е ефе едееедебед ец ец ецеееде ебедец ецедефеце«ец ецедеце

Size: px
Start display at page:

Download "е ефе едееедебед ец ец ецеееде ебедец ецедефеце«ец ецедеце"

Transcription

1 едеге е е ецедедеце, 2009, 43, 5, ег LTR-appleappleapple - apple applefl apple, apple- appleapple е appleapple apple - LINE (long interspersed elements) е 3 7 apple apple LINE apple apple apple- fl, apple apple appleapple- е -fl ( appleappleapple Gag) е fl appleapple-, fl apple apple appleapple е, applefl - apple fl apple fl apple- LINE, apple fl 15 [24] LINE apple apple apple- ; fl - apple appleapple [5] ед appleapple L1 [6] ед apple -, fl- fl fl fl, fl- L1 appleapple apple 5'- еф - fl applefl, apple apple appleapple fl appleеде едефец е ефе едееедебед ец ец ецеееде ебедец ецедефеце«ец ецедеце 2009 appleapple*, ец flapple е apple е,, ее apple ееapplefl apple apple fl appleappleapple appleflfl - apple apple appleapple (short interspersed elements, SINE) е apple apple appleapple apple, appleapple appleapple apple - ед, apple appleapple fl - applefl : apple SINE, fl, fl SHORT INTERSPERSED REPETITIVE SEQUENCES (SINEs) AND THEIR USE AS A PHYLOGENET- IC TOOL, by D A Kramerov*, N S Vassetzky (Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; * The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed Their structure, origin, and functioning in the genome are discussed The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples Key words: short interspersed elements, SINEs, evolution, phylogeny * еде едефец е ефе едееедебед е fl appleflfl - - fl apple apple- ееfl appleflfl apple, apple flfl : -apple appleappleapple -apple apple apple apple- ееfl -apple apple applefl (cut and paste), apple apple apple, apple apple е appleapple apple applefl, apple apple apple flfl, - applefl apple apple appleapple ( applefl, copy and paste), -apple, flfl appleapple- apple, apple ( ) apple (long terminal repeat, LTR) [1] еф- appleappleapple 8 apple apple apple fl, apple apple apple appleapple (appleapple) * е : 795

2 796 7SL PHK (A) n B1 LINE еф SINE е е 1 appleapple apple appleapple: B1 () е SINE () apple apple; apple flfl fl applefl applefl - applefl fl L1 ее -,, applefl apple apple, fl ефfl fl fl appleapple, appleappleapple apple apple applefl - apple (SINE, short interspersed elements) apple appleapple е«apple SINE flfl - fl fl fl apple - fl 1030%, - applefl fl SINE SINE, fl apple, apple - apple [7] SINE - applefl, apple, apple, apple ( appleapple apple) SINE apple fl applefl - fl apple apple LINE (apple 1) [8, 9] еф apple, SINE applefl ееapple apple appleapple- 1 B2, apple [10 13], Alu apple [14] applefl - SINE, fl -, apple apple- B1 Alu 7SL е, е ее-, - applefl- appleapple apple [15] ееapple 1 apple fl SL е, -, - (apple 1) 1 fl -, А А Alu apple 1 - apple - apple еф apple, Alu flflfl apple SINE е«apple apple- 7SL е, е B2 apple е,, е ееapple 2 е, apple - applefl, 3'- apple- fl - fl SINE applefl (apple 1), fl е -appleapple-, е -apple apple applefl е apple appleapple appleappleapple [7], apple apple apple- apple, applefl 5S appleе apple apple fl apple Danio rerio [16] apple apple appleapple applefl -, applefl 5S appleе, SINE apple [17] - [18] apple apple apple - apple appleapple

