Nucleomorph comparative genomics

Endosymbiosis

Volumn 9783709113035, Issue , 2014, Pages 197-213

  Tanifuji, Goro ^a   Archibald, John M ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84901461349     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1303-5_11     Document Type: Chapter

References (78)

1. Archibald JM (2007) Nucleomorph genomes: structure, function, origin and evolution. Bioessays 29:392-402
2. Archibald JM, Lane CE (2009) Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. J Hered 100:582-590
3. Bock R, Timmis JN (2008) Reconstructing evolution: gene transfer from plastids to the nucleus. Bioessays 30:556-566
4. Burki F, Shalchian-Tabrizi K, Pawlowski J (2008) Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Bio Lett 4:366-369
5. Burki F, Inagaki Y, Brate J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K (2009) Largescale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol 1:231-238
6. Cavalier-Smith T (2002) Nucleomorphs: enslaved algal nuclei. Curr Opin Microbiol 5:612-619
7. Cavalier-Smith T, Couch JA, Thorsteinsen KE, Gilson P, Deane JA, Hill DRA, McFadden GI (1996) Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny. Eur J Phycol 31:315-328
8. Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJM, Herman EK, Klute MJ, Nakayama T, Oborńk M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale C, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Korený L, Kroth PG, Liu Y, Malik S-B, Maier UG, McRose D, Mock T, Neilson JAD, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM (2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492:59-65
9. Daley DO, Whelan J (2005) Why genes persist in organelle genomes. Genome Biol 6:110
10. Deane JA, Isabbelle M, Strachan IM, Saunders GW, Hill DRA, McFadden GI (2002) Cryptomonad evolution: nuclear 18SrDNA phycologeny versus cell morphology and pigmentation. J Phycol 38:1236-1244
11. Deber CM, Liu LP, Wang C (1999) Perspective: peptides as mimics of transmembrane segments in proteins. J Pept Res 54:200-205
12. Degnan PH, Lazarus AB, Wernegreen JJ (2005) Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res 15:1023-1033
13. Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynie S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piegu B, Ball SG, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Vande Peer Y, Moreau H (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA 103:11647-11652
14. Dolezal P, Likic V, Tachezy J, Lithgow T (2006) Evolution of the molecular machines for protein import into mitochondria. Science 313:314-318
15. Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PSG, Hara Y, Archibald JM (2009) The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biol Evol 1:439-448
16. Douglas SE, Penny SL (1999) The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. J Mol Evol 48:236-244
17. Douglas SE, Durnford DG, Morden CW (1990) Nucleotide sequence of the gene for the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase from Cryptomonas phi : evidence supporting the polyphyletic origin of plastids. J Phycol 26:500-508
18. Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu XN, Reith M, Cavalier-Smith T, Maier UG (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410:1091-1096
19. Eschbach S, Hofmann CJB, Maier UG, Sitte P, Hansmann P (1991) A eukaryotic genome of 660 Kb: electrophoretic karyotype of nucleomorph and cell nucleus of the cryptomonad alga, Pyrenomonas salina. Nucleic Acids Res 19:1779-1781
20. Gagat P, Mackiewicz P, Body? A (2013) Secondary endosymbioses. In: Löffelhardt W (ed) Endosymbiosis. Springer, Vienna, pp xx-yy
21. Gibbs SP (1978) Chloroplasts of euglena may have evolved from symbiotic green-algae. Can J Bot 56:2883-2889
22. Gilson PR, McFadden GI (2002) Jam packed genomes-a preliminary, comparative analysis of nucleomorphs. Genetica 115:13-28
23. Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI (2006) Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proc Natl Acad Sci USA 103:9566-9571
24. Gould SB, Waller RR, McFadden GI (2008) Plastid evolution. Annu Rev Plant Biol 59:491-517
25. Gray MW, Doolittle WF (1982) Has the endosymbiont hypothesis been proven? Microbiol Rev 46:1-42
26. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283:1476-1481
27. Gray MW, Lang BF, Burger G (2004) Mitochondria of protists. Annu Rev Genet 38:477-524
28. Greenwood A (1974) The cryptophyta in relation to phylogeny and photosynthesis. In: Proceedings of the 8th International Congress on Electron Microscopy, vol 2, pp 566-567
29. Hackett JD, Anderson DM, Erdner DL, Bhattacharya D (2004) Dinoflagellates: a remarkable evolutionary experiment. Am J Bot 91:1523-1534
30. Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ (2009) Phylogenomic analyses support the monophyly of excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci USA 106:3859-3864
31. Hibberd DJ, Norris RE (1984) Cytology and ultrastructure of Chlorarachnion reptans (Chlorarachniophyta divisio nova, Chlorarachniophyceae classis nova). J Phycol 20:310-330
32. Hirakawa Y, Burki F, Keeling PJ (2012) Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and plastid in chlorarachniophytes. J Cell Sci 125(Pt 24):6176-6184
33. Hoef-Emden K (2005) Multiple independent losses of photosynthesis and differing evolutionary rates in the genus Cryptomonas (cryptophyceae): combined phylogenetic analyses of DNA sequences of the nuclear and the nucleomorph ribosomal operons. J Mol Evol 60:183-195
34. Hoef-Emden K, Marin B, Melkonian M (2002) Nuclear and nucleomorph SSU rDNA phylogeny in the cryptophyta and the evolution of cryptophyte diversity. J Mol Evol 55:161-179
35. Ishida K, Cao Y, Hasegawa M, Okada N, Hara Y (1997) The origin of chlorarachniophyte plastids, as inferred from phylogenetic comparisons of amino acid sequences of EF-Tu. J Mol Evol 45:682-687
