Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

Gene

Volumn 449, Issue 1-2, 2010, Pages 70-76

  Ogino, Kazutoyo ^a   Tsuneki, Kazuhiko ^a   Furuya, Hidetaka ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

Dicyemid; Exon intron structure; Intron evolution; Intron shortening

Indexed keywords

ARTICLE; CONTROLLED STUDY; ENDOPARASITE; EUKARYOTE; EXON; GENE SEQUENCE; GENOME ANALYSIS; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SPECIES DIFFERENTIATION; SPLICEOSOME;

ANIMALS; EXONS; GENOME; INTRONS; PARASITES; SPLICEOSOMES;

ANIMALIA; BIGELOWIELLA NATANS; CEPHALOPODA; CHLORARACHNIOPHYCEAE; DICYEMA; DICYEMIDA; EUKARYOTA; INVERTEBRATA; LOPHOTROCHOZOA; MESOZOA; MOLLUSCA; OIKOPLEURA DIOICA; TAKIFUGU RUBRIPES; VERTEBRATA;

EID: 70350416452     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.09.002     Document Type: Article

References (58)

1. Abrahamsen M.S., et al. Complete genome sequence of the apicomplexan Cryptosporidium parvum. Science 304 (2004) 441-445
2. Adam D.R. The Giardia lamblia genome. Int. J. Parasitol. 30 (2000) 475-484
3. Aparicio S., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297 (2002) 1301-1310
4. Aruga J., Odaka Y.S., Kamiya A., and Furuya H. Dicyema Pax6 and Zic tool-kit genes in a highly simplified bilaterian. BMC Evol. Biol. 7 (2007) 201
5. Aury J.M., et al. Global trends of whole genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444 (2006) 172-178
6. Carlton J.M., et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315 (2007) 207-212
7. Carmel L., Rogozin I.B., Wolf Y.I., and Koonin E.V. Patterns of intron gain and conservation in eukaryotic genes. BMC Evol. Biol. 7 (2007) 192
8. Castillo-Davis C.I., Mekhedov S.L., Hatl D.L., Koonin E.V., and Kondrashov F.A. Selection for short introns in highly expressed genes. Nat. Genet. 31 (2002) 415-418
9. Cocquet J., Chong A., Zhang G., and Veitia R.A. Reverse transcriptase template switching and false alternative transcripts. Genomics 88 (2006) 127-131
10. Comeron J.M. Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 167 (2004) 1293-1304
11. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 14 (2004) 1188-1190
12. Derelle, E. et al., 2006. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.
13. Deutsch M., and Long M. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27 (1999) 3219-3228
14. Douglas S., et al. The highly reduced genome of an enslaved algal nucleus. Nature 410 (2001) 1091-1096
15. Fahey M.E., and Higgins D.G. Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis. J. Mol. Evol. 65 (2007) 349-357
16. Fedorov A., Merican A.F., and Gilbert W. Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 16128-16133
17. Furuya H., and Tsuneki K. Developmental patterns of the hermaphroditic gonad in dicyemid mesozoans (Phylum Dicyemida). Invertebr. Biol. 126 (2007) 295-306
18. Furuya H., Tsuneki K., and Koshida Y. Two new species of the genus Dicyema (Mesozoa) from octopuses of Japan with notes on D. misakiense and D. acuticephalum. Zool. Sci. 9 (1992) 423-437
19. Furuya H., Tsuneki K., and Koshida Y. The cell lineages of two types of embryo and a hermaphroditic gonad in dicyemid mesozoans. Dev. Growth Differ. 38 (1996) 453-463
20. Furuya H., Hochberg F.G., and Tsuneki K. Developmental patterns and cell lineages of vermiform embryos in dicyemid mesozoans. Biol. Bull. 201 (2001) 405-416
21. Furuya H., Hochberg F.G., and Tsuneki K. Reproductive traits of dicyemids. Mar. Biol. 142 (2003) 693-706
22. Furuya H., Hochberg F.G., and Tsuneki K. Cell number and cellular composition in infusoriform larvae of dicyemid mesozoans (Phylum Dicyemida). Zool. Sci. 21 (2004) 877-889
23. Furuya H., Hochberg F.G., and Tsuneki K. Cell number and cellular composition in vermiform larvae of dicyemid mesozoans (Phylum Dicyemida). J. Zool. 272 (2007) 284-298
24. Ghedin E., et al. Draft genome of the filarial nematode parasite Brugia malayi. Science 317 (2007) 1756-1760
25. Gilson P.R., Su V., Slamovits C.H., Reith M.E., Keeling P.J., and McFadden G.I. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 9566-9571
26. Haas B.J., et al. Complete reannotation of the Arabidopsis genome: method, tools, protocols, and the final release. BMC Biol. 3 (2005) 7
