Genome enablement of the notothenioidei: Genome size estimates from 11 species and BAC libraries from 2 representative taxa

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 314 B, Issue 5, 2010, Pages 369-381

  Taxa, Representative ^a   William Detrich, H ^a   Stuart, Andrew ^b   Schoenborn, Michael ^b   Parker, Sandra K ^a   Methé, Barbara A ^c   Amemiya, Chris T ^b,d  

^a NORTHEASTERN UNIVERSITY   (United States)

^b BENAROYA RESEARCH INSTITUTE   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954321343     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.21341     Document Type: Article

References (91)

1. Albertson RC, Cresko W, Detrich III HW, Postlethwait JH. 2009. Evolutionary mutant models for human disease. Trends Genet 25:74-81.
2. Amemiya CT, Ota T, Litman GW. 1996. Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. In: Lai E, Birren B, editors. Analysis of nonmammalian genomes. San Diego: Academic Press. p 223-256.
3. Arumuganathan K, Searle ED. 1991. Estimation of nuclear DNA contents in plants by flow cytometry. Plant Mol Biol 9:229-241.
4. Balushkin AV. 2000. Morphology, classification, and evolution of notothenioid fishes of the Southern Ocean (Notothenioidei, Perciformes). J Ichthyol 40:S74-S109.
5. Bargelloni L, Marcato S, Patarnello T. 1998. Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperature. Proc Natl Acad Sci USA 95:8670-8675.
6. Bucciarelli G, Bernardi G, Bernardi G. 2002. An ultracentrifugation analysis of two hundred fish genomes. Gene 295:153-162.
7. Buckley BA, Place SP, Hofmann GE. 2004. Regulation of heat shock genes in isolated hepatocytes from an Antarctic fish, Trematomus bernacchii. J Exp Biol 207:3649-3656.
8. Chen L, DeVries AL, Cheng C-HC. 1997. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic noththe-nioid fish. Proc Natl Acad Sci USA 94:3811-3816.
9. Chen Z, Cheng CH, Zhang J, Cao L, Chen L, Zhou L, Jin Y, Ye H, Deng C, Dai Z, Xu Q, Hu P, Sun S, Shen Y, Chen L. 2008. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc Natl Acad Sci USA 105:12944-12949.
10. Cheng C-HC. 1998. Origin and mechanism of evolution of antifreeze glycoproteins in polar fishes. In: di Prisco G, Pisano E, Clarke A, editors. Fishes of Antarctica. A biological overview. Milano, Italy: Springer. p 311-328.
11. 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 401:443-444.
12. Cheng C-HC, Detrich III HW. 2007. Molecular ecophysiology of Antarctic notothenioid fishes. Phil T Roy Soc B 362:2215-2232.
13. Clarke A. 1990. Temperature and evolution: Southern Ocean cooling and the Antarctic marine fauna. In: Kerry KR, Hempel G, editors. Antarctic ecosystems: ecological change and conservation. Berlin: Springer. p 9-22.
14. Cocca E, Ratnayake-Lecamwasam M, Parker SK, Camardella L, Ciaramella M, di Prisco G, Detrich III HW. 1995. Genomic remnants of a-globin genes in the hemoglobinless Antarctic icefishes. Proc Natl Acad Sci USA 92:1817-1821.
15. Cocca E, Detrich III HW, Parker SK, di Prisco G. 2000. A cluster of four globin genes from the Antarctic fish Notothenia coriiceps. J Fish Biol 57:33-50.
16. Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. 2006. The ''fish-specific'' Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 23:121-136.
17. Cui J, Ren X, Yu Q. 1991. Nuclear DNA content variation in fishes. Cytologia 56:425-429.
18. 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 Part A 301:228-234.
19. D'Avino R, di Prisco G. 1988. Antarctic fish hemoglobin: an outline of the molecular structure and oxygen binding properties-I. molecular structure. Comp Biochem Physiol B 90:579-584.
20. DeConto RM, Pollard D. 2003. Rapid Cenozoic glaciation of Antarctica induced by declining atmospheric CO2. Nature 421:245-249.
21. Detrich III HW. 2007. The unusual cardiovascular system of the hemoglobinless Antarctic icefishes. In: Aird WC, editor. Endothelial biomedicine. Cambridge: Cambridge University Press. p 74-78.
22. Detrich III HW, Johnson KA, Marchese-Ragona SP. 1989. Polymerization of Antarctic fish tubulins at low temperatures: energetic aspects. Biochemistry 28:10085-10093.
23. Detrich III HW, Fitzgerald TJ, Dinsmore JH, Marchese-Ragona SP. 1992. Brain and egg tubulins from Antarctic fishes are functionally and structurally distinct. J Biol Chem 267:18766-18775.