36. Ishida K, Green BR, Cavalier-Smith T (1999) Diversification of a chimaeric algal group, the chlorarachniophytes: phylogeny of nuclear and nucleomorph small-subunit rRNA genes. Mol Biol Evol 16:321-331
37. Ishida K, Endo H, Koike S (2011a) Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp. Phycol Res 59:120-122
38. Ishida K, Yabuki A, Ota S (2011b) Amorphochlora amoebiformis gen. et comb. nov. (Chlorarachniophyceae). Phycol Res 59:52-53
39. Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450-453
40. Khan H, Parks N, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM (2007) Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Mol Biol Evol 24:1832-1842
41. Lane CE, Archibald JM (2006) Novel nucleomorph genome architecture in the cryptomonad genus Hemiselmis. J Eukaryot Microbiol 53:515-521
42. Lane CE, Archibald JM (2008) New marine members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae). J Phycol 44:439-450
43. Lane CE, Khan H, MacKinnon M, Fong A, Theophilou S, Archibald JM (2006) Insight into the diversity and evolution of the cryptomonad nucleomorph genome. Mol Biol Evol 23:856-865
44. Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM (2007) Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc Natl Acad Sci USA 104:19908-19913
45. Löffelhardt W (2013) The single primary endosymbiotic event. In: Löffelhardt W (ed) Endosymbiosis. Springer, Vienna, pp xx-yy
46. Ludwig M, Gibbs SP (1985) DNA is present in the nucleomorph of cryptomonads-further evidence that the chloroplast evolved from a eukaryotic endosymbiont. Protoplasma 127:9-20
47. Martin W (2003) The smoking gun of gene transfer. Nat Genet 33:442
48. Martin W, Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol 118:9-17
49. Martin W, Schnarrenberger C (1997) The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis. Curr Genet 32:1-18
50. Martin W, Mustafa AZ, Henze K, Schnarrenberger C (1996) Higher-plant chloroplast and cytosolic fructose-1, 6-bisphosphatase isoenzymes: origins via duplication rather than prokaryoteeukaryote divergence. Plant Mol Biol 32:485-491
51. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 99:12246-12251
52. Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:653-657
53. McFadden GI, Gilson PR, Hill DRA (1994) Goniomonas-ribosomal RNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur J Phycol 29:29-32
54. McFadden GI, Gilson PR, Waller RF (1995) Molecular phylogeny of chlorarachniophytes based on plastid ribosomal RNA and rbcL sequences. Arch Protistenkd 145:231-239
55. Moore CE, Archibald JM (2009) Nucleomorph genomes. Annu Rev Genet 43:251-264
56. Moran NA (1996) Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA 93:2873-2878
57. Moran NA, McCutcheon JP, Nakabachi A (2008) Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42:165-190
58. Moreira D, Lopezarchilla AI, Amils R, Marin I (1994) Characterization of 2 New thermoacidophilic microalgae-genome organization and comparison with Galdieria sulphuraria. FEMS Microbiol Lett 122:109-114
59. Muravenko OV, Selyakh IO, Kononenko NV, Stadnichuk IN (2001) Chromosome numbers and nuclear DNA contents in the red microalgae Cyanidium caldarium and three Galdieria species. Eur J Phycol 36:227-232
60. Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267
61. Ota S, Ueda K, Ishida K (2007) Norrisiella sphaerica gen. et sp nov., a new coccoid chlorarachniophyte from Baja California, Mexico. J Plant Res 120:661-670
62. Patron NJ, Inagaki Y, Keeling PJ (2007) Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol 17:887-891
63. Phipps KD, Donaher NA, Lane CE, Archibald JM (2008) Nucleomorph karyotype diversity in the freshwater cryptophyte genus Cryptomonas. J Phycol 44:11-14
64. Podlevsky JD, Bley CJ, Omana RV, Qi XD, Chen JJL (2008) The telomerase database. Nucleic Acids Res 36:D339-D343
65. Rensing SA, Goddemeier M, Hofmann CJB, Maier UG (1994) The presence of a nucleomorph hsp70 gene is a common feature of cryptophyta and chlorarachniophyta. Curr Genet 26:451-455
66. Reyes-Prieto A, Weber APM, Bhattacharya D (2007) The origin and establishment of the plastid in algae and plants. Annu Rev Genet 41:147-168
67. Saccone C, Gissi C, Reyes A, Larizza A, Sbisa E, Pesole G (2002) Mitochondrial DNA in metazoa: degree of freedom in a frozen event. Gene 286:3-12
68. Shalchian-Tabrizi K, Brate J, Logares R, Klaveness D, Berney C, Jakobsen KS (2008) Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environ Microbiol 10:2635-2644
69. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407:81-86
70. Silver TD, Koike S, Yabuki A, Kofuji R, Archibald JM, Ishida KI (2007) Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae. J Eukaryot Microbiol 54:403-410
71. Silver TD, Moore CE, Archibald JM (2010) Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algae. J Eukaryot Microbiol 57:453-459
72. Smith DR (2009) Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol Biol 71:627-639
73. Tanifuji G (2011) Reductive genome evolution in nucleomorphs (in Japanese). Jpn J Protozool 44:89-102
74. Tanifuji G, Onodera NT, Hara Y (2010) Nucleomorph genome diversity and its phylogenetic implications in cryptomonad algae. Phycol Res 58:230-237
75. Tanifuji G, Onodera NT, Wheeler TJ, Dlutek M, Donaher N, Archibald JM (2011) Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. Genome Biol Evol 3:44-54
76. van Dooren GG, Schwartzbach SD, Osafune T, McFadden GI (2001) Translocation of proteins across the multiple membranes of complex plastids. Biochim Biophys Acta 1541:34-53
77. Whatley JM, Whatley FR (1981) Chloroplast evolution. New Phytol 87:233-247
78. Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KFX, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324:268-272