BmSE, a SINE family with 3′ ends of (ATTT) repeats in domesticated silkworm (Bombyx mori)

Jinshan Xu^{a, b},
Tie Liu^c,
Dong Li^c,
Ze Zhang^c,
Qinyou Xia^c,
Zeyang Zhou^{a, b, c
, ,}

a.
Laboratory of Animal Biology, Chongqing Normal University, Chongqing 400047, China
b.
Engineering Research Center of Bioactive Substances, Chongqing Normal University, Chongqing 400047, China
c.
Institute of Sericulture and System Biology, Southwest University, Chongqing 400716, China

More Information

Corresponding author: E-mail address: zyzhou@cqnu.edu.cn (Zeyang Zhou)

摘要

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Abstract: Short interspersed elements (SINEs), which are mainly composed of Bm1, are abundant in the domesticated silkworm. A 294 bp novel SINE family, designated as BmSE, was identified by mining the database of the complete Bombyx mori genome. A representational BmSE element is flanked by an 11 bp target site duplication sequence posterior poly (A) at the 3′ end and has the sequence motifs of an internal promoter of RNA polymerase III, which are similar to that of Bm1. The repetitive elements of BmSE are widely distributed in all 28 chromosomes of the genome and share the common (ATTT) repeats at the ends. GC-content distribution shows that BmSE tends to accumulate preferably in the region of higher AT content than that of Bm1. A high proportion of the BmSEs are mapped to the coding sequence introns, whereas several elements are also present in the UTR of some transcripts, indicating that BmSEs are indeed exonized with UTRs. Of the 615 identified structural variants (SVs) of BmSE among the 40 domesticated and wild silkworms, only 230 SVs were found in the domesticated silkworms, indicating that many recent SV events of BmSE occurred after domestication, which was probably due to its mobilization. Our analysis might assist in developing BmSE as a potential marker and in understanding the evolutionary roles of SINEs in the domesticated silkworm.
- domesticated silkworm /
- SINE /
- distribution /
- structural variant

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参考文献(38)