24. Detrich III HW, Parker SK, Williams Jr RC, Nogales E, Downing KH. 2000. Cold adaptation of microtubule assembly and dynamics: structural interpretation of primary sequence changes present in the aand b-tubulins of Antarctic fishes. J Biol Chem 275: 37038-37047.
25. Dettaï A, Lecointre G. 2004. In search of notothenioid (Teleostei) relatives. Antarct Sci 16:71-85.
26. De Vries AL, Eastman JT. 1978. Lipid sacs as a buoyancy adaptation in an Antarctic fish. Nature 271:352-353.
27. 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.
28. di Prisco G. 1998. Molecular adaptations of Antarctic fish hemoglobins. In: di Prisco G, Pisano E, Clarke A, editors. Fishes of Antarctica. A biological overview. Milano: Springer. p 339-353.
29. di Prisco G, Eastman JT, Giordano D, Parisi E, Verde C. 2007. Biogeography and adaptation of Notothenioid fish: hemoglobin function and globin-gene evolution. Gene 398:143-155.
30. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2007. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17:1697-1706.
31. Eastman JT. 1993. Antarctic fish biology: evolution in a unique environment. San Diego: Academic Press.
32. Eastman JT. 1997. Phyletic divergence and specialization for pelagic life in the Antarctic notothenioid fish Pleuragramma antarcticum. Comp Biochem Physiol 118A:1095-1101.
33. Eastman JT. 1999. Aspects of the biology of the icefish Dacodraco hunteri (Notothenioidei, Channichthyidae) in the Ross Sea, Antarctica. Polar Biol 21:194-196.
34. Eastman JT. 2000. Antarctic notothenioid fishes as subjects for research in evolutionary biology. Antarct Sci 12:276-287.
35. Eastman JT. 2005. The nature of the diversity of Antarctic fishes. Polar Biol 28:93-107.
36. 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 Antarctic: a biological overview. Milano: Springer. p 3-26.
37. Eastman JT, DeVries AL. 1981. Buoyancy adaptations in a swimbladderless Antarctic fish. J Morphol 167:91-102.
38. Eastman JT, McCune AR. 2000. Fishes on the Antarctic continental shelf: evolution of a marine species flock? J Fish Biol 57A:84-102.
39. Fjell CD, Bosdet I, Schein JE, Jones SJ, Marra MA. 2003. Internet Contig Explorer (iCE)-a tool for visualizing clone fingerprint maps. Genome Res 13:1244-1249.
40. Hardie DC, Hebert PD. 2003. The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes. Genome 46:683-706.
41. Hardie DC, Hebert PD. 2004. Genome-size evolution in fishes. Can J Fish Aquat Sci 61:1636-1646.
42. Hinegardner R. 1968. Evolution of cellular DNA content in teleost fishes. Am Nat 102:517-523.
43. Hinegardner R, Rosen DE. 1972. Cellular DNA content and the evolution of teleostean fishes. Am Nat 106:621-644.
44. 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: 2331-2339.
45. Hureau JC, Petit D, Fine JM, Marneux M. 1977. New cytological, biochemical, and physiological data on the colorless blood of the Channichthyidae (Pisces, Teleosteans, Peciformes). In: Llano GA, editor. Adaptations within Antarctic ecosystems. Washington, DC: Smithsonian Institution. p 459-477.
46. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462-467.
47. Kennett JP. 1977. Cenozoic evolution of Antarctic glaciation, the circum-Antarctic ocean, and their impact on global paleoceanography. J Geophys Res 82:3843-3860.
48. Kim CB, Amemiya C, Bailey W. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc Natl Acad Sci USA 97: 1655-1660.
49. 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 207:4633-4649.
50. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: Repbase Submitter and Censor. BMC Bioinformatics 7:474
51. Kunzmann A, Caruso C, di Prisco G. 1991. Haematological studies on a high-Antarctic fish: Bathydraco marri Norman. J Exp Mar Biol Ecol 152:243-255.
52. 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.
53. Livermore R, Nankivell A, Eagles G, Morris P. 2005. Paleogene opening of the Drake Passage. Earth Planet Sci Lett 236:459-470.
54. 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 203:2105-2115.
55. Meyer A, Schartl M. 1999. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 11:699-704.
56. Mirsky AE, Ris H. 1951. The deoxyribonucleic acid content of animal cells and its evolutionary significance. J Gen Physiol 34:451-462.
57. Montgomery J, Clements K. 2000. Disaptation and recovery in the evolution of Antarctic fishes. Trends Ecol Evol 15:267-271.
