Antarctic notothenioid fishes: Genomic resources and strategies for analyzing an adaptive radiation

Integrative and Comparative Biology

Volumn 50, Issue 6, 2010, Pages 1009-1017

  Detrich III, H W ^a   Amemiya, Chris T ^b,c  

^a NORTHEASTERN UNIVERSITY   (United States)

^b BENAROYA RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ADAPTATION; ANIMAL; ANTARCTICA; BACTERIAL ARTIFICIAL CHROMOSOME; BONE MINERALIZATION; CHEMISTRY; CONFERENCE PAPER; DISEASE MODEL; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GENOME; HISTOLOGY; INTERSPERSED REPEAT; METABOLIC BONE DISEASE; MOLECULAR EVOLUTION; PERCIFORMES; PHYLOGENY; PHYSIOLOGY;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ANTARCTIC REGIONS; BONE DISEASES, METABOLIC; CALCIFICATION, PHYSIOLOGIC; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DISEASE MODELS, ANIMAL; DNA; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENE LIBRARY; GENOME; INTERSPERSED REPETITIVE SEQUENCES; PERCIFORMES; PHYLOGENY;

BACTERIA (MICROORGANISMS); CHAENOCEPHALUS ACERATUS; CHANNICHTHYIDAE; NOTOTHENIA CORIICEPS; NOTOTHENIIDAE; PERCIDAE; PERCIFORMES; PISCES; SALANGINI;

EID: 78649509931     PISSN: 15407063     EISSN: 15577023     Source Type: Journal    
DOI: 10.1093/icb/icq071     Document Type: Conference Paper

References (69)

