Evaluation of models of the mechanisms underlying intron loss and gain in aspergillus fungi

Journal of Molecular Evolution

Volumn 71, Issue 5-6, 2010, Pages 364-373

  Zhang, Lei Ying ^a   Yang, Yu Fei ^a   Niu, Deng Ke ^a  

^a BEIJING NORMAL UNIVERSITY   (China)

Author keywords

Aspergillus; Double strand break repair; mRNA mediated intron loss; Orthologous genes; Parallel intron gain; Self primed reverse transcription

Indexed keywords

MESSENGER RNA; MITOCHONDRIAL DNA; POLYADENYLIC ACID;

ARTICLE; ASPERGILLUS; BIOLOGICAL MODEL; DUPLICATE GENE; GENE CONVERSION; GENE EXPRESSION REGULATION; GENETICS; INTRON; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ASPERGILLUS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, MITOCHONDRIAL; GENE CONVERSION; GENES, DUPLICATE; INTRONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; POLY A; RNA, MESSENGER;

ASPERGILLUS; FUNGI;

EID: 78649999037     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9391-6     Document Type: Article

References (58)

1. N Ahmadinejad T Dagan N Gruenheit W Martin T Gabaldon 2010 Evolution of spliceosomal introns following endosymbiotic gene transfer BMC Evol Biol 10 57 10.1186/1471-2148-10-57 20178587
2. MK Basu IB Rogozin O Deusch T Dagan W Martin EV Koonin 2008 Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues Mol Biol Evol 25 111 119 1:CAS:528:DC%2BD1cXit12jsb4%3D 10.1093/molbev/msm234 17974547
3. L Carmel YI Wolf IB Rogozin EV Koonin 2007 Three distinct modes of intron dynamics in the evolution of eukaryotes Genome Res 17 1034 1044 1:CAS:528:DC%2BD2sXnvVWkur0%3D 10.1101/gr.6438607 17495008 (Pubitemid 47026350)
4. F Catania M Lynch 2008 Where do introns come from? PLoS Biol 6 e283 10.1371/journal.pbio.0060283 19067485
5. F Catania X Gao DG Scofield 2009 Endogenous mechanisms for the origins of spliceosomal introns J Hered 100 591 596 1:CAS:528:DC%2BD1MXhtVGrsbnI 10.1093/jhered/esp062 19635762
6. J Coulombe-Huntington J Majewski 2007 Characterization of intron loss events in mammals Genome Res 17 23 32 1:CAS:528:DC%2BD2sXms1KhsQ%3D%3D 10.1101/gr.5703406 17108319 (Pubitemid 46041662)
7. J Coulombe-Huntington J Majewski 2007 Intron loss and gain in Drosophila Mol Biol Evol 24 2842 2850 1:CAS:528:DC%2BD1cXnsVGhtA%3D%3D 10.1093/molbev/ msm235 17965454
8. SJ de Souza 2003 The emergence of a synthetic theory of intron evolution Genetica 118 117 121 10.1023/A:1024193323397 12868602 (Pubitemid 36821043)
9. LK Derr JN Strathern DJ Garfinkel 1991 RNA-mediated recombination in S. cerevisiae Cell 67 355 364 1:CAS:528:DyaK3MXmsV2ntrY%3D 10.1016/0092-8674(91) 90187-4 1655280
10. TH Eickbush AV Furano 2002 Fruit flies and humans respond differently to retrotransposons Curr Opin Genet Dev 12 669 1:CAS:528:DC%2BD38XosFOhsrc%3D 10.1016/S0959-437X(02)00359-3 12433580 (Pubitemid 35335985)
11. A Farlow E Meduri M Dolezal L Hua C Schlotterer 2010 Nonsense-mediated decay enables intron gain in Drosophila PLoS Genet 6 e1000819 10.1371/journal.pgen.1000819 20107520