[1]	Adams, D.S., Eickbush, T.H., Herrera, R.J. et al. J. Mol. Biol., 187 (1986),pp. 465-478
[2]	Dewannieux, M., Esnault, C., Heidmann, T. LINE-mediated retrotransposition of marked Alu sequences Nat. Genet., 35 (2003),pp. 41-48
[3]	Eickbush, T.H. Transposing without ends: the non-LTR retrotransposable elements New Biol., 4 (1992),pp. 430-440
[4]	Felsenstein, J. PHYLIP—Phylogeny Inference Package (Version 3.2) Cladistics, 5 (1989),pp. 164-166
[5]	Galli, G., Hofstette, H., Bimstiel, M.L. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements Nature, 294 (1981),pp. 626-631
[6]	Hamada, M., Kido, Y., Himberg, M. et al. 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 (1997),pp. 355-367
[7]	Hasan, G., Turner, M.J., Cordingley, J.S. Cell, 37 (1984),pp. 333-341
[8]	Kajikawa, M., Okada, N. LINEs mobilize SINEs in the eel through a shared 3′ sequence Cell, 111 (2002),pp. 433-444
[9]	Kajikawa, M., Okada, N. Isolation and characterization of active LINE and SINEs from the eel Mol. Biol. Evol., 22 (2005),pp. 673-682
[10]	Kido, Y., Aono, M., Yamaki, T. et al. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution Proc. Natl. Acad. Sci. USA, 88 (1991),pp. 2326-2330
[11]	Kimura, R.H., Choudary, P.V., Schmid, C.W. Silkworm Bm1 SINE RNA increases following cellular insults Nucleic Acids Res., 27 (1999),pp. 3380-3387
[12]	Kramerov, D.A., Vassetzky, N.S. Short retroposon in eukaryotic genome Int. Rev. Cytol., 247 (2005),pp. 165-221
[13]	Lander, E.S., Linton, L.M., Birren, B. et al. Initial sequencing and analysis of the human genome Nature, 409 (2001),pp. 860-921
[14]	Luan, D.D., Korman, M.H., Jakubczak, J.L. et al. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition Cell, 72 (1993),pp. 595-605
[15]	Lowe, T.M., Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res., 25 (1997),pp. 955-964
[16]	Maichele, A.J., Farwell, N.J., Chamberlain, J.S. A B2 repeat insertion generates altemate structures of the mouse muscle Y-phosphorylase kinase gene Genomics, 16 (1993),pp. 139-149
[17]	Nakajima, Y., Hashido, K., Tsuchida, K. et al. J. Mol. Evol., 48 (1999),pp. 577-585
[18]	Ogiwara, I., Miya, M., Ohshima, K. et al. Retropositional Parasitism of SINEs on LINEs: identification of SINEs and LINEs in Elasmobranchs Mol. Biol. Evol., 16 (1999),pp. 1238-1250
[19]	Ohshima, K., Okada, N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail Cytogenet. Genome Res., 110 (2005),pp. 475-490
[20]	Ohshima, K., Hamada, M., Terai, Y. et al. 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 (1996),pp. 3756-3764
[21]	Okada, N. SINEs: short interspersed repeated elements of the eukaryotic genome Trends Ecol. Evol., 6 (1991),pp. 358-361
[22]	Okada, N., Hamada, M., Ogiwara, I. et al. SINEs and LINEs share common 3′ sequences: a review Gene, 205 (1997),pp. 229-243
[23]	Piskurek, O., Austin, C.C., Okada, N. Sauria SINEs: novel short interspersed retroposable elements that are widespread in reptile genomes J. Mol. Evol., 62 (2006),pp. 630-644
[24]	Rho, M., Tang, H. MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes Nucleic Acids Res., 37 (2009),pp. 1-12
[25]	Schmid, C.W., Maraia, R. Transcriptional regulation and transpositional selection of active SINE sequences Curr. Opin. Genet. Dev., 2 (1992),pp. 874-882
[26]	Sela, N., Mersch, B., Gal-Mark, N. et al. Comparative analysis of transposed elements' insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome Genome Biol., 8 (2007),pp. R1271-R12719
[27]	Shedlock, A.M., Okada, N. SINE insertions: powerful tools for molecular systematics Bioessays, 22 (2000),pp. 148-160
[28]	Smit, A. F. A., Hubley, R., and Green, P. (1996–2004). RepeatMasker Open-3.0 (http://www.repeatmsker.org).
[29]	Sun, F.J., Fleurdepine, S., Cecile, B.A. et al. Common evolutionary trends for SINE RNA structures Trends Genet., 23 (2006),pp. 26-33
[30]	Takasaki, N., Murata, S., Saitoh, M. et al. Species-specific amplification of tRNAderived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids Proc. Natl. Acad. Sci. USA, 91 (1994),pp. 10153-10157
[31]	Thompson, J.D., Higgins, D.G., Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res., 22 (1994),p. 4673
[32]	Tsuchimoto, S., Hirao, Y., Ohtsubo, E. et al. New SINE families from rice, OsSN, with poly(A) at the 3′ ends Genes Genet. Syst., 83 (2008),pp. 227-236
[33]	Ullu, E., Tschudi, C. Alu sequences are processed 7SL RNA genes Nature, 312 (1984),pp. 171-172
[34]	Wang, J., Wong, G.K., Ni, P.X. et al. RePS: a sequence assembler that masks exact repeats identified from the shotgun data Genome Res., 2 (2002),pp. 824-831
[35]	Weiner, A.M. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome Cell, 22 (1980),pp. 209-218
[36]	Wichman, H.A., Van den Bussche, R.A., Hamilton, M.J. et al. Transposable elements and the evolution of genome organization in mammals Genetica, 86 (1992),pp. 287-293
[37]	Xia, Q., Wang, J., Zhou, Z. et al. Insect Biochem. Mol. Biol., 38 (2008),pp. 1036-1045
[38]	Xia, Q.Y., Guo, Y., Zhang, Z. et al. Science, 326 (2009),pp. 433-436