3 еде едефец е ефе едееедебед ец ец ецеееде ебедец 797 apple е, apple apple apple applefl е -apple III, е -apple II, - applefl appleappleapple, apple, LINE apple appleapple appleappleapplefl е -apple III, apple- applefl е [19, 20] еф, SINE appleappleapplefl apple, apple- apple е -apple II, appleapple е -apple- III, applefl appleapple е, 5S appleе, 7SL е, apple applefl apple appleappleapple [7, 21] еф apple, apple appleapple е SINE fl fl fl - - appleapple SINE apple- apple, apple -, applefl appleapple appleappleapplefl, appleapple apple appleapple appleapple е -- apple III SINE, apple е 7SL е, appleapple 11,, apple apple SINE, 5S appleе, appleapple apple, IE appleapple flfl apple apple apple appleapple fl apple- apple е -apple III ец, apple- applefl, flfl е -apple, appleapplefl apple еф [19, 21] ецapple, SINE appleapple е, appleapplefl applefl apple fl еф-- apple 3'- apple fl SINE applefl -- ее appleapple - apple appleapple- apple [22] ег, apple 2- apple-, appleapple appleapple-, еф еф SINE flfl еф +, SINE apple- apple еф еф ефappleapplefl B2 SINE fl еф-, 3'- - applefl е applefl () [23] fl applefl еф е appleapple applefl - apple е -apple III ее(), apple- fl appleapple SINE, - apple applefl е apple apple apple - fl А А SINE apple apple ( apple SINE ) apple : apple fl apple 35 (apple 2) SINE -, apple apple 30100, 3'-- apple LINE (apple 2) [24], appleapple Bov-B, CR-1, L2, RSg-1 apple apple ег-, е SINE fl appleapple LINE, apple apple appleapple е apple SINE - apple -, apple LINE- L1 fl, - () - е SINE, appleapple [25, 26] ее apple applefl apple SINE apple - [27, 28] е SINE appleapple LINE appleappleapplefl flapple, - fl, appleapple-, - SINE е apple, - fl е applefl, 3'- apple appleapple apple appleapple ее apple apple- appleapplefl apple apple apple apple apple -apple apple - applefl fl fl SINE, applefl applefl apple 816 (target site duplication, TSD) applefl fl TSD applefl apple apple appleapplefl - fl apple ее apple appleapple apple TSD, appleapple SINE applefl apple SINE, apple ееfl apple, appleflfl - appleapple apple apple, apple appleapple flfl apple Ther-1 SINE apple, Ther-1, applefl Alu apple applefl [29], fl А apple А fl - apple appleapple:, apple Alu applefl; apple apple apple, SINE, flfl apple, - applefl [30] ецеееде ебедец еде едефец е ефе едееедебедед ецедефеце«ец ецедеце 90- apple apple apple- appleapple apple apple - apple

4 798 OPC1 LINE OPC2 SINE fl fl SINE ефappleapplefl е -apple II ефappleapplefl е -apple III PK LINE ефappleflfl едapplefl appleapplefl applefl едapplefl appleapple LINE е 2 apple apple appleapple еде applefl apple fl (); apple flfl apple apple apple apple, - fl apple apple apple А NatureА, applefl apple [31] apple - flapple, apple- apple,, apple applefl apple- apple apple apple ед,, - flapple, - fl applefl, apple apple apple, flapple - appleapple apple fl apple apple [3234] ец fl apple -, applefl,, е apple apple ед fl -, fl apple е apple apple, - apple 90- apple SINE apple [3537] fl, -, apple SINE, е -apple - apple apple (еее ), - SINE, apple- applefl apple apple apple,, apple - apple 3 1, 2 3 apple - SINE, 4 apple applefl, SINE 1 2, 3 4 е fl apple apple, - apple apple 3 ец apple, apple apple apple - apple appleapple appleapple- apple, fl - apple apple, apple [38] applefl еее apple - apple appleapple е -apple III apple fl SINE, apple apple, applefl еее -apple, apple apple apple apple apple apple - fl apple SINE, fl - SINE, apple - fl appleapple apple-

5 еде едефец е ефе едееедебед ец ец ецеееде ебедец apple apple- applefl fl [40] ее apple apple apple apple- apple apple apple flapple [41] apple -, applefl Afrotheria [33] apple, apple, fl apple, apple apple apple, apple apple - fl apple fl - apple - apple appleapple AfroSINE [42] е apple apple fl Afrotheria, apple -apple, fl applefl Supraprimates ( Euarchontoglires) [33] - - applefl еб еб ееapplefl fl applefl ееappleapple ' ееappleapple ' SINE е 3 ец apple appleapple fl еб appleapple /' /' fl apple appleapple apple apple flfl apple appleapple еее applefl ее apple - apple, apple- - е 4 appleapple apple fl applefl apple А А apple, fl apple Romer [39], - appleapple apple appleapple apple е apple, B1-dID, - applefl apple- B1-dID apple apple - : (Sciuridae), (Aplodontidae) (Gliridae) apple Romer apple apple apple () apple ( apple 4 ) ец appleapplefl B1-dID

6 800 B1 ID B4 45SH 45S1 B2 B1-dID IDL-Geo DIP Cricetidae Muridae Spalacidae Rhizomyidae Dipodidae Zapodidae Geomyidae Heteromyidae Gliridae Aplodontidae Sciuridae Castoridae Hystricidae Anomaluridae Hydrochoeridae Caviidae Dasyproctidae DIP B2, 45S1 B4, 45SH IDL-Geo B1-dID е 4 е apple apple ее apple apple appleapple apple - apple [37, 40, 46, 7274] apple apple flfl apple appleapple еб fl Gliridae Romer [39]

