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Ahn SJ, Kim JY, Kim MS, Lee HH. Cloning and characterization of Tc1 family-derived PPTN related transposons from ridged-eye flounder (Pleuronichthys cornutus) and inshore hagfish (Eptatretus burgeri). Genes Genomics 2013. [DOI: 10.1007/s13258-013-0068-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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2
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Brownlie JC, Johnson NM, Whyard S. The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons. Mol Genet Genomics 2005; 273:92-101. [PMID: 15702348 DOI: 10.1007/s00438-005-1110-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2004] [Accepted: 01/03/2005] [Indexed: 10/25/2022]
Abstract
The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae.
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Affiliation(s)
- J C Brownlie
- CSIRO Division of Entomology, GPO Box 1700, Canberra, ACT, 2601, Australia.
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3
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Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DHA, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 2003; 1:E45. [PMID: 14624247 PMCID: PMC261899 DOI: 10.1371/journal.pbio.0000045] [Citation(s) in RCA: 650] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2003] [Accepted: 09/04/2003] [Indexed: 11/19/2022] Open
Abstract
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes. With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome evolution
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MESH Headings
- Animals
- Biological Evolution
- Caenorhabditis/genetics
- Caenorhabditis elegans/genetics
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Cluster Analysis
- Codon
- Conserved Sequence
- Evolution, Molecular
- Exons
- Gene Library
- Genome
- Genomics/methods
- Interspersed Repetitive Sequences
- Introns
- MicroRNAs/genetics
- Models, Genetic
- Models, Statistical
- Molecular Sequence Data
- Multigene Family
- Open Reading Frames
- Physical Chromosome Mapping
- Plasmids/metabolism
- Protein Structure, Tertiary
- Proteins/chemistry
- RNA/chemistry
- RNA, Ribosomal/genetics
- RNA, Spliced Leader
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Lincoln D Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA..
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4
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Turcotte K, Bureau T. Phylogenetic analysis reveals stowaway-like elements may represent a fourth family of the IS630-Tc1-mariner superfamily. Genome 2002; 45:82-90. [PMID: 11908672 DOI: 10.1139/g01-127] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630-Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630-Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.
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Affiliation(s)
- Kime Turcotte
- Department of Biology, McGill University, Montreal, Canada
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5
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Leaver MJ. A family of Tc1-like transposons from the genomes of fishes and frogs: evidence for horizontal transmission. Gene 2001; 271:203-14. [PMID: 11418241 DOI: 10.1016/s0378-1119(01)00530-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tc1-like transposons are very widely distributed within the genomes of animal species. They consist of an inverted repeat sequence flanking a transposase gene with homology to the mobile DNA element, Tc1 of the nematode Caenorhabditis elegans. These elements seem particularly to infest the genomes of fish and amphibian species where they can account for 1% of the total genome. However, all vertebrate Tc1-like elements isolated so far are non-functional in that they contain multiple frameshifts within their transposase coding regions. Here I describe a Tc1-like transposon (PPTN) from the genome of a marine flatfish species (Pleuronectes platessa) which bears conserved inverted repeats flanking an apparently intact transposase gene. Closely related, although degenerate, Tc1-like transposons were also isolated from the genomes of Atlantic salmon (SSTN, Salmo salar) and frog (RTTN, Rana temporaria). Consensual nucleic acid sequences were derived by comparing several individual isolates from each species and conceptual amino acid sequences were thence derived for their transposases. Phylogenetic analysis of these sequences with previously isolated Tc1-like transposases shows that the elements from plaice, salmon and frog comprise a new subfamily of Tc1-like transposons. Each member is distinct in that it is not found in the genomes of the other species tested. Plaice genomes contain about 300 copies of PPTN, salmon 1200 copies of SSTN and frog genomes about 500 copies of RTTN. The presence of these closely related elements in the genomes of fish and frog species, representing evolutionary lines, which diverged more than 400 million years ago, is not consistent with a vertical transmission model for their distributions.
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Affiliation(s)
- M J Leaver
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK.
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Hoekstra R, Otsen M, Tibben J, Lenstra JA, Roos MH. Non-autonomous transposable elements in the genome of the parasitic nematode Haemonchus contortus. Mol Biochem Parasitol 2000; 106:163-8. [PMID: 10743620 DOI: 10.1016/s0166-6851(99)00195-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- R Hoekstra
- Department of Molecular Recognition, Institute for Animal Science and Health (ID-Lelystad), Netherlands.