12. AL Feiber J Rangarajan JC Vaughn 2002 The evolution of single-copy Drosophila nuclear 4f-rnp genes: Spliceosomal intron losses create polymorphic alleles J Mol Evol 55 401 413 1:CAS:528:DC%2BD38XnsVers7s%3D 10.1007/s00239-002-2336-y 12355261
13. GR Fink 1987 Pseudogenes in yeast? Cell 49 5 6 1:CAS:528: DyaL1cXovVGktw%3D%3D 10.1016/0092-8674(87)90746-X 3549000
14. X Gao M Lynch 2009 Ubiquitous internal gene duplication and intron creation in eukaryotes Proc Natl Acad Sci USA 49 20818 20823 10.1073/pnas.0911093106
15. T Hankeln H Friedl I Ebersberger J Martin ER Schmidt 1997 A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain Gene 205 151 160 1:CAS:528:DyaK1cXmt12itA%3D%3D 10.1016/S0378-1119(97) 00518-0 9461389 (Pubitemid 28029609)
16. RA Hoskins JW Carlson C Kennedy D Acevedo M Evans-Holm E Frise KH Wan S Park M Mendez-Lago F Rossi A Villasante P Dimitri GH Karpen SE Celniker 2007 Sequence finishing and mapping of Drosophila melanogaster heterochromatin Science 316 1625 1628 1:CAS:528:DC%2BD2sXmtl2jsLg%3D 10.1126/science.1139816 17569867 (Pubitemid 46982037)
17. JL Huppert 2008 Thermodynamic prediction of RNA-DNA duplex-forming regions in the human genome Mol Biosyst 4 686 691 1:CAS:528:DC%2BD1cXmtVamtbg%3D 10.1039/b800354h 18493667 (Pubitemid 351706312)
18. M Irimia JL Rukov D Penny J Vinther J Garcia-Fernandez SW Roy 2008 Origin of introns by 'intronization' of exonic sequences Trends Genet 24 378 381 1:CAS:528:DC%2BD1cXoslChs7c%3D 10.1016/j.tig.2008.05.007 18597887
19. DC Jeffares T Mourier D Penny 2006 The biology of intron gain and loss Trends Genet 22 16 22 1:CAS:528:DC%2BD28Xkt1Wn 10.1016/j.tig.2005.10.006 16290250 (Pubitemid 43011993)
20. DC Jeffares CJ Penkett J Bahler 2008 Rapidly regulated genes are intron poor Trends Genet 24 375 378 1:CAS:528:DC%2BD1cXoslChs7k%3D 10.1016/j.tig.2008. 05.006 18586348
21. DG Knowles A McLysaght 2006 High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes Mol Biol Evol 23 1548 1557 1:CAS:528:DC%2BD28XnslCitbY%3D 10.1093/molbev/msl017 16720694 (Pubitemid 44297413)
22. CE Lane K van den Heuvel C Kozera BA Curtis BJ Parsons S Bowman JM Archibald 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 1:CAS:528:DC%2BD1cXhs1Wntw%3D%3D 10.1073/pnas.0707419104 18077423
23. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins 2007 Clustal W and clustal X version 2.0 Bioinformatics 23 2947 2948 1:CAS:528: DC%2BD2sXhtlaqsL%2FM 10.1093/bioinformatics/btm404 17846036 (Pubitemid 350162903)
24. Lawson MJ, Jiao J, Fan WG, Zhang LQ (2009) A pattern analysis of gene conversion literature. Comp Funct Genom 2009:761512
25. W Li AE Tucker W Sung WK Thomas M Lynch 2009 Extensive, recent intron gains in Daphnia populations Science 326 1260 1262 1:CAS:528:DC%2BD1MXhsVKhtbbL 10.1126/science.1179302 19965475
26. H Lin W Zhu J Silva X Gu CR Buell 2006 Intron gain and loss in segmentally duplicated genes in rice Genome Biol 7 R41 10.1186/gb-2006-7-5-r41 16719932 (Pubitemid 43885063)
27. A Llopart JM Comeron FG Brunet D Lachaise M Long 2002 Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection Proc Natl Acad Sci USA 99 8121 8126 1:CAS:528:DC%2BD38XkvVGjurc%3D 10.1073/pnas.122570299 12060758 (Pubitemid 34651016)