7 еде едефец е ефе едееедебед ец ец ецеееде ебедец 801 apple apple fl appleapple [43, 44] ед, apple apple applefl, apple, apple, apple apple apple 7SL е, apple apple [45],, - apple apple, applefl applefl apple, - 7SL е apple apple SINE 1 apple Alu apple appleapple SINE, - еф, apple apple 1 apple apple - 1 apple apple fl apple apple, fl fl appleapplefl apple- apple apple apple - apple apple [46] appleappleapple appleapple -, - apple appleapple applefl SINE apple - apple [47] е - еее - apple fl, - apple SINE (apple 5) apple apple apple, apple SINE fl applefl apple - apple apple, SINE, apple SINE, apple apple,, apple -, apple apple - apple- flapple- е apple apple fl fl - fl apple [48] - [49] apple (/) SINE Alu apple fl fl apple, applefl apple apple ( apple [30] ) fl apple, appleapple,, applefl - apple (Cetacea) applefl apple apple applefl apple (Artiodactyla) еф apple, fl, fl [50, 51] ее apple apple apple apple apple - flapple [32] ецapple-sine-еее, apple fl apple appleapple- е, apple-sineеее, fl еее, apple - apple apple SINE ееappleapple apple apple, apple, apple fl SINE (apple 6) apple apple- fl apple еее applefl apple, apple - fl apple applefl е apple fl apple [52] apple apple- fl appleapple [53], fl- [5456], flapple [57] apple [58] apple, apple appleapple fl apple appleapple fl apple, fl, applefl А appleа еф apple, apple apple, apple apple apple ( ), apple appleapple - appleapple apple ед ( apple apple) apple appleapple apple, apple- apple е apple apple, ее, apple appleapple- -, apple fl (rare genomic changes), apple apple fl, apple LINE apple apple, applefl -, [59] -, apple appleapple apple -, apple apple, SINE apple ( apple fl - ) apple - apple apple - fl apple applefl, apple apple appleapple fl 1 -, SINE applefl, applefl 4

8 еее SINE е 5 ец apple appleapple fl apple apple apple fl apple apple apple apple appleapple apple, fl SINE appleflfl apple applefl, apple apple appleapple apple apple applefl applefl - apple SINE - apple 3 apple appleapple apple- fl apple, apple, apple SINE apple ( apple - apple) еф, fl apple apple appleapple- appleapple appleflfl apple, applefl- apple SINE, applefl apple appleapple- appleapple apple [60] [61], - fl fl fl apple appleapple еф apple - fl apple apple appleapple ефfl fl apple -, apple, apple- applefl ( fl- apple,

9 еде едефец е ефе едееедебед ец ец ецеееде ебедец fl д fl д fl д fl д еее д д е 6 ец apple appleapple fl ецapple-sine-еее apple apple- apple SINE apple apple apple д д apple appleapple apple),, -, apple TSD ее apple- 051% apple-, fl apple Alu, fl, apple- SINE [62] ед apple - fl, apple, appleflfl apple apple apple appleapple applefl - е,, 3'- - LINE, appleapple SINE ед apple- apple - ед fl - - applefl apple apple е -apple apple apple - SINE, apple apple apple fl, applefl е, - [63] еф, apple appleapple- ID apple, Vic-1 apple Das-1 apple-, applefl е, apple apple еф apple, apple apple appleapple - ( apple fl) apple apple apple appleappleapple- appleflapple fl appleapple apple apple fl -apple LTR-appleappleapple [64] apple apple appleapple, fl,, apple - LINE ( LINE Bov-B [18, 65]), appleapple apple- apple apple appleapple ( - А apple apple SINEА appleapple [65]), - apple apple - LINE, apple apple applefl apple appleapple apple apple SINE - apple appleapple apple- appleapple [66] apple appleapple SmaI appleappleapple apple, apple, apple, apple, applefl apple - е - apple [66] apple- apple, fl, apple fl: apple appleapple- apple - apple apple, apple apple, А А apple flflfl apple, - fl apple - apple, apple apple- apple fl,, 4*