58. 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 11:655-661.
59. 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 16:559-564.
60. Near TJ, Cheng CH. 2008. Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences. Mol Phylogenet Evol 47:832-840.
61. Near TJ, Russo SE, Jones CD, DeVries AL. 2003. Ontogenetic shift in buoyancy and habitat in the Antarctic toothfish, Dissostichus mawsoni (Perciformes: Nototheniidae). Polar Biol 26:124-128.
62. 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 32:881-891.
63. Near TJ, Parker SK, Detrich III HW. 2006. A genomic fossil reveals key steps in hemoglobin loss by the antarctic icefishes. Mol Biol Evol 23:2008-2016.
64. Near TJ, Kendrick BJ, Detrich III HW, Jones CD. 2007. Confirmation of neutral buoyancy in Aethotaxis mitopteryx DeWitt (Notothenioidei: Nototheniidae). Polar Biol 30:443-447.
65. 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 203:1287-1297.
66. 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.
67. Paluh JL, Killilea AN, Detrich III HW, Downing KH. 2004. Meiosis-specific failure of cell cycle progression in fission yeast by mutation of a conserved b-tubulin residue. Mol Biol Cell 15:1160-1171.
68. Parker SK, Detrich III HW. 1998. Evolution, organization, and expression of a-tubulin genes in the Antarctic fish Notothenia coriiceps: a tandem gene cluster generated by recent gene duplication, inversion, and divergence. J Biol Chem 273:34358-34369. Place SP,
69. Hofmann GE. 2005. Constitutive expression of a stressinducible heat shock protein gene, hsp70, in phylogenetically distant Antarctic fish. Polar Biol 28:261-267.
70. 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 -Reg Integr Comp Physiol 287:R429-R436.
71. Romisch K, Collie N, Soto N, Logue J, Lindsay M, Scheper W, Cheng C-HC. 2003. Protein translocation across the endoplasmic reticulum membrane in cold-adapted organisms. J Cell Sci 116:2875-2883.
72. Ruud JT. 1954. Vertebrates without erythrocytes and blood pigment. Nature 173:848-850.
73. Schein JE, Kucaba TA, Sekhon M, Smailus D, Waterston RH, Marra MA. 2004. High-throughput BAC fingerprinting. In: Zhao S, Stodolsky M, editors. Bacterial artificial chromosomes, volume 1: library construction, physical mapping, and sequencing. Totowa, NY: Humana Press, Inc. p 143-156.
74. Scher HD, Martin EE. 2006. Timing and climatic consequences of the opening of Drake Passage. Science 312:428-430.
75. 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 104:2767-2772.
76. 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 209:1791-1802.
77. 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 94:3420-3424.
78. Smit AFA, Hubley R, Green P. 2004. RepeatMasker Open-3.0.
79. Smith AD, Xuan Z, Zhang MQ. 2008. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9:128.
80. Smith JJ, Putta S, Zhu W. 2009. Genic regions of a large salamander genome contain long introns and novel genes. BMC Genomics 10:19.
81. Somero GN, DeVries AL. 1967. Temperature tolerance of some Antarctic fishes. Science 156:257-258.
82. Strong SJ, Ohta Y, Litman GW, Amemiya CT. 1997. Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res 25:3959-3961.
83. 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 177:857-866.
84. Vialli M. 1957. Volume et contenu en ADN par noyau. Exp Cell Res 4:284-293.
85. Vinograd AE. 1998. Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry 31:100-109.
86. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N. 2006. 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7:275.
87. Williams Jr RC, Correia JJ, DeVries AL. 1985. Formation of microtubules at low temperature by tubulin from Antarctic fish. Biochemistry 24:2790-2798.
88. Wittbrodt J, Meyer A, Schartl M. 1998. More genes in fish? BioEssays 20:511-515.
89. Xing J, Wang H, Belancio VP, Cordaux R, Deininger PL, Batzer MA. 2006. Emergence of primate genes by retrotransposonmediated sequence transduction. Proc Natl Acad Sci USA 103:17608-17613.
90. Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686-693.
91. Zhao Y, Ratnayake-Lecamwasam M, Parker SK, Cocca E, Camardella L, di Prisco G, Detrich III HW. 1998. The major adult a-globin gene of Antarctic teleosts and its remnants in the hemoglobinless icefishes: calibration of the mutational clock for nuclear genes. J Biol Chem 273:14745-14752.