Natural selection maintains the transcribed LTR retrotransposons in Nosema bombycis

Journal of Genetics and Genomics

Volumn 37, Issue 5, 2010, Pages 305-314

  Xiang, Heng ^a   Pan, Guoqing ^a   Zhang, Ruizhi ^a   Xu, Jinshan ^b   Li, Tian ^a   Li, Wenle ^a   Zhou, Zeyang ^a,b   Xiang, Zhonghuai ^a  

^a SOUTHWEST UNIVERSITY   (China)

^b CHONGQING NORMAL UNIVERSITY   (China)

Author keywords

LTR retrotransposon; microsporidia; positive selection; purifying selection; transcribed

Indexed keywords

COMPLEMENTARY DNA; GAG PROTEIN; GENE PRODUCT; POL PROTEIN; PROTEIN GYPSY; PROTEINASE; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA LIBRARY; GENE DELETION; GENE INSERTION; GENETIC TRANSCRIPTION; LONG TERMINAL REPEAT; NATURAL SELECTION; NONHUMAN; NOSEMA; NOSEMA BOMBYCIS; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN MOTIF; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; STOP CODON; SYNTENY;

AMINO ACID SEQUENCE; FUNGAL PROTEINS; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; NOSEMA; PHYLOGENY; RETROELEMENTS; SELECTION, GENETIC; SEQUENCE ALIGNMENT; TERMINAL REPEAT SEQUENCES; TRANSCRIPTION, GENETIC;

EUKARYOTA; MICROSPORIDIA; NOSEMA BOMBYCIS;

EID: 77952682149     PISSN: 16738527     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1673-8527(09)60048-5     Document Type: Article

References (41)