10 804 fl А«А» ецapplefl SINE fl А«+А» fl А«+А» е 7 apple apple apple apple, apple apple apple appleapple - apple apple ее apple SINE apple fl appleapple [67], apple- apple apple appleapple applefl apple apple, - Schistosoma japonicum [68, 69] ед apple apple appleapple apple apple, ( appleapple) А apple appleа [70] - apple apple apple- apple appleflfl apple applefl, SINE -, apple apple - appleapple- apple LINE еф apple, apple SINE apple apple apple appleapple ( apple apple), apple SINE fl apple, apple - apple appleapple ед fl, apple apple- SINE - fl apple е fl, appleapple : apple apple apple - apple apple ( fl SINE apple ) appleflfl apple applefl applefl apple apple- (apple 7) fl, - apple apple apple [71] ее apple- apple-, applefl apple- fl apple applefl apple apple- apple fl -, apple, appleappleapple - SINE, apple fl appleapple apple -, fl - fl fl applefl apple applefl applefl, - applefl apple еб apple apple applefl fl apple, apple flfl, apple- apple apple - fl applefl apple applefl apple apple fl - fl SINE - fl apple applefl appleapple applefl apple apple apple appleapple fl fl apple -, apple, fl fl,, apple fl apple, apple

11 еде едефец е ефе едееедебед ец ец ецеееде ебедец 805 ееецед ецефе ефеге 1 Havecker ER, Gao X, Voytas DF 2004 The diversity of LTR retrotransposons Genome Biol 5, Malik HS, Eickbush TH 2000 NeSL-1, an ancient lineage of site-specific non-ltr retrotransposons from Caenorhabditis elegans Genetics 154, Lovsin N, Gubensek F, Kordis D 2001 Evolutionary dynamics in a novel L2 clade of non-ltr retrotransposons in Deuterostomia Mol Biol Evol 18, Burke WD, Malik HS, Rich SM, et al 2002 Ancient lineages of non-ltr retrotransposons in the primitive eukaryote, Giardia lamblia Mol Biol Evol 19, Eickbush TH, Jamburuthugoda VK 2008 The diversity of retrotransposons and the properties of their reverse transcriptases Virus Res 134, Ostertag EM, Kazazian HH, Jr 2001 Biology of mammalian L1 retrotransposons Annu Rev Genet 35, Kramerov DA, Vassetzky NS 2005 Short retroposons in eukaryotic genomes Int Rev Cytol 247, Kajikawa M, Okada N 2002 LINEs mobilize SINEs in the eel through a shared 3' sequence Cell 111, Dewannieux M, Esnault C, Heidmann T 2003 LINEmediated retrotransposition of marked Alu sequences Nat Genet 35, Kramerov DA, Grigoryan AA, Ryskov AP, et al 1979 Long double-stranded sequences (dsrna-b) of nuclear pre-mrna consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments Nucleic Acids Res 6, Haynes SR, Toomey TP, Leinwand L, et al 1981 The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element Mol Cell Biol 1, Krayev AS, Kramerov DA, Skryabin KG, et al 1980 The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA Nucleic Acids Res 8, Krayev AS, Markusheva TV, Kramerov DA, et al 1982 Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing Nucleic Acids Res 10, Deininger PL, Jolly DJ, Rubin CM, et al 1981 Base sequence studies of 300 nucleotide renatured repeated human DNA clones J Mol Biol 151, Ullu E, Tschudi C 1984 Alu sequences are processed 7SL RNA genes Nature 312, Kapitonov VV, Jurka J 2003 A Novel Class of SINE elements derived from 5S rrna Mol Biol Evol 20, Nishihara H, Smit AF, Okada N 2006 Functional noncoding sequences derived from SINEs in the mammalian genome Genome Res 16, Gogolevsky KP, Vassetzky NS, Kramerov DA 2008 Bov-B-mobilized SINEs in vertebrate genomes Gene 407, Haynes SR, Jelinek WR 1981 Low molecular weight RNAs transcribed in vitro by RNA polymerase III from Alu-type dispersed repeats in Chinese hamster DNA are also found in vivo Proc Natl Acad Sci USA 78, Kramerov DA, Lekakh IV, Samarina OP, et al 1982 The sequences homologous to major interspersed repeats B1 and B2 of mouse genome are present in mrna and small cytoplasmic poly(a) + RNA Nucleic Acids Res 10, Schramm L, Hernandez N 2002 Recruitment of RNA polymerase III to its target promoters Genes Dev 16, Borodulina OR, Kramerov DA 2001 Short interspersed elements (SINEs) from insectivores Two classes of mammalian SINEs distinguished by A-rich tail structure Mamm Genome 12, Borodulina OR, Kramerov DA 2008 Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner RNA 14, Ohshima K, Hamada M, Terai Y, et al 1996 The 3' ends of trna-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements Mol Cell Biol 16, Dewannieux M, Heidmann T 2005 L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells J Mol Biol 349, Dewannieux M, Heidmann T 2005 Role of poly(a) tail length in Alu retrotransposition Genomics 86, Luan DD, Korman MH, Jakubczak JL, et al 1993 Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non- LTR retrotransposition Cell 72, Jurka J 1997 Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons Proc Natl Acad Sci USA 94, International Human Genome Sequencing Consortium 2001 Initial sequencing and analysis of the human genome Nature 409, Batzer MA, Deininger PL 2002 Alu repeats and human genomic diversity Nat Rev Genet 3, DА»Erchia AM, Gissi C, Pesole G, et al 1996 The guinea-pig is not a rodent Nature 381, Murphy WJ, Eizirik E, OА»Brien SJ, et al 2001 Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294, Murphy WJ, Eizirik E, Johnson WE, et al 2001 Molecular phylogenetics and the origins of placental mammals Nature 409, Dunn CW, Hejnol A, Matus DQ, et al 2008 Broad phylogenomic sampling improves resolution of the animal tree of life Nature 452, apple ец, appleapple 1993 ец- appleapple 2 fl fl - apple apple 29, apple ец, appleapple 1994 ец- apple appleapple - appleapple е 335, Serdobova IM, Kramerov DA 1998 Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny J Mol Evol 46, Borodulina OR, Kramerov DA 1999 Wide distribution of short interspersed elements among eukaryotic genomes FEBS Lett 457, Romer AS 1966 Vertebrate paleontology Chicago: University Chicago Press