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7
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Hoekstra R, Otsen M, Lenstra JA, Roos MH. Characterisation of a polymorphic Tc1-like transposable element of the parasitic nematode Haemonchus contortus. Mol Biochem Parasitol 1999; 102:157-66. [PMID: 10477184 DOI: 10.1016/s0166-6851(99)00094-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hctc1, a member of the Tc1-family of transposable elements was isolated from the parasitic nematode Haemonchus contortus. Hctc1 is 1590 bp long, is flanked by 55 bp inverted repeats and carries a single open reading frame of a 340 amino acid transposase-like protein. Hctc1 is similar to Tc1 of Caenorhabditis elegans and elements Tcb1 and Tcb2 of Caenorhabditis briggsae in the inverted terminal repeats, the open reading frame, as well as the target insertion sequence. Furthermore, the copy number of Hctc1 is comparable with the Tc1 copy number in low copy strains of C. elegans. The sequence of Hctc1 is highly variable in H. contortus due to deletions, insertions and point mutations, with at least five distinct length variants of Hctc1. Most of the Hctc1 variation was within rather than between H. contortus populations. The high level of sequence variation is probably due to variation generally found for members of the Tc1-family, as well as a high background level of genetic variation of H. contortus.
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Affiliation(s)
- R Hoekstra
- Department of Molecular Recognition, Institute for Animal Science and Health (ID-DLO), Lelystad, The Netherlands.
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8
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Abstract
The sequencing of the 100 Mb Caenorhabditis elegans genome-containing approximately 14,000 genes-is approximately 50% complete. One of its most interesting features is its compactness; introns and intergenic distances are unusually small and, surprisingly, approximately 25% of genes are contained in polycistronic transcription units (operons) with only approximately 100 bp between genes.
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Affiliation(s)
- T Blumenthal
- Department of Biology, Indiana University, Bloomington 47405, USA.
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Affiliation(s)
- R H Plasterk
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam.
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10
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Affiliation(s)
- R H Plasterk
- Netherlands Cancer Institute, Division of Molecular Biology, Amsterdam, The Netherlands
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11
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Glayzer DC, Roberts IN, Archer DB, Oliver RP. The isolation of Ant1, a transposable element from Aspergillus niger. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:432-8. [PMID: 8552048 DOI: 10.1007/bf00287105] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A transposable element has been isolated from the industrially important fungus Aspergillus niger (strain N402). The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. It had inserted at a TA site and appeared to have duplicated the target site upon insertion. The isolated element was found to be 4798 bp in length and contained 37-bp inverted, imperfect, terminal repeats (ITRs). The sequence of the central region of the element revealed an open reading frame (designated ORF1) which showed similarity, at the amino acid level, to the transposase of the Tc1/mariner class of DNA transposons. Another sequence within the central region of the element showed similarity to the 3' coding and downstream untranslated region of the amyA gene of A. niger. Sequence homology and structural features indicate that this element, which has been named Ant1 (A. niger transposon 1), is related to the Tc1/mariner group of DNA transposons. Ant1 is apparently present as a single copy in strain N402 of A. niger.
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Affiliation(s)
- D C Glayzer
- Norwich Molecular Plant Pathology Group, School of Biological Sciences, University of East Anglia, Norwich Research Park, UK
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12
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Marín I, Fontdevila A. Characterization of Gandalf, a new inverted-repeat transposable element of Drosophila koepferae. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:423-33. [PMID: 7565606 DOI: 10.1007/bf02191642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The cloning and characterization of Gandalf, a new DNA-transposing mobile element obtained from the Drosophila koepferae (repleta group) genome is described. A fragment of Gandalf was found in a middle repetitive clone that shows variable chromosomal localization. Restriction, Southern blot, PCR and sequencing analyses have shown that most Gandalf copies are about 1 kb long, are flanked by 12 bp inverted terminal repeats and contain subterminal repetitive regions on both sides of the element. As with other elements of the DNA-transposing type (known as the 'Ac family'), the Gandalf element generates 8 bp direct duplications at the insertion point. Coding region analysis has shown that the longer open reading frame found in Gandalf copies could encode part of a protein. However, whether or not the 1 kb copies of the element are actually the active transposons remains to be elucidated. Gandalf shows a very low copy number in D. buzzatii, a sibling species of D. koepferae. An attempt to induce interspecific hybrid dysgenesis in hybrids of these two species has been unsuccessful.