1. Abrahamsen M.S., Templeton T.J., Enomoto S., Abrahante J.E., Zhu G., Lancto C.A., Deng M., Liu C., Widmer G., and Tzipori S. Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304 (2004) 441-445
2. Akiyoshi D.E., Morrison H.G., Lei S., Feng X., Zhang Q., Corradi N., Mayanja H., Tumwine J.K., Keeling P.J., and Weiss L.M. Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi. PLoS Pathog. 5 (2009) e1000261
3. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
4. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J., Dehal P., Christoffels A., Rash S., Hoon S., and Smit A. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297 (2002) 1301-1310
5. Arkhipova I.R., Pyatkov K.I., Meselson M., and Evgen'ev M.B. Retroelements containing introns in diverse invertebrate taxa. Nat. Genet. 33 (2003) 123-124
6. Boeke J.D., and Stoye J.P. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In: Coffin J.M., Hughes S.H., and Varmus H.E. (Eds). Retroviruses Vol. 8 (1997), Cold Spring Harbor Laboratory Press, Plainview, NY 343-435
7. Bringaud F., Ghedin E., Blandin G., Bartholomeu D.C., Caler E., Levin M.J., Baltz T., and El-Sayed N.M. Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements. Mol. Biol. Evol. 145 (2006) 158-170
8. Capy P., Langin T., Anxolabehere D., and Bazin C. Dynamics and Evolution of Transposable Elements (1996), Thomson Learning, Austin, TX
9. Carlton J.M., Angiuoli S.V., Suh B.B., Kooij T.W., Pertea M., Silva J.C., Ermolaeva M.D., Allen J.E., Selengut J.D., and Koo H.L. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419 (2002) 512-519
10. Cook J.M., Martin J., Lewin A., Sinden R.E., and Tristem M. Systematic screening of Anopheles mosquito genomes yields evidence for a major clade of Pao-like retrotransposons. Insect Mol. Biol. 9 (2000) 109-117
11. Crollius H.R., Jaillon O., Dasilva C., Ozouf-Costaz C., Fizames C., Fischer C., Bouneau L., Billault A., Quetier F., and Saurin W. Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res. 10 (2000) 939-949
12. DeMarco R., Kowaltowski A.T., Machado A.A., Soares M.B., Gargioni C., Kawano T., Rodrigues V., Madeira A., Wilson R.A., and Menck C.F.M. Saci-1,-2, and-3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. J. Virol. 78 (2004) 2967-2978
13. Eickbush T.H., and Malik H.S. Origins and evolution of retrotransposons. In: Craig N., Craigie R., Gellert M., and Lambowitz A. (Eds). Mobile DNA II, Chap. 49 (2002), American Society of Microbiology Press, Washington, D.C. 1111-1114
14. Eickbush T.H., and Furano A.V. Fruit flies and humans respond differently to retrotransposons. Curr. Opin. Genet. Dev. 12 (2002) 669-674
15. Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W., Carlton J.M., Pain A., Nelson K.E., and Bowman S. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419 (2002) 498-511
16. Grandbastien M.A. Retroelements in higher plants. Trends Genet. 8 (1992) 103-108
17. Katinka M.D., 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., and Vivares C.P. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414 (2001) 450-453
18. Kazazian H.H. Mobile elements: drivers of genome evolution. Science 303 (2004) 1626-1632
19. Laha T., Loukas A., Smyth D.J., Copeland C.S., and Brindley P.J. The fugitive LTR retrotransposon from the genome of the human blood fluke, Schistosoma mansoni. Int. J. Parasitol. 34 (2004) 1365-1375
20. Liu J.B., Pan G.Q., Cheng D.J., Xia Q.Y., Zhou Z.Y., and Xiang Z.H. Construction of Nosema bombycis (N.b) cDNA library and analysis of ESTs sequence from partial clones. Acta Sericologica Sinica 30 (2004) 363-366
21. Ma J., Devos K.M., and Bennetzen J.L. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14 (2004) 860-869
22. Mount S.M., and Rubin G.M. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol. Cell Biol. 5 (1985) 1630-1638
23. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York City, NY
24. Orgel L.E., and Crick F.H.C. Selfish DNA: the ultimate parasite. Nature 284 (1980) 604-607
25. Petrov D.A. Evolution of genome size: new approaches to an old problem. Trends Genet. 17 (2001) 23-28
26. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
27. Slamovits C.H., Fast N.M., Law J.S., and Keeling P.J. Genome compaction and stability in microsporidian intracellular parasites. Curr. Biol. 14 (2004) 891-896
28. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
29. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
30. Toh H., Kikuno R., Hayashida H., Miyata T., Kugimiya W., Inouye S., Yuki S., and Saigo K. Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus. EMBO J. 4 (1985) 1267-1272
31. Volff J.N., Hornung U., and Schartl M. Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements. Mol. Genet. Genomics 265 (2001) 711-720
32. Volff J.N., Bouneau L., Ozouf-Costaz C., and Fischer C. Diversity of retrotransposable elements in compact pufferfish genomes. Trends Genet. 19 (2003) 674-678
33. Volff J.N., Lehrach H., Reinhardt R., and Chourrout D. Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. Mol. Biol. Evol. 21 (2004) 2022-2033
34. Whitcomb J.M., and Hughes S.H. Retroviral reverse transcription and integration: progress and problems. Annu. Rev. Cell Biol. 8 (1992) 275-306
35. Williams B.A.P., Lee R.C.H., Becnel J.J., Weiss L.M., Fast N.M., and Keeling P.J. Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities. BMC Genomics 9 (2008) 200
36. Xiong Y., and Eickbush T.H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9 (1990) 3353-3362
37. Xu J., Pan G., Fang L., Li J., Tian X., Li T., Zhou Z., and Xiang Z. The varying microsporidian genome: existence of long-terminal repeat retrotransposon in domesticated silkworm parasite Nosema bombycis. Int. J. Parasitol. 36 (2006) 1049-1056
38. Xu P., Widmer G., Wang Y., Ozaki L.S., Alves J.M., Serrano M.G., Puiu D., Manque P., Akiyoshi D., and Mackey A.J. The genome of Cryptosporidium hominis. Nature 431 (2004) 1107-1112
39. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics (Oxford, England) 13 (1997) 555-556
40. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24 (2007) 1586-1591
41. Yang Z., Wong W.S.W., and Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22 (2005) 1107-1118