12 Kramerov D, Vassetzky N, Serdobova I 1999 The evolutionary position of dormice (Gliridae) in Rodentia determined by a novel short retroposon Mol Biol Evol 16, Adkins RM, Walton AH, Honeycutt RL 2003 Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes Mol Phylogenet Evol 26, Nikaido M, Nishihara H, Hukumoto Y, et al 2003 Ancient SINEs from African endemic mammals Mol Biol Evol 20, Nishihara H, Terai Y, Okada N 2002 Characterization of novel Alu- and trna-related SINEs from the tree shrew and evolutionary implications of their origins Mol Biol Evol 19, Vassetzky NS, Ten OA, Kramerov DA 2003 B1 and related SINEs in mammalian genomes Gene 319, Kriegs JO, Churakov G, Jurka J, et al 2007 Evolutionary history of 7SL RNA-derived SINEs in Supraprimates Trends Genet 23, Veniaminova NA, Vassetzky NS, Kramerov DA 2007 B1 SINEs in different rodent families Genomics 89, Nishihara H, Okada N 2008 Retroposons: genetic footprints on the evolutionary paths of life Methods Mol Biol 422, Perna NT, Batzer MA, Deininger PL, et al 1992 Alu insertion polymorphism: a new type of marker for human population studies Hum Biol 64, Murata S, Takasaki N, Saitoh M, et al 1993 Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution Proc Natl Acad Sci USA 90, Shimamura M, Yasue H, Ohshima K, et al 1997 Molecular evidence from retroposons that whales form a clade within even-toed ungulates Nature 388, Nikaido M, Rooney AP, Okada N 1999 Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales Proc Natl Acad Sci USA 96, Buntjer JB 1997 Mammalian species identification by interspersed repeat PCR fingerprinting Utrecht Netherlands: Utrecht Univ 53,, appleapple 2002 ед fl apple-sine-еее 38, Bannikova AA, Bulatova NS, Krysanov EY, et al 2003 DNA Polymorphism within Sorex araneus and two congeneric species as inferred from inter-sine- PCR Mammalia 67, Bannikova AA, Lebedev VS, Kramerov DA, et al 2006 Phylogeny and systematics of the Crocidura suaveolens species group: corroboration and controversy between nuclear and mitochondrial DNA markers Mammalia 70, Shafer AB, Stewart DT 2007 Phylogenetic relationships among Nearctic shrews of the genus Sorex (Insectivora, Soricidae) inferred from combined cytochrome b and inter-sine fingerprint data using Bayesian analysis Mol Phylogenet Evol 44, apple,, е fl, et al 2006 flapple- appleapple flapple Darevskia raddei (Lacertidae: Sauria): apple applefl flapple fl 41, е fl,, е apple, et al 2008 apple - inter-sine-еее 44, Rokas A, Holland PW 2000 Rare genomic changes as a tool for phylogenetics Trends Ecol Evol 15, Roy-Engel AM, Carroll ML, El-Sawy M, et al 2002 Non-traditional Alu evolution and primate genomic diversity J Mol Biol 316, Rothenburg S, Eiben M, Koch-Nolte F, et al 2002 Independent integration of rodent identifier (ID) elements into orthologous sites of some RT6 alleles of Rattus norvegicus and Rattus rattus J Mol Evol 55, van de Lagemaat LN, Gagnier L, Medstrand P, et al 2005 Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates Genome Res 15, Borodulina OR, Kramerov DA 2005 PCR-based approach to SINE isolation: simple and complex SINEs Gene 349, Hua-Van A, Le Rouzic A, Maisonhaute C, et al 2005 Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences Cytogenet Genome Res 110, Kordis D, Gubensek F 1995 Horizontal SINE transfer between vertebrate classes Nat Genet 10, Hamada M, Kido Y, Himberg M, et al 1997 A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs Genetics 146, Takasaki N, Yamaki T, Hamada M, et al 1997 The salmon SmaI family of short interspersed repetitive elements (SINEs): interspecific and intraspecific variation of the insertion of SINEs in the genomes of chum and pink salmon Genetics 146, Melamed P, Chong KL, Johansen MV 2004 Evidence for lateral gene transfer from salmonids to two Schistosome species Nat Genet 36, Matveev V, Nishihara H, Okada N 2007 Novel SINE families from salmons validate Parahucho (Salmonidae) as a distinct genus and give evidence that SINEs can incorporate LINE-related 3'-tails of other SINEs Mol Biol Evol 24, Piskurek O, Okada N 2007 Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals Proc Natl Acad Sci USA 104, Terai Y, Takahashi K, Nishida M, et al 2003 Using SINEs to probe ancient explosive speciation: А hiddenа radiation of African cichlids? Mol Biol Evol 20, Gogolevskaya IK, Kramerov DA 2002 Evolutionary history of 45SI RNA and indication that it is functional J Mol Evol 54, Gogolevskaya IK, Koval AP, Kramerov DA 2005 Evolutionary history of 45SH RNA Mol Biol Evol 22, Gogolevsky KP, Kramerov DA 2006 Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents Gene 373, 6774

