Repetitive sequences (repeats) represent a significant fraction of the eukaryotic genomes and can be divided into tandem repeats, segmental duplications, and interspersed repeats on the basis of their sequence characteristics and how they are formed. Most interspersed repeats are derived from transposable elements (TEs). Eukaryotic TEs have been subdivided into two major classes according to the intermediate they use to move. The transposition and amplification of TEs have a great impact on the evolution of genes and the stability of genomes. However, identification and classification of TEs are complex and difficult due to the fact that their structure and classification are complex and diverse compared with those of other types of repeats. Here, we briefly introduced the function and classification of TEs, and summarized three different steps for identification, classification and annotation of TEs in eukaryotic genomes: (1) assembly of a repeat library, (2) repeat correction and classification, and (3) genome annotation. The existing computational approaches for each step were summarized and the advantages and disadvantages of the approaches were also highlighted in this review. To accurately identify, classify, and annotate the TEs in eukaryotic genomes requires combined methods. This review provides useful information for biologists who are not familiar with these approaches to find their way through the forest of programs.
XU Hong-En, ZHANG Hua-Hao, HAN Min-Jin, SHEN Yi-Hong, HUANG Xian-Zhi, XIANG Zhong-Huai, ZHANG Ze
. Computational approaches for identification and classification of transposable elements in eukaryotic genomes[J]. Hereditas(Beijing), 2012
, 34(8)
: 1009
-1019
.
DOI: 10.3724/SP.J.1005.2012.01009
[1] Britten RJ, Kohne DE. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science, 1968, 161 (3841): 529-540.
[2] Waring M, Britten RJ. Nucleotide sequence repetition: a rapidly reassociating fraction of mouse DNA. Science, 1966, 154(3750): 791-794.
[3] Rubin CM, Houck CM, Deininger PL, Friedmann T, Schmid CW. Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature, 1980, 284(5754): 372 -374.
[4] Singer MF. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell, 1982, 28(3): 433-434.
[5] Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Chen YJ. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822): 860-921.
[6] Li YC, Korol AB, Fahima T, Beiles A, Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol, 2002, 11(12): 2453- 2465.
[7] Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity, 2009, 104(6): 520-533.
[8] Charlesworth B, Sniegowski P, Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature, 1994, 371(6494): 215-220.
[9] Eichler EE. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet, 2001, 17(11): 661-669.
[10] Feschotte C, Pritham EJ. Computational analysis and paleogenomics of interspersed repeats in eukaryotes. In: Stojanovic N, ed. Computational genomics: current methods. London: Taylor & Francis, 2007: 31-54.
[11] Wessler SR. Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci USA, 2006, 103(47): 17600-17601.
[12] Kidwell MG. Transposable elements and the evolution of genome size in eukaryotes. Genetica, 2002, 115(1): 49-63.
[13] Kazazian HH Jr. Mobile elements: drivers of genome evolution. Science, 2004, 303 (5664): 1626-1632.
[14] Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res, 1998, 8(5): 464-478.
[15] Kapitonov VV, Jurka J. Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA, 2003, 100(11): 6569- 6574.
[16] Osanai-Futahashi M, Suetsugu Y, Mita K, Fujiwara H. Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori. Insect Biochem Mol Biol, 2008, 38(12): 1046-1057.
[17] SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The paleontology of intergene retrotransposons of maize. Nat Genet, 1998, 20(1): 43-45.
[18] Pardue ML, Rashkova S, Casacuberta E, DeBaryshe PG, George JA, Traverse KL. Two retrotransposons maintain telomeres in Drosophila. Chromosome Res, 2005, 13(5): 443- 453.
[19] Gregory TR. Synergy between sequence and size in large-scale genomics. Nature Rev Genet, 2005, 6(9): 699-708.
[20] 陈建军, 王瑛. 植物基因组大小进化的研究进展. 遗传, 2009, 31(5): 464-470.
[21] Bennetzen JL. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev, 2005, 15(6): 621-627.
[22] 陈志伟, 吴为人. 植物中的反转录转座子及其应用. 遗传, 2004, 26(1): 122-126.
[23] Bennetzen JL. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol, 2000, 42(1): 251-269.
[24] Devine SE, Chissoe SL, Eby Y, Wilson RK, Boeke JD. A transposon-based strategy for sequencing repetitive DNA in eukaryotic genomes. Genome Res,
