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PMID: 11282973 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

The complex repeats of Dictyostelium discoideum.

Genome research ·Vol. 11 ·No. 4 ·2001-04-00 ·Pages 585-94

Glöckner G, Szafranski K, Winckler T, Dingermann T, Quail MA, Cox E, Eichinger L, Noegel AA, Rosenthal A

Abstract

In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species. Several of the most abundant small complex repeats and transposons (DIRS-1; TRE3-A,B; TRE5-A; skipper; Tdd-4; H3R) have been described previously. In our analysis we have identified additional elements. Thus, we can now present a complete list of complex repetitive elements in D. discoideum. All elements add up to 10% of the genome. Some of the newly described elements belong to established classes (TRE3-C, D; TRE5-B,C; DGLT-A,P; Tdd-5). However, we have also defined two new classes of DNA transposable elements (DDT and thug) that have not been described thus far. Based on the nucleotide amount, we calculated the least copy number in each family. These vary between <10 up to >200 copies. Unique sequences adjacent to the element ends and truncation points in elements gave a measure for the fragmentation of the elements. Furthermore, we describe the diversity of single elements with regard to polymorphisms and conserved structures. All elements show insertion preference into loci in which other elements of the same family reside. The analysis of the complex repeats is a valuable data resource for the ongoing assembly of whole D. discoideum chromosomes.

MeSH Terms
Animals DNA Transposable Elements/genetics DNA, Protozoan/genetics Dictyostelium/genetics Genes, Protozoan/genetics Interspersed Repetitive Sequences/genetics Molecular Sequence Data Mutagenesis, Insertional/genetics Phylogeny Polymorphism, Genetic/genetics RNA, Protozoan/genetics Repetitive Sequences, Nucleic Acid/genetics Retroelements/genetics
Chemicals
DNA Transposable Elements DNA, Protozoan RNA, Protozoan Retroelements
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Glöckner G
IMB Jena, Department of Genome Analysis, D-07745 Jena, Germany. [email protected]
Szafranski K
Winckler T
Dingermann T
Quail M A
Cox E
Eichinger L
Noegel A A
Rosenthal A
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.162201
Email
[email protected]
Published
2001-04-00
Pages
585-94
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC311061
Subset
IM
Databases
GENBANK
AF135841, AF298201, AF298202, AF298203, AF298204, AF298205, AF298206, AF298207, AF298208, AF298209, AF298210, AF298624
External Links
PubMed source DOI: 10.1101/gr.162201 PMC Full Text View journal details
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