ЗВАВЩ ЙЩЖЩГЙ АВ ЕЙКЩИРЕИВАОЗЗЛ КВА ВИВА Е РЩЗВЖО ҐЩХНГҐО Л ИЩК ЕЕГ

ЗВАВЩ ЙЩЖЩГЙ АВ ЕЙКЩИРЕИВАОЗЗЛ КВА ВИВА Е РЩЗВЖО ҐЩХНГҐО Л ИЩК ЕЕГ ЖВЩДНБИЗОБ ПЕВВРЕБ, 2006, 40, 2,. 378382 Н Д 577.21 Дapple ъfl ЗВАВЩ ЙЩЖЩГЙ АВ ЕЙКЩИРЕИВАОЗЗЛ КВА ВИВА Е РЩЗВЖО ҐЩХНГҐО Л ИЩК ЕЕГ 2006. Й. О. Д, В. И. Пapple, А. А. Рapple*,. О. Дappleapple Е flapple ъ

More information

THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD

THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD Manyuan Long*,Esther Betrán,Kevin Thornton and Wen Wang Genome data have revealed great variation in the numbers of genes in different organisms,

More information

Review. Which genetic marker for which conservation genetics issue? Nucleic acids. 1 Introduction. Contents. Electrophoresis 2004, 25, 2165 2176 2165

Review. Which genetic marker for which conservation genetics issue? Nucleic acids. 1 Introduction. Contents. Electrophoresis 2004, 25, 2165 2176 2165 Electrophoresis 2004, 25, 2165 2176 2165 Review Qiu-Hong Wan 1 Hua Wu 1 Tsutomu Fujihara 2 Sheng-Guo Fang 1 1 College of Life Sciences, State Conservation Center for Gene Resources of Endangered Wildlife,

More information

Can Viruses Make Us Human? 1

Can Viruses Make Us Human? 1 Can Viruses Make Us Human? 1 LUIS P. VILLARREAL Director, Center for Virus Research University of California at Irvine THIS QUESTION WILL SEEM preposterous to most. Viruses are molecular genetic parasites

More information

Base Compositional Bias and Phylogenetic Analyses: A Test of the Flying DNA Hypothesis

Base Compositional Bias and Phylogenetic Analyses: A Test of the Flying DNA Hypothesis MOLECULAR PHYLOGENETICS AND EVOLUTION Vol. 3, No. 3, December, pp. 408 46, 998 ARTICLE NO. FY98053 Base Compositional Bias and Phylogenetic Analyses: A Test of the Flying DNA Hypothesis Ronald A. Van Den

