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PMID: 10899147 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Rice transposable elements: a survey of 73,000 sequence-tagged-connectors.

Genome research ·Vol. 10 ·No. 7 ·2000-07-00 ·Pages 982-90

Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, Dean RA, Wing RA

Abstract

As part of an international effort to sequence the rice genome, the Clemson University Genomics Institute is developing a sequence-tagged-connector (STC) framework. This framework includes the generation of deep-coverage BAC libraries from O. sativa ssp. japonica c.v. Nipponbare and the sequencing of both ends of the genomic DNA insert of the BAC clones. Here, we report a survey of the transposable elements (TE) in >73,000 STCs. A total of 6848 STCs were found homologous to regions of known TE sequences (E<10(-5)) by FASTX search of STCs against a set of 1358 TE protein sequences obtained from GenBank. Of these TE-containing STCs (TE-STCs), 88% (6027) are related to retroelements and the remaining are transposase homologs. Nearly all DNA transposons known previously in plants were present in the STCs, including maize Ac/Ds, En/Spm, Mutator, and mariner-like elements. In addition, 2746 STCs were found to contain regions homologous to known miniature inverted-repeat transposable elements (MITEs). The distribution of these MITEs in regions near genes was confirmed by EST comparisons to MITE-containing STCs, and our results showed that the association of MITEs with known EST transcripts varies by MITE type. Unlike the biased distribution of retroelements in maize, we found no evidence for the presence of gene islands when we correlated TE-STCs with a physical map of the CUGI BAC library. These analyses of TEs in nearly 50 Mb of rice genomic DNA provide an interesting and informative preview of the rice genome.

MeSH Terms
Arabidopsis/genetics Capsid/genetics Carrier Proteins/genetics Chromosomes, Bacterial/genetics DNA Transposable Elements/genetics DNA, Plant/genetics DNA-Binding Proteins/genetics Gene Library Genes, Plant Genome, Plant Multigene Family/genetics Oryza/genetics Physical Chromosome Mapping Plant Proteins Plant Viruses/genetics Plants, Toxic Repetitive Sequences, Nucleic Acid/genetics Sequence Homology, Nucleic Acid Sequence Tagged Sites Tobacco/genetics Transposases
Chemicals
Carrier Proteins DNA Transposable Elements DNA, Plant DNA-Binding Proteins Plant Proteins ferredoxin-NADP reductase-binding protein, Zea mays mariner transposases Transposases
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Mao L
Clemson University Genomics Institute, South Carolina 29634 USA.
Wood T C
Yu Y
Budiman M A
Tomkins J
Woo S
Sasinowski M
Presting G
Frisch D
Goff S
Dean R A
Wing R A
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.10.7.982
Published
2000-07-00
Pages
982-90
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC310901
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.10.7.982 PMC Full Text View journal details
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