1. Albertson RC, Cresko W, Detrich HW III, Postlethwait JH. 2009. Evolutionary mutant models for human disease. Trends Genet 25:74-81.
2. Albertson RC, Yan YL, Titus TA, Pisano E, Vacchi M, Yelick PC, Detrich HW III, Postlethwait JH. 2010. Molecular pedomorphism underlies craniofacial skeletal evolution in Antarctic notothenioid fishes. BMC Evol Biol 10:4.
3. Amemiya CT, Gomez-Chiarri M. 2006. Comparative genomics in vertebrate evolution and development. J Exp Zool A Comp Exp Biol 305:672-82.
4. Amemiya CT, Zhong TP, Silverman GA, Fishman MC, Zon LI. 1999. Zebrafish YAC, BAC, and PAC genomic libraries. Methods Cell Biol 60:235-58.
5. Balushkin AV. 2000. Morphology, classification, and evolution of notothenioid fishes of the Southern Ocean (Notothenioidei, Perciformes). J Ichthyol 40: S74-109.
6. Birney E, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
7. Bucciarelli G, Bernardi G, Bernardi G. 2002. An ultracentrifugation analysis of two hundred fish genomes. Gene 295:153-62.
8. Buckley BA, Place SP, Hofmann GE. 2004. Regulation of heat shock genes in isolated hepatocytes from an Antarctic fish, Trematomus bernacchii. J Exp Biol 207:3649-56.
9. Chan YF, et al. 2010. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327:302-5.
10. Cheng C-HC, Chen L. 1999. Evolution of an antifreeze glycoprotein: a blood protein that keeps Antarctic fish from freezing arose from a digestive enzyme. Nature 401:443-4.
11. Chen Z, et al. 2008. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc Natl Acad Sci USA 105:12944-49.
12. Chen L, DeVries AL, Cheng C-HC. 1997. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notohthenioid fish. Proc Natl Acad Sci USA 94:3811-6. (Pubitemid 27180454)
13. Cocca E, Detrich HW III, Parker SK, di Prisco G. 2000. A cluster of four globin genes from the Antarctic fish Notothenia coriiceps. J Fish Biol 57:33-50.
14. Cocca E, Ratnayake-Lecamwasam M, Parker SK, Camardella L, Ciaramella M, di Prisco G, Detrich HW III. 1995. Genomic remnants of a-globin genes in the hemoglobinless antarctic icefishes. Proc Natl Acad Sci USA 92:1817-21.
15. Danke J, Miyake T, Powers T, Schein J, Shin H, Bosdet I, Erdmann M, Caldwell R, Amemiya CT. 2004. Genome resource for the Indonesian coelacanth, Latimeria menadoensis. J Exp Zool A Comp Exp Biol 301:228-34. (Pubitemid 38345458)
16. DeConto RM, Pollard D. 2003. Rapid Cenozoic glaciation of Antarctica induced by declining atmospheric CO2. Nature 421:245-9.
17. Detrich HW III, Fitzgerald TJ, Dinsmore JH, Marchese-Ragona SP. 1992. Brain and egg tubulins from Antarctic fishes are functionally and structurally distinct. J Biol Chem 267:18766-75.
18. Detrich HW III, Johnson KA, Marchese-Ragona SP. 1989. Polymerization of Antarctic fish tubulins at low temperatures: energetic aspects. Biochemistry 28:10085-93.
19. Detrich HW III, Parker SK, Williams RC Jr, Nogales E, Downing KH. 2000. Cold adaptation of microtubule assembly and dynamics: structural interpretation of primary sequence changes present in the a-and b-tubulins of Antarctic fishes. J Biol Chem 275:37038-47.
20. Detrich HW III, Stuart A, Schoenborn M, Parker SK, Methe BA, Amemiya CT. 2010. Genome enablement of the Notothenioidei: genome size estimates from eleven species and BAC libraries from two representative taxa. J Exp Zool B Mol Dev Evol 314:369-81.
21. Dettäi A, Lecointre G. 2004. In search of notothenioid (Teleostei) relatives. Antarctic Sci 16:71-85.
22. DeWitt HH. 1971. Coastal and deep-water benthic fishes of the Antarctic. In: Bushnell VC, editor. Antarctic Map Folio Series, Folio 15. New York: American Geographical Society. p. 1-10.
23. Eastman JT. 1993. Antarctic fish biology: evolution in a unique environment. San Diego: Academic Press.
24. Eastman JT. 1997. Phyletic divergence and specialization for pelagic life in the Antarctic notothenioid fish Pleuragramma antarcticum. Comp Biochem Physiol 118 A: 1095-101.
25. Eastman JT. 1999. Aspects of the biology of the icefish Dacodraco hunteri (Notothenioidei, Channichthyidae) in the Ross Sea, Antarctica. Polar Biol 21:194-6.
26. Eastman JT. 2000. Antarctic notothenioid fishes as subjects for research in evolutionary biology. Antarctic Sci 12:276-87.
27. Eastman JT. 2005. The nature of the diversity of Antarctic fishes. Polar Biol 28:93-107.
28. Eastman JT, Clarke A. 1998. A comparison of adaptive radiations of Antarctic fish with those of non-Antarctic fish. In: di Prisco G, Pisano E, Clarke A, editors. Fishes of Antartica: a biological overview. Milano: Springer-Verlag. p. 3-26.
29. Eastman JT, McCune AR. 2000. Fishes on the Antarctic continental shelf: evolution of a marine species flock? J Fish Biol 57 A: 84-102.
30. Gould SJ. 1992. Ontogeny and phylogeny-revisited and reunited. Bioessays 14:275-279.
31. Hardie DC, Hebert PD. 2003. The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes. Genome 46:683-706.
32. Hardie DC, Hebert PD. 2004. Genome-size evolution in fishes. Can J Fish Aq Sci 61:1636-46.
33. Hinegardner R, Rosen DE. 1972. Cellular DNA content and the evolution of teleostean fishes. Am Naturalist 106:621-44.
34. Hofmann GE, Buckley BA, Airaksinen S, Keen JE, Somero GN. 2000. Heat-shock protein expression is absent in the antarctic fish Trematomus bernacchii (family Nototheniidae). J Exp Biol 203:2331-9.
35. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462-7.
