.W., Harkins, K.R., Maddox, J.M., Ayres, N.M., Sharma, D.P., and Firoozabady, E. 1983. Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science, 220: 1049-1051. doi:10.1126/science.220. 4601.1049. PMID:17754551.
15. Gambi, M.C., Ramella, L., Sella, G., Protto, P., and Aldieri, E. 1997. Variation in genome size of benthic polychaetes: systematic and ecological relationships. J. Mar. Biol. Assoc. U.K. 77: 1045-1057.
16. González-Tizón, A., Martínez-Lage, A., Ausio, J., and Méndez, J. 2000. Polyploidy in a natural population of mussel, Mytilus trossulus. Genome, 43: 409-411. doi:10.1139/gen-43-2-409. PMID: 10791832.
17. Grandbastien, M.-A., Audeon, C., Bonnivard, E., Casacuberta, J.M., Chalhoub, B., Costa, A.-P.P., et al. 2005. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110: 229-241. doi:10.1159/000084957. PMID:16093677.
18. Gregory, T.R. 2003. Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma. Biol. J. Linn. Soc. 79: 329-339. doi:10.1046/j.1095-8312.2003. 00191.x.
19. Gregory, T.R. 2005a. The C-value enigma in plants and animals: a review of parallels and an appeal for partnership. Ann. Bot. (Lond.), 95: 133-146. doi:10.1093/aob/mci009. PMID: 15596463.
20. Gregory, T.R. 2005b. Synergy between sequence and size in large-scale genomics. Nat. Rev. Genet. 6: 699-708. doi:10.1038/nrg1674. PMID:16151375.
21. Gregory, T.R. 2008. Animal Genome Size database [online]. Available from http://www.genomesize.com [accessed October 2008].
22. Gregory, T.R., and Witt, J.D.S. 2008. Population size and genome size in fishes: a closer look. Genome, 51: 309-313. doi:10.1139/G08-003. PMID:18356967.
23. Gregory, T.R., Hebert, P.D., and Kolasa, J. 2000. Evolutionary implications of the relationship between genome size and body size in flatworms and copepods. Heredity, 84: 201-208. doi:10.1046/j.1365-2540.2000.00661. x. PMID:10762390.
24. Greilhuber, J. 1998. Intraspecific variation in genome size: a critical reassessment. Ann. Bot. (Lond.), 82: 27-35. doi:10.1006/anbo.1998.0725.
25. Hardie, D.C., and Hebert, P.D.N. 2003. The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes. Genome, 46: 683-706. doi:10.1139/g03-040. PMID:12897876.
26. Jollivet, D. 1996. Specific and genetic diversity at deep-sea hydrothermal vents: an overview. Biodivers. Conserv. 5: 1619-1653. doi:10.1007/BF00052119.
27. Kidwell, M.G. 2002. Transposable elements and the evolution of genome size in eukaryotes. Genetica, 115: 49-63. doi:10.1023/A:1016072014259. PMID:12188048.
28. Knight, C.A., Molinari, N.A., and Petrov, D.A. 2005. The large genome constraint hypothesis: evolution, ecology and phenotype. Ann. Bot. (Lond.), 95: 177-190. doi:10.1093/aob/mci011.PMID:15596465.
29. Kumar, A., and Rai, K.S. 1990. Intraspecific variation in nuclear DNA content among world populations of a mosquito, Aedes albopictus (Skuse). Theor. Appl. Genet. 79: 748-752. doi:10.1007/BF00224239.
30. Lampert, K.P., Lamatsch, D.K., Fischer, P., and Schartl, M. 2008. A tetraploid Amazon molly, Poecilia formosa. J. Hered. 99: 223-226. doi:10.1093/jhered/esm102. PMID:18209110.
31. Lécher, P., Defaye, D., and Noel, P. 1995. Chromosomes and nuclear DNA of Crustacea. Invertebr. Reprod. Dev. 27: 85-114.