28. Y-H Loh S Brenner B Venkatesh 2008 Investigation of loss and gain of introns in the compact genomes of Pufferfishes (Fugu and Tetraodon) Mol Biol Evol 25 526 535 1:CAS:528:DC%2BD1cXjt1CltLY%3D 10.1093/molbev/msm278 18089580 (Pubitemid 351301907)
29. M Long C Rosenberg W Gilbert 1995 Intron phase correlations and the evolution of the intron/exon structure of genes Proc Natl Acad Sci USA 92 12495 12499 1:CAS:528:DyaK28Xhtl2rtw%3D%3D 10.1073/pnas.92.26.12495 8618928 (Pubitemid 26014096)
30. J Mak L Kleiman 1997 Primer tRNAs for reverse transcription J Virol 71 8087 8095 1:CAS:528:DyaK2sXmvV2itbo%3D 9343157
31. HG Morrison AG McArthur FD Gillin SB Aley RD Adam GJ Olsen AA Best WZ Cande F Chen MJ Cipriano BJ Davids SC Dawson HG Elmendorf AB Hehl ME Holder SM Huse UU Kim E Lasek-Nesselquist G Manning A Nigam JEJ Nixon D Palm NE Passamaneck A Prabhu CI Reich DS Reiner J Samuelson SG Svard ML Sogin 2007 Genomic minimalism in the early diverging intestinal parasite Giardia lamblia Science 317 1921 1926 1:CAS:528:DC%2BD2sXhtVOlt73L 10.1126/science.1143837 17901334 (Pubitemid 47509437)
32. T Mourier DC Jeffares 2003 Eukaryotic intron loss Science 300 1393 1:CAS:528:DC%2BD3sXks1ygtLo%3D 10.1126/science.1080559 12775832 (Pubitemid 36638151)
33. CB Nielsen B Friedman B Birren CB Burge JE Galagan 2004 Patterns of intron gain and loss in fungi PLoS Biol 2 e422 10.1371/journal.pbio.0020422 15562318 (Pubitemid 40280526)
34. D-K Niu 2007 Protecting exons from deleterious R-loops: a potential advantage of having introns Biol Direct 2 11 10.1186/1745-6150-2-11 17459149 (Pubitemid 46711867)
35. D-K Niu W-R Hou S-W Li 2005 mRNA-mediated intron losses: evidence from extraordinarily large exons Mol Biol Evol 22 1475 1481 1:CAS:528: DC%2BD2MXksFGktbk%3D 10.1093/molbev/msi138 15788745 (Pubitemid 40734198)
36. K Paigen P Petkov 2010 Mammalian recombination hot spots: properties, control and evolution Nat Rev Genet 11 221 233 1:CAS:528:DC%2BC3cXitFCrsLc%3D 10.1038/nrg2712 20168297
37. M Plohl A Luchetti N Mestrovic B Mantovani 2008 Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin Gene 409 72 82 1:CAS:528: DC%2BD1cXnsl2ltA%3D%3D 10.1016/j.gene.2007.11.013 18182173
38. NH Putnam M Srivastava U Hellsten B Dirks J Chapman A Salamov A Terry H Shapiro E Lindquist VV Kapitonov J Jurka G Genikhovich IV Grigoriev SM Lucas RE Steele JR Finnerty U Technau MQ Martindale DS Rokhsar 2007 Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization Science 317 86 94 1:CAS:528:DC%2BD2sXnt1Sjtbo%3D 10.1126/science.1139158 17615350 (Pubitemid 47056460)
39. F Rodriguez-Trelles R Tarro FJ Ayala 2006 Origins and evolution of spliceosomal introns Annu Rev Genet 40 47 76 1:CAS:528:DC%2BD2sXnslKi 10.1146/annurev.genet.40.110405.090625 17094737 (Pubitemid 44956779)
40. SW Roy 2004 The origin of recent introns: transposons? Genome Biol 5 251 10.1186/gb-2004-5-12-251 15575977 (Pubitemid 40073693)
41. SW Roy 2009 Intronization, de-intronization and intron sliding are rare in Cryptococcus BMC Evol Biol 9 192 10.1186/1471-2148-9-192 19664208
