Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Tong, Chaobo ^a,b   Gan, Xiaoni ^a,b   He, Shunping ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CYPRINID; EVOLUTIONARY BIOLOGY; GENETIC MARKER; GENOME; NUCLEIC ACID; PHYLOGENETICS; POLYMERASE CHAIN REACTION; REAL TIME; TAXONOMY;

ACIPENSERIFORMES; CYPRINIDAE; CYPRINIFORMES; DANIO RERIO; HYPOPHTHALMICHTHYS; HYPOPHTHALMICHTHYS NOBILIS; OSTEICHTHYES; OSTEOGLOSSIFORMES; PISCES; POLYPTERIFORMES; SILURIFORMES;

ANIMAL; ARTICLE; CYPRINIFORMES; GENETICS; LONG INTERSPERSED REPEAT; MOLECULAR EVOLUTION; POLYADENYLATION; POLYMERASE CHAIN REACTION; SHORT INTERSPERSED REPEAT; ZEBRA FISH;

ANIMALS; CYPRINIDAE; EVOLUTION, MOLECULAR; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; POLYADENYLATION; POLYMERASE CHAIN REACTION; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; ZEBRAFISH;

EID: 77951543876     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-115     Document Type: Article

References (25)

1. Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation. C Tong B Guo S He, BMC genomics 2009 10 83 10.1186/1471-2164-10-83 19224649
2. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. MF Singer, Cell 1982 28 3 433 434 10.1016/0092-8674(82) 90194-5 6280868
3. Origins of repeated DNA. J Rogers, Nature 1985 317 6040 765 766 10.1038/317765a0 4058584
4. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. AM Weiner PL Deininger A Efstratiadis, Annual review of biochemistry 1986 55 631 661 10.1146/annurev.bi. 55.070186.003215 2427017
5. Retroposons - seeds of evolution. J Brosius, Science (New York, NY) 1991 251 4995 753
6. Transposing without ends: the non-LTR retrotransposable elements. TH Eickbush, The New biologist 1992 4 5 430 440 1325183
7. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. DD Luan MH Korman JL Jakubczak TH Eickbush, Cell 1993 72 4 595 605 10.1016/0092-8674(93)90078-5 7679954
8. The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements. K Ohshima M Hamada Y Terai N Okada, Mol Cell Biol 1996 16 7 3756 3764 8668192
9. Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs. I Ogiwara M Miya K Ohshima N Okada, Mol Biol Evol 1999 16 9 1238 1250 10486979
10. SINEs and LINEs share common 3' sequences: a review. N Okada M Hamada I Ogiwara K Ohshima, Gene 1997 205 1-2 229 243 10.1016/S0378-1119(97)00409-5 9461397
11. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. K Ohshima N Okada, Cytogenet Genome Res 2005 110 1-4 475 490 10.1159/000084981 16093701
12. Evolution of the active sequences of the HpaI short interspersed elements. Y Kido M Saitoh S Murata N Okada, J Mol Evol 1995 41 6 986 995 10.1007/BF00173180 8587145
13. V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. I Ogiwara M Miya K Ohshima N Okada, Genome research 2002 12 2 316 324 10.1101/gr.212302 11827951
14. CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. N Gilbert D Labuda, Proceedings of the National Academy of Sciences of the United States of America 1999 96 6 2869 2874 10.1073/pnas.96.6.2869 10077603
15. Fauna Sinica, Osteichthys: Cypriniformes (Part II). YY Chen, Science Press, Beijing 1998
16. Molecular Cloning: A Laboratory Manual. J Sambrook EF Fritsch T Maniatis, Cold Spring Harbor Laboratory Press, New York second 1989
17. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics (Oxford, England) 2001 17 8 754 755 10.1093/bioinformatics/17.8.754 11524383
18. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics (Oxford, England) 2003 19 12 1572 1574 10.1093/bioinformatics/btg180 12912839
19. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. X Wang J Li S He, Molecular phylogenetics and evolution 2007 42 1 157 170 10.1016/j.ympev.2006.06.014 16919973
20. Mitochondrial phylogeny of European cyprinids: implications for their systematics, reticulate evolution, and colonization time. A Gilles G Lecointre E Faure R Chappaz G Brun, Mol Phylogenet Evol 1998 10 132 143 10.1006/mpev.1997.0480 9751923
21. Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region. ALG Gilles A Miquelis M Loerstcher R Chappaz G Brun, Mol Phylogenet Evol 2001 19 22 33 10.1006/mpev.2000.0916 11286488
22. Human Alu subfamilies and their methylation revealed by blot hybridization. CW Schmid, Nucleic acids research 1991 19 20 5613 5617 10.1093/nar/19.20.5613 1945838
23. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. WM Liu CW Schmid, Nucleic acids research 1993 21 6 1351 1359 10.1093/nar/21.6.1351 8464725
24. Transcriptional regulation and transpositional selection of active SINE sequences. C Schmid R Maraia, Current opinion in genetics & development 1992 2 6 874 882 10.1016/S0959-437X(05)80110-8 1335809
25. Characterization of species-specifically amplified SINEs in three salmonid species - chum salmon, pink salmon, and kokanee: the local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. N Takasaki L Park M Kaeriyama AJ Gharrett N Okada, J Mol Evol 1996 42 2 103 116 10.1007/BF02198835 8919862