32. Lesage, P., and Todeschini, A.L. 2005. Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet. Genome Res. 110: 70-90. doi:10.1159/000084940. PMID:16093660.
33. Libertini, A., Panozzo, M., and Zenere, R. 1993. Chromosome number and genome size in the Antarctic whelk, Neobuccinum eatoni (Smith) (Prosobranchia, Neogastropoda). Chromosome Inf. Serv. 55: 5-6.
34. Marescalchi, O., Scali, V., and Zuccoti, M. 1998. Flow-cytometric analyses of intraspecific genome size variations in Bacillus atticus (Insecta, Phasmatodea). Genome, 41: 629-635. doi:10.1139/gen-41-5-629.
35. McLaren, I.A., Sévigny, J.S., and Frost B.W. 1989. Evolutionary and ecological significance of genome sizes in the copepod genus Pseudocalanus. Rev. Can. Zool. 67: 565-569. doi:10.1139/z89-080.
36. Nyholm, S.V., Robidart, J., and Girguis, P.R. 2008. Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae. Biol. Bull. 214: 255-265. PMID:18574102.
37. Rasch, E.M., and Wyngaard, G.A. 1996. Differences in DNA levels during early cleavage stages of Mesocyclops edax and Mesocyclops longisetus (Crustacea, Copepoda). Mol. Biol. Cell, 7: 694.
38. Rasch, E.M., and Wyngaard, G.A. 2006a. Genome sizes of cyclopoid copepods (Crustacea): evidence of evolutionary constraint. Biol. J. Linn. Soc. 87: 625-635. doi:10.1111/j.1095-8312.2006.00610.x.
39. Rasch, E.M., and Wyngaard, G.A. 2006b. Changes in nuclear morphology associated with elevated DNA levels during gametogenesis in cyclopoid copepods with chromatin diminution. Invertebr. Biol. 125: 56-69. doi:10.1111/j.1744-7410.2006.00041.x.
40. Rees, D.J., Dufresne, F., Glémet, H., and Belzile, C. 2007. Amphipod genome sizes: first estimates for Arctic species reveal genomic giants. Genome, 50: 151-158. doi:10.1139/G06-155. PMID:17546080.
41. Rees, D.J., Belzile, C., Glémet, H., and Dufresne, F. 2008. Large genomes among caridean shrimp. Genome, 51: 159-163. doi:10.1139/G07-108. PMID:18356950.
42. Rheinsmith, E.L., Hinegardner, R., and Bachmann, K. 1974. Nuclear DNA amounts in crustacea. Comp. Biochem. Physiol. B, 48: 343-348. doi:10.1016/0305-0491(74)90269-7. PMID:4847621.
43. Rodríguez-Juíz, A.M., Torrado, M., and Méndez, J. 1996. Genomesize variation in bivalve molluscs determined by flow cytometry. Mar. Biol. (Berl.), 126: 489-497. doi:10.1007/BF00354631.
44. Sarradin, P., Caprais, J., Riso, R., Kerouel, R., and Aminot, A. 1999. Chemical environment of the hydrothermal mussel communities in the Lucky Strike and Menez Gwen vent fields, Mid Atlantic Ridge. Cah. Biol. Mar. 40: 93-104.
45. Sella, G., Redi, C.A., Ramella, L., Soldi, R., and Premoli, M.C. 1993. Genome size and karyotype length in some interstitial polychaete species of the genus Ophryotrocha (Dorvilleidae). Genome, 36: 652-657. doi:10.1139/g93-086. PMID:18470014.
46. Sellars, M.J., Degnan, B.M., and Preston, N.P. 2006. Production of triploid Kuruma shrimp, Marsupenaeus (Penaeus) japonicus (Bate) nauplii through inhibition of polar body I, or polar body I and II extrusion using 6-dimethylaminopurine. Aquaculture, 256: 337-345. doi:10.1016/j. aquaculture.2006.02.052.