36. Kennett JP. 1977. Cenozoic evolution of Antarctic glaciation, the circum-Antarctic ocean, and their impact on global paleoceanography. J Geophys Res 82:3843-60.
37. Kiss AJ, Mirarefi AY, Ramakrishnan S, Zukoski CF, DeVries AL, Cheng CH. 2004. Cold-stable eye lens crystallins of the Antarctic nototheniid toothfish Dissostichus mawsoni Norman. J Exp Biol 207:4633-49.
38. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7:474.
39. Lecointre G, Bonillo C, Ozouf-Costaz C, Hureau J-C. 1997. Molecular evidence for the origins of Antarctic fishes: paraphyly of the Bovichtidae and no indication for the monophyly of the Notothenioidei (Teleostei). Polar Biol 18:193-208.
40. Livermore R, Nankivell A, Eagles G, Morris P. 2005. Paleogene opening of the Drake Passage. Earth Planet Sci Lett 236:459-70.
41. Logue JA, De Vries AL, Fodor E, Cossins AR. 2000. Lipid compositional correlates of temperature-adaptive interspecific differences in membrane physical structure. J Exp Biol 203:2105-15.
42. Miyake T, Amemiya CT. 2004. BAC libraries and comparative genomics of aquatic chordate species. Comp Biochem Physiol C Toxicol Pharmacol 138:233-44.
43. Montgomery J, Clements K. 2000. Disaptation and recovery in the evolution of Antarctic fishes. Trends Ecol Evol 15:267-71.
44. Morescalchi A, Hureau JC, Olmo E, Ozouf-Costaz C, Pisano E, Stanyon R. 1992. A multiple sex-chromosome system in Antarctic ice-fishes. Polar Biol 11:655-61.
45. Morescalchi A, Morescalchi MA, Odierna G, Stingo V, Capriglione T. 1996. Karyotype and genome size of zoarcids and notothenioids (Teleostei, Perciformes) from the Ross Sea: cytotaxonomic implications. Polar Biol 16:559-64.
46. Near TJ, Cheng CH. 2008. Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences. Mol Phylogenet Evol 47:832-40.
47. Near TJ, Kendrick BJ, Detrich HW III, Jones CD. 2007. Confirmation of neutral buoyancy in Aethotaxis mitopteryx DeWitt (Notothenioidei: Nototheniidae). Polar Biol 30:443-7.
48. Near TJ, Parker SK, Detrich HW III. 2006. A genomic fossil reveals key steps in hemoglobin loss by the Antarctic icefishes. Mol Biol Evol 23:2008-16.
49. Near TJ, Pesavento JJ, Cheng CH. 2004. Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA. Mol Phylogenet Evol 32:881-91.
50. O'Brien KM, Sidell BD. 2000. The interplay among cardiac ultrastructure, metabolism and the expression of oxygen-binding proteins in Antarctic fishes. J Exp Biol 203:1287-97.
51. Osoegawa K, Woon PY, Zhao B, Frengen E, Tateno M, Catanese JJ, de Jong PJ. 1998. An improved approach for construction of bacterial artificial chromosome libraries. Genomics 52:1-8.
52. Paluh JL, Killilea AN, Detrich HW III, Downing KH. 2004. Meiosis-specific failure of cell cycle progression in fission yeast by mutation of a conserved b-tubulin residue. Mol Biol Cell 15:1160-71.
53. Place SP, Hofmann GE. 2005. Constitutive expression of a stress-inducible heat shock protein gene, hsp70, in phylogenetically distant Antarctic fish. Polar Biol 28:261-7.
54. Place SP, Zippay ML, Hofmann GE. 2004. Constitutive roles for inducible genes: evidence for the alteration in expression of the inducible hsp70 gene in Antarctic notothenioid fishes. Am J Physiol Regul Integr Comp Physiol 287: R429-36.
55. Romisch K, Collie N, Soto N, Logue J, Lindsay M, Scheper W, Cheng C-HC. 2003. Protein translocation across the endoplasmic reticulum membrane in coldadapted organisms. J Cell Sci 116:2875-83.
56. Ruud JT. 1954. Vertebrates without erythrocytes and blood pigment. Nature 173:848-50.
57. Scher HD, Martin EE. 2006. Timing and climatic consequences of the opening of Drake Passage. Science 312:428-30.
58. Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV. 2007. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci USA 104:2767-72.
59. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794-7.
60. Sidell BD, O'Brien KM. 2006. When bad things happen to good fish: the loss of hemoglobin and myoglobin expression in Antarctic icefishes. J Exp Biol 209:1791-802.
61. Sidell BD, Vayda ME, Small DJ, Moylan TJ, Londraville RL, Yuan ML, Rodnick KJ, Eppley ZA, Costello L. 1997. Variable expression of myoglobin among the hemoglobinless Antarctic icefishes. Proc Natl Acad Sci USA 94:3420-4.
62. Smit A F A, Hubley R, Green P. 2004. Repeat Masker Open-3.0. 1996-2010, available from: http://www.repeatmasker.org.
63. Todgham AE, Hoaglund EA, Hofmann GE. 2007. Is cold the new hot? Elevated ubiquitin-conjugated protein levels in tissues of Antarctic fish as evidence for cold-denaturation of proteins in vivo. J Comp Physiol [B] 177:857-66.
64. Vialli M. 1957. Volume et contenu en ADN par noyau. Exp Cell Res Suppl 4:284-93.
65. Vinograd AE. 1998. Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry 31:100-9.
66. Williams RC Jr, Correia JJ, DeVries AL. 1985. Formation of microtubules at low temperature by tubulin from Antarctic fish. Biochemistry 24:2790-8.
67. Yang XW, Model P, Heintz N. 1997. Homologous recombination based modification in Escherichia coli and germline transmission in transgenic mice of a bacterial artificial chromosome. Nat Biotechnol 15:859-65.
68. Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686-93.
69. Zhao Y, Ratnayake-Lecamwasam M, Parker SK, Cocca E, Camardella L, di Prisco G, Detrich HW III. 1998. The major adult α-globin gene of Antarctic teleosts and its remnants in the hemoglobinless icefishes: calibration of the mutational clock for nuclear genes. J Biol Chem 273:14745-52.