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Affiliation(s)
- I Marín
- Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Spain
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13
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Izsvák Z, Ivics Z, Hackett PB. Characterization of a Tc1-like transposable element in zebrafish (Danio rerio). MOLECULAR & GENERAL GENETICS : MGG 1995; 247:312-22. [PMID: 7770036 DOI: 10.1007/bf00293199] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have characterized Tdr1, a family of Tc1-like transposable elements found in the genome of zebrafish (Danio rerio). The copy number and distribution of the sequence in the zebrafish genome have been determined, and by these criteria Tdr1 can be classified as a moderately repetitive, interspersed element. Examination of the sequences and structures of several copies of Tdr1 revealed that a particular deletion derivative, 1250 bp long, of the transposon has been amplified to become the dominant form of Tdr1. The deletion in these elements encompasses sequences encoding the N-terminal portion of the putative Tdr1 transposase. Sequences corresponding to the deleted region were also detected, and thus allowed prediction of the nucleotide sequence of a hypothetical full-length element. Well conserved segments of Tc1-like transposons were found in the flanking regions of known fish genes, suggesting that these elements have a long evolutionary history in piscine genomes. Tdr1 elements have long, 208 bp inverted repeats, with a short DNA motif repeated four times at the termini of the inverted repeats. Although different from that of the prototype C. elegans transposon Tc1, this inverted repeat structure is shared by transposable elements from salmonid fish species and two Drosophila species. We propose that these transposons form a subgroup within the Tc1-like family. Comparison of Tc1-like transposons supports the hypothesis that the transposase genes and their flanking sequences have been shaped by independent evolutionary constraints. Although Tc1-like sequences are present in the genomes of several strains of zebrafish and in salmonid fishes, these sequences are not conserved in the genus Danio, thus raising the possibility that these elements can be exploited for gene tagging and genome mapping.
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Affiliation(s)
- Z Izsvák
- Department of Genetics and Cell Biology, University of Minnesota, St. Paul 55108, USA
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14
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Radice AD, Bugaj B, Fitch DH, Emmons SW. Widespread occurrence of the Tc1 transposon family: Tc1-like transposons from teleost fish. MOLECULAR & GENERAL GENETICS : MGG 1994; 244:606-12. [PMID: 7969029 DOI: 10.1007/bf00282750] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We characterized five transposable elements from fish: one from zebrafish (Brachydanio rerio), one from rainbow trout (Salmo gairdneri), and three from Atlantic salmon (Salmo salar). All are closely similar in structure to the Tc1 transposon of the nematode Caenorhabditis elegans. A comparison of 17 Tc1-like transposons from species representing three phyla (nematodes, arthropods, and chordates) showed that these elements make up a highly conserved transposon family. Most are close to 1.7 kb in length, have inverted terminal repeats, have conserved terminal nucleotides, and each contains a single gene encoding similar polypeptides. The phylogenetic relationships of the transposons were reconstructed from the amino acid sequences of the conceptual proteins and from DNA sequences. The elements are highly diverged and have evidently inhibited the genomes of these diverse species for a long time. To account for the data, it is not necessary to invoke recent horizontal transmission.
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Affiliation(s)
- A D Radice
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
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15
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van Luenen HG, Plasterk RH. Target site choice of the related transposable elements Tc1 and Tc3 of Caenorhabditis elegans. Nucleic Acids Res 1994; 22:262-9. [PMID: 8127662 PMCID: PMC523575 DOI: 10.1093/nar/22.3.262] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have investigated the target choice of the related transposable elements Tc1 and Tc3 of the nematode C. elegans. The exact locations of 204 independent Tc1 insertions and 166 Tc3 insertions in an 1 kbp region of the genome were determined. There was no phenotypic selection for the insertions. All insertions were into the sequence TA. Both elements have a strong preference for certain positions in the 1 kbp region. Hot sites for integration are not clustered or regularly spaced. The orientation of the integrated transposon has no effect on the distribution pattern. We tested several explanations for the target site preference. If simple structural features of the DNA (e.g. bends) would mark hot sites, we would expect the patterns of the two related transposons Tc1 and Tc3 to be similar; however we found them to be completely different. Furthermore we found that the sequence at the donor site has no effect on the choice of the new insertion site, because the insertion pattern of a transposon that jumps from a transgenic donor site is identical to the insertion pattern of transposons jumping from endogenous genomic donor sites. The most likely explanation for the target choice is therefore that the primary sequence of the target site is recognized by the transposase. However, alignment of the Tc1 and Tc3 integration sites does not reveal a strong consensus sequence for either transposon.
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Affiliation(s)
- H G van Luenen
- The Netherlands Cancer Institute, Division of Molecular Biology, Amsterdam
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16
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Sulston J, Du Z, Thomas K, Wilson R, Hillier L, Staden R, Halloran N, Green P, Thierry-Mieg J, Qiu L. The C. elegans genome sequencing project: a beginning. Nature 1992; 356:37-41. [PMID: 1538779 DOI: 10.1038/356037a0] [Citation(s) in RCA: 404] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.
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Affiliation(s)
- J Sulston
- MRC Laboratory of Molecular Biology, Cambridge, UK
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