47. Shank, T.M., Fornari, D.J., Von Damm, K.L., Lilley, M.D., Haymon, R.M., and Lutz, R.A. 1998. Temporal and spatial patterns of biological community development at nascent deep-sea hydrothermal vents (9°50′N, East Pacific Rise). Deep Sea Res. Part II Top. Stud. Oceanogr. 45: 465-515. doi:10.1016/S0967-0645(97)00089-1.
48. Shank, T.M., Black, M.B., Halanych, K.M., Lutz, R.A., and Vrijenhoek, R.C. 1999. Miocene radiation of deep-sea hydrothermal vent shrimp (Caridea: Bresiliidae): evidence from mitochondrial cytochrome oxidase subunit I. Mol. Phylogenet. Evol. 13: 244-254. doi:10.1006/mpev.1999.0642. PMID:10603254.
49. Siljak-Yakovlev, S., Solic, M.E., Catrice, O., Brown, S.C., and Papes, D. 2005. Nuclear DNA content and chromosome number in some diploid and tetraploid Centaurea (Asteraceae: Cardueae) from the Dalmatia region. Plant Biol. 7: 397-404. doi:10.1055/s-2005-865693. PMID:16025412.
50. Soldi, R., Ramella, L., Gambi, M.C., Sordino, P., and Sella, G. 1994. Genome size in polychaetes: relationship with body length and life habit. In Actes de la 4ième Conférence Internationale des Polychètes. Edited by J.-C. Dauvin, L. Laubier, and D.J. Reish. Mémoires du M.N.H.N., Paris. pp. 129-135.
51. Steel, R.G.D., and Torrie, J.H. 1980. Analysis of covariance. In Principles and procedures of statistics: a biometrical approach. McGraw-Hill, New York. pp. 401-437.
52. Tsutsui, N.D., Suarez, A.V., Spagna, J.C., and Johnston, J.S. 2008. The evolution of genome size in ants. BMC Evol. Biol. 8: 64. [online.] doi:10.1186/1471-2148-8-64. PMID:18302783.
53. Van Dover, C.L., and Trask, J.L. 2000. Diversity at deep-sea hy-drothermal vent and intertidal mussel beds. Mar. Ecol. Prog. Ser. 195: 169-178. doi:10.3354/meps195169.
54. Van Dover, C.L., German, C.R., Speer, K.G., Parson, L.M., and Vrijenhoek, R.C. 2002. Evolution and biogeography of deep-sea vent and seep invertebrates. Science, 295: 1253-1257. doi:10. 1126/science.1067361. PMID:11847331.
55. Vieira, C., Lepetit, D., Dumont, S., and Biémont, C. 1999. Wake up of transposable elements following Drosophila simulans worldwide colonization. Mol. Biol. Evol. 16: 1251-1255. PMID:10486980.
56. Vieira, C., Nardon, C., Arpin, C., Lepetit, D., and Biémont, C. 2002. Evolution of genome size in Drosophila. Is the invader's genome being invaded by transposable elements? Mol. Biol. Evol. 19: 1154-1161. PMID:12082134.
57. Wessler, S.R. 1996. Turned on by stress. Plant retrotransposons. Curr. Biol. 6: 959-961. doi:10.1016/S0960-9822(02)00638-3. PMID:8805314.
58. Wyngaard, G.A., and Rasch, E.M. 2000. Patterns of genome size in the copepoda. Hydrobiologia, 417: 43-56. doi:10.1023/A:1003855322358.
59. Yi, S., and Streelman, J.T. 2005. Genome size is negatively correlated with effective population size in ray-finned fish. Trends Genet. 21: 643-646. doi:10.1016/j.tig.2005.09.003. PMID: 16213058.
60. Zhang, X., and Onozato, H. 2004. Hydrostatic pressure treatment during the first mitosis does not suppress the first cleavage but the second one. Aquaculture, 240: 101-113. doi:10.1016/j. aquaculture.2004.07.004.