27. Irimia M., and Roy S.W. Evolutionary convergence on highly-conserved 3′ intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet. 4 (2008) 1-14
28. Jeffares D.C., Mourier T., and Penny D. The biology of intron gain and loss. Trends Genet. 22 (2006) 16-22
29. Katayama T., Wada H., Furuya H., Satoh N., and Yamamoto M. Phylogenetic position of the dicyemid Mesozoa inferred from 18S rDNA sequences. Biol. Bull. 189 (1995) 81-90
30. Katinka M.D., et al. Genome sequence and gene compaction of the eukaryote parasite Eucephalitozoon cuniculi. Nature 414 (2001) 450-453
31. King N., et al. . The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451 (2008) 783-788
32. Kobayashi M., Furuya H., and Holland W.H. Dicyemids are higher animals. Nature 401 (1999) 762
33. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinformatics 5 (2004) 150-163
34. Kupfer D.M., et al. Introns and splicing elements of five diverse fungi. Eukaryotic Cell. 3 (2004) 1088-1100
35. Lanier W., Moustafa A., Bhattacharya D., and Comeron J.M. EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes. Plos One 3 (2008) e2171
36. Lapan E.A., and Morowitz H.J. The dicyemid Mesozoa as an integrated system for morphogenetic studies: 1. Description, isolation and maintenance. J. Exp. Zool. 193 (1975) 147-160
37. Long M., and Deutsch M. Association of intron phase with conservation at splice site sequences and evolution of spliceosomal introns. Mol. Biol. Evol. 16 (1999) 1528-1534
38. Noto T., and Endoh H. A "chimera" theory on the origin of dicyemid mesozoans: evolution driven by frequent lateral gene transfer from host to parasite. BioSystems 73 (2004) 73-83
39. Ogino K., Tsuneki K., and Furuya H. The expression of tubulin and tektin genes in dicyemid mesozoans (Phylum: Dicyemida). J. Parasitol. 93 (2007) 608-618
40. Ogino K., Tsuneki K., and Furuya H. Cloning of chitinase-like cDNA from dicyemid mesozoans (Phylum: Dicyemida). J. Parasitol. 93 (2007) 1403-1415
41. Pawlowski J., Montoya-Burgos J.I., Fahrni J.F., Wüest J., and Zaninetti L. Origin of the Mesozoa inferred from 18s rRNA gene sequences. Mol. Biol. Evol. 13 (1996) 1128-1132
42. Putnam N.H., et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317 (2007) 86-94
43. Raible F., et al. Vertebrate-type intron rich genes in the marine annelid Platynereis dumerilii. Science 310 (2005) 1325-1326
44. Ren W.Y., Vorst O., Fiers M.W.E.J., Stiekema W.J., and Nap J.P. In plants, highly expressed genes are the least compact. Trends Genet. 22 (2006) 528-532
45. Rogozin I.B., Wolf Y.I., Sorokin A.V., Mirkin B.G., and Koonin E.V. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13 (2003) 1512-1517
46. Roy S.W., and Gilbert W. Complex early genes. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 1986-1991
47. Roy S.W., and Gilbert W. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat. Rev. Genet. 7 (2006) 211-221
48. Roy S.W., and Irimia M. When good transcripts go bad: artifactual RT-PCR splicing and genome analysis. Bioessays 30 (2008) 601-605
49. Sakharkar M., Passetti F., de Souza J.E., Long M., and de Souza S.J. ExInt: an exon intron database. Nucleic Acids Res. 30 (2002) 191-194
50. Schneider T.D., and Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18 (1990) 6097-6100
51. Seo H.C., et al. Miniature genome in the marine chordata Oikopleura dioica. Science 294 (2001) 2506
52. Sharp P.A. Speculations on RNA splicing. Cell 23 (1981) 643-646
53. Sheth N., Roca X., Hastings M.L., Roeder T., Krainer A.R., and Sachidanandam R. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res. 34 (2006) 3955-3967
54. Srivastava M., et al. The Trichoplax genome and the nature of placozoans. Nature 454 (2008) 955-960
55. Sverdlov A.V., Rogozin I.B., Babenko V.N., and Koonin E.V. Conservation versus parallel gains in intron evolution. Nucleic Acids Res. 33 (2005) 1741-1748
56. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
57. Van Beneden É. Recherches sur les Dicyémides, survivants actuels d'un embranchement des Mésozoaires. Bulletins de l'Académie Royale de Belgique 42 (1876) 3-111
58. Vinogradov A.E. Intron length and codon usage. J. Mol. Evol. 52 (2001) 2-5