More information

Tracking the Evolution of the Elusive Andean Mountain Cat (Oreailurus jacobita) From Mitochondrial DNA

Tracking the Evolution of the Elusive Andean Mountain Cat (Oreailurus jacobita) From Mitochondrial DNA Tracking the Evolution of the Elusive Andean Mountain Cat (Oreailurus jacobita) From Mitochondrial DNA W. E. Johnson, M. Culver, J. A. Iriarte, E. Eizirik, K. L. Seymour, and S. J. O Brien Rarely observed

More information

Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1

Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1 Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1 Ziheng Yang Department of Animal Science, Beijing Agricultural University Felsenstein s maximum-likelihood

More information

Genetic Variation and Human Evolution Lynn B. Jorde, Ph.D. Department of Human Genetics University of Utah School of Medicine.

Genetic Variation and Human Evolution Lynn B. Jorde, Ph.D. Department of Human Genetics University of Utah School of Medicine. Genetic Variation and Human Evolution Lynn B. Jorde, Ph.D. Department of Human Genetics University of Utah School of Medicine. The past two decades have witnessed an explosion of human genetic data. Innumerable

More information

Review. Bioinformatics - a definition 1. As submitted to the Oxford English Dictionary

Review. Bioinformatics - a definition 1. As submitted to the Oxford English Dictionary N.M. Luscombe, D. Greenbaum, M. Gerstein Department of Molecular Biophysics and Biochemistry Yale University New Haven, USA Review What is bioinformatics? An introduction and overview Abstract: A flood

More information

BLOCK-iT Products: Powerful tools to advance RNAi analysis

BLOCK-iT Products: Powerful tools to advance RNAi analysis BLOCK-iT RNAi Products BLOCK-iT Products: Powerful tools to advance RNAi analysis With BLOCK-iT RNAi Technology you can: Get powerful blocking and easily generate functional RNAi data Effectively prepare

More information

Real-time PCR for mrna quantitation

Real-time PCR for mrna quantitation Real-time PCR for mrna quantitation Marisa L. Wong and Juan F. Medrano BioTechniques 39:75-85 (July 2005) Real-time PCR has become one of the most widely used methods of gene quantitation because it has

More information

TRENDS in Ecology & Evolution Vol.16 No.1 January 2001. RNA sequences: addressing the interdependence

TRENDS in Ecology & Evolution Vol.16 No.1 January 2001. RNA sequences: addressing the interdependence 37 12 Swofford, D.L. et al. (1996) Phylogenetic inference. n Molecular Systematics (illis, D.M. et al., eds), pp. 407 514, Sinauer ssociates 13 uelsenbeck, J.P. and randall, K.. (1997) Phylogeny estimation

More information

Replication Patterns of Specific Viruses

Replication Patterns of Specific Viruses WBV15 6/27/03 11:09 PM Page 229 Replication Patterns of Specific Viruses IV PART REPLICATION OF POSITIVE-SENSE RNA VIRUSES REPLICATION OF POSITIVE-SENSE RNA VIRUSES WHOSE GENOMES ARE TRANSLATED AS THE

More information

The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals

The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals Journal of Biogeography, 30, 71 86 The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals Leonora P. Costa Museum of Vertebrate

More information

VIRAL SAFETY EVALUATION OF BIOTECHNOLOGY PRODUCTS DERIVED FROM CELL LINES OF HUMAN OR ANIMAL ORIGIN Q5A(R1)

VIRAL SAFETY EVALUATION OF BIOTECHNOLOGY PRODUCTS DERIVED FROM CELL LINES OF HUMAN OR ANIMAL ORIGIN Q5A(R1) INTERNATIONAL CONFERENCE ON HARMONISATION OF TECHNICAL REQUIREMENTS FOR REGISTRATION OF PHARMACEUTICALS FOR HUMAN USE ICH HARMONISED TRIPARTITE GUIDELINE VIRAL SAFETY EVALUATION OF BIOTECHNOLOGY PRODUCTS

More information

Why do we have linear chromosomes? A matter of Adam and Eve

Why do we have linear chromosomes? A matter of Adam and Eve Mutation Research 434 Ž 1999. 99 107 www.elsevier.comrlocaterdnarepair Community address: www.elsevier.comrlocatermutres Minireview Why do we have linear chromosomes? A matter of Adam and Eve Fuyuki Ishikawa

