Nucleomorph genome sequence of the cryptophyte alga chroomonas mesostigmatica CCMP1168 reveals lineage-specific gene loss and genome complexity

Genome Biology and Evolution

Volumn 4, Issue 11, 2012, Pages 1162-1175

  Moore, Christa E ^a   Curtis, Bruce ^a   Mills, Tyler ^a   Tanifuji, Goro ^a   Archibald, John M ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Comparative genomics; Cryptophyte; Endosymbiosis; Genome reduction; Nucleomorph

Indexed keywords

ALGAE; CHROOMONAS MESOSTIGMATICA; CRYPTOPHYTA; EUKARYOTA;

ARTICLE; CELL CULTURE; CHROMOSOME; CHROMOSOME MAP; CRYPTOPHYTA; DNA SEQUENCE; GENE DELETION; GENETIC VARIABILITY; GENETICS; GENOME; GENOME SIZE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; SYMBIOSIS;

CELLS, CULTURED; CHROMOSOME MAPPING; CHROMOSOMES; CRYPTOPHYTA; EVOLUTION, MOLECULAR; GENE DELETION; GENETIC SPECIATION; GENETIC VARIATION; GENOME; GENOME SIZE; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SYMBIOSIS;

EID: 84876063172     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs090     Document Type: Article

References (41)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
2. Archibald JM. 2007. Nucleomorph genomes: structure, function, origin, and evolution. BioEssays 29:392-402.
3. Archibald JM, Lane CE. 2009. Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. J Hered. 100: 582-590.
4. Bolte K, et al. 2011. Making new out of old: Recycling and modification of an ancient protein translocation system during eukaryotic evolution. Bioessays 33:368-376.
5. Bonfield JK, Smith KF, Staden R. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:4992-4999.
6. Cao K, Nakajima R, Meyer HH, Zheng Y. 2003. The AAA-ATPase Cdc48/ p97 regulates spindle disassembly at the end of mitosis. Cell 115: 355-367.
7. Cavalier-Smith T. 2000. Membrane heredity and early chloroplast evolution. Trends Plant Sci. 5:174-182.
8. Cavalier-Smith T. 2002. Nucleomorphs: enslaved algal nuclei. Curr Opin Microbiol. 5:612-619.
9. Conaway RC, Brower CS, Conaway JW. 2002. Emerging roles of ubiquitin in transcription regulation. Science 296:1254-1258.
10. 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.
11. Douglas S, et al. 2001. The highly reduced genome of an enslaved algal nucleus. Nature 410:1091-1096.
12. Eschbach S, Hofmann CJ, 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.
13. Finley D, Chau V. 1991. Ubiquitination. Annu Rev Cell Biol. 7:25-69.
14. Gardner RG, Nelson ZW, Gottschling DE. 2005. Ubp10/Dot4p regulates the persistence of ubiquitinated histone H2B: distinct roles in telomeric silencing and general chromatin. Mol Cell Biol. 25:6123-6139.
15. Gilson PR, McFadden GI. 2002. Jam packed genomes-a preliminary, comparative analysis of nucleomorphs. Genetica 115:13-28.
16. Gilson PR, et al. 2006. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proc Natl Acad Sci U S A. 103:9566-9571.
17. Gould SB, et al. 2006a. Protein targeting into the complex plastids of cryptophytes. J Mol Evol. 62:674-681.
18. Gould SB, et al. 2006b. Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms. Mol Biol Evol. 23:2413-2422
19. Grainger RJ, Beggs JD. 2005. Prp8 protein: at the heart of the spliceosome. RNA 11:533-557.
20. Gray MW, Schnare MN. 1990. Evolution of the modular structure of rRNA. In: Hill WE, et al. editors. The ribosome: structure, function and evolution. Washington: American Society for Microbiology. p. 589-597.
21. Hoef-Emden K. 2008. Molecular phylogeny of the phycocyanin-containing cryptophytes: evolution of biliproteins and geographical distribution. J Phycol. 44:985-993.
22. Ishida K, Endo H, Koike S. 2011. Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp. Phycol Res. 59:120-122.
23. Jentsch S, McGrath JP, Varshavsky A. 1987. The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme. Nature 329:131-134.
24. Katinka MD, et al. 2001. Genome sequence and gene compaction of the eukaryotic parasite Encephalitozoon cuniculi. Nature 414:450-453.
25. Lane CE, Archibald JM. 2006. Novel nucleomorph genome architecture in the cryptomonad genus Hemiselmis. J Eukaryot Microbiol. 53: 515-521.
26. Lane CE, et al. 2006. Insight into the diversity and evolution of the cryptomonad nucleomorph genome. Mol Biol Evol. 23:856-865.
27. Lane CE, et al. 2007. Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc Natl Acad Sci U S A. 104:19908-19913.
28. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
29. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
30. Moore CE, Archibald JM. 2009. Nucleomorph genomes. Annu Rev Genet. 43:251-264.
31. Patron NJ, Rogers MB, Keeling PJ. 2006. Comparative rates of evolution in endosymbiotic nuclear genomes. BMC Evol Biol. 6:46.
32. Phipps KD, Donaher NA, Lane CE, Archibald JM. 2008. Nucleomorph karyotype diversity in the freshwater cryptophyte genus Cryptomonas. J Phycol. 44:11-14.
33. 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.
34. Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ. 2007. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol Biol Evol. 24:54-62.
35. Rutherford K, et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
36. Silver TD, et al. 2007. Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae. J Eukaryot Microbiol. 54:403-410.
37. Slamovits CH, Fast NM, Law JS, Keeling PJ. 2004. Genome compaction and stability in microsporidian intracellular parasites. Curr Biol. 14: 891-896.
38. Tanifuji G, Onodera NT, Hara Y. 2010. Nucleomorph genome diversity and its phylogenetic implications in cryptomonad algae. Phycol Res. 58: 230-237.
39. Tanifuji G, et al. 2011. Complete nucleomorph genome sequences of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. Genome Biol Evol. 3:44-54.
40. Yoon HS, Hackett JD, Pinto G, Bhattacharya D. 2002. The single, ancient origin of chromist plastids. Proc Natl Acad Sci U S A. 99: 15507-15512.
41. Zauner S, et al. 2000. Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph. Proc Natl Acad Sci U S A. 97:200-205.