42. SW Roy W Gilbert 2005 The pattern of intron loss Proc Natl Acad Sci USA 102 713 718 1:CAS:528:DC%2BD2MXis1Cqs7Y%3D 10.1073/pnas.0408274102 15642949 (Pubitemid 40282731)
43. SW Roy W Gilbert 2005 Rates of intron loss and gain: implications for early eukaryotic evolution Proc Natl Acad Sci USA 102 5773 5778 1:CAS:528:DC%2BD2MXjslaktLg%3D 10.1073/pnas.0500383102 15827119 (Pubitemid 40559635)
44. SW Roy W Gilbert 2006 The evolution of spliceosomal introns: patterns, puzzles and progress Nat Rev Genet 7 211 221 16485020
45. SW Roy DL Hartl 2006 Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number Genome Res 16 750 756 1:CAS:528:DC%2BD28XlvVeiurc%3D 10.1101/gr.4845406 16702411 (Pubitemid 43830695)
46. SW Roy M Irimia 2009 Mystery of intron gain: new data and new models Trends Genet 25 67 73 1:CAS:528:DC%2BD1MXhs1ais74%3D 10.1016/j.tig.2008.11.004 19070397
47. SW Roy D Penny 2006 Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution Genome Res 16 1270 1275 1:CAS:528:DC%2BD28XhtVOmtrbP 10.1101/gr.5410606 16963708 (Pubitemid 44506960)
48. SW Roy D Penny 2006 Smoke without fire: most reported cases of intron gain in Nematodes instead reflect intron losses Mol Biol Evol 23 2259 2262 1:CAS:528:DC%2BD28Xht1ejtbzP 10.1093/molbev/msl098 16943250 (Pubitemid 44737116)
49. SW Roy D Penny 2007 Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana Mol Biol Evol 24 171 181 1:CAS:528:DC%2BD2sXnvFWmsw%3D%3D 10.1093/molbev/msl159 17065597 (Pubitemid 46026292)
50. SW Roy M Irimia D Penny 2006 Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes Mol Biol Evol 23 1824 1827 1:CAS:528:DC%2BD28XhtVWgs73O 10.1093/molbev/msl061 16847043 (Pubitemid 44412868)
51. Scherer S (2008) A short guide to the human genome. Cold Spring Harbor Laboratory Press, New York
52. TJ Sharpton DE Neafsey JE Galagan JW Taylor 2008 Mechanisms of intron gain and loss in Cryptococcus Genome Biol 9 R24 10.1186/gb-2008-9-1-r24 18234113 (Pubitemid 351903429)
53. JE Stajich FS Dietrich 2006 Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans Eukaryot Cell 5 789 793 1:CAS:528:DC%2BD28XlsVGgt70%3D 10.1128/EC.5.5.789-793.2006 16682456 (Pubitemid 43794478)
54. JE Stajich FS Dietrich SW Roy 2007 Comparative genomic analysis of fungal genomes reveals intron-rich ancestors Genome Biol 8 R223 10.1186/gb-2007-8-10- r223 17949488 (Pubitemid 351917454)
55. L Szekvolgyi A Nicolas 2010 From meiosis to postmeiotic events: homologous recombination is obligatory but flexible FEBS J 277 571 589 1:CAS:528:DC%2BC3cXhsFarsrY%3D 10.1111/j.1742-4658.2009.07502.x 20015080
56. JN Volff L Bouneau C Ozouf-Costaz C Fischer 2003 Diversity of retrotransposable elements in compact pufferfish genomes Trends Genet 19 674 678 1:CAS:528:DC%2BD3sXpt1emsb4%3D 10.1016/j.tig.2003.10.006 14642744 (Pubitemid 37464841)
57. MD Wilkerson Y Ru VP Brendel 2009 Common introns within orthologous genes: software and application to plants Brief Bioinform 10 631 644 1:CAS:528:DC%2BD1MXhsVKntbjF 10.1093/bib/bbp051 19933210
58. Williams RL (1975) The shoot apex and leaf growth. Cambridge University Press, London