More information

Real-Time PCR UNIT 10.3 OVERVIEW AND PRINCIPLES

Real-Time PCR UNIT 10.3 OVERVIEW AND PRINCIPLES UNIT.3 Dean Fraga, 1 Tea Meulia, 2 and Steven Fenster 3 1 College of Wooster, Wooster, Ohio 2 Ohio Agricultural Research and Development Center, Wooster, Ohio 3 Ashland University, Ashland, Ohio OVERVIEW

More information

Identification of an UP element consensus sequence for bacterial promoters

Identification of an UP element consensus sequence for bacterial promoters Proc. Natl. Acad. Sci. USA Vol. 95, pp. 9761 9766, August 1998 Biochemistry Identification of an UP element consensus sequence for bacterial promoters SHAWN T. ESTREM, TAMAS GAAL, WILMA ROSS, AND RICHARD

More information

Quantification strategies in real-time PCR

Quantification strategies in real-time PCR A-Z of quantitative PCR (Editor: SA Bustin) Chapter3. Quantification strategies in real-time PCR 87 Quantification strategies in real-time PCR Michael W. Pfaffl Chaper 3 pages 87-112 in: A-Z of quantitative

More information

Real-Time PCR UNIT 10.3 OVERVIEW AND PRINCIPLES

Real-Time PCR UNIT 10.3 OVERVIEW AND PRINCIPLES UNIT.3 Real-Time PCR Dean Fraga, 1 Tea Meulia, 2 and Steven Fenster 3 1 College of Wooster, Wooster, Ohio 2 Ohio Agricultural Research and Development Center, Wooster, Ohio 3 Ashland University, Ashland,

More information

Chemistry Guide. DNA Sequencing by Capillary Electrophoresis Applied Biosystems Chemistry Guide Second Edition

Chemistry Guide. DNA Sequencing by Capillary Electrophoresis Applied Biosystems Chemistry Guide Second Edition Chemistry Guide DNA Sequencing by Capillary Electrophoresis Applied Biosystems Chemistry Guide Second Edition Chemistry Guide DNA Sequencing by Capillary Electrophoresis Applied Biosystems Chemistry Guide

More information

Detecting DNA Base Modifications Using Single Molecule, Real-Time Sequencing

Detecting DNA Base Modifications Using Single Molecule, Real-Time Sequencing Detecting DA Using Single Molecule, Real-Time Sequencing Introduction Base modifications are important to the understanding of biological processes such as gene expression, host-pathogen interactions,

More information

Phylogenetic and Taxonomic Relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus

Phylogenetic and Taxonomic Relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus ZOOLOGICAL SCIENCE 23: 323 331 (2006) 2006 Zoological Society of Japan Phylogenetic and Taxonomic Relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae),

More information

Artificial life: organization, adaptation and complexity from the bottom up

Artificial life: organization, adaptation and complexity from the bottom up Review TRENDS in Cognitive Sciences Vol.7 No.11 November 2003 505 Artificial life: organization, adaptation and complexity from the bottom up Mark A. Bedau Department of Philosophy, Reed College, 3023

More information

Imaging the developing brain: what have we learned about cognitive development?

Imaging the developing brain: what have we learned about cognitive development? Review TRENDS in Cognitive Sciences Vol.9 No.3 March 2005 Imaging the developing brain: what have we learned about cognitive development? B.J. Casey 1, Nim Tottenham 1, Conor Liston 1 and Sarah Durston

More information

Alien Plants Introduced by Different Pathways Differ in Invasion Success: Unintentional Introductions as a Threat to Natural Areas

Alien Plants Introduced by Different Pathways Differ in Invasion Success: Unintentional Introductions as a Threat to Natural Areas Alien Plants Introduced by Different Pathways Differ in Invasion Success: Unintentional Introductions as a Threat to Natural Areas Petr Pyšek 1,2 *, Vojtěch Jarošík 1,2, Jan Pergl 1,3 1 Department of Invasion

More information

Competing interests statement The authors declare that they have no competing financial interests.

Competing interests statement The authors declare that they have no competing financial interests. The ages for MJG-I, MJG-II and MJG-III are considerably older than previous age estimates of Palaeolithic sites in northern China 1 and indicate that humans might have reached northeast Asia earlier than

More information

Dating Phylogenies with Sequentially Sampled Tips

Dating Phylogenies with Sequentially Sampled Tips Syst. Biol. 62(5):674 688, 2013 The Author(s) 2013. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com

More information

Agricultural Biotechnology. (A Lot More than Just GM Crops)

Agricultural Biotechnology. (A Lot More than Just GM Crops) Agricultural Biotechnology (A Lot More than Just GM Crops) 1 All living organisms have the ability to improve themselves through natural means in order to adapt to changing environmental conditions. However,

More information