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Vol. 10, Issue 7, 982-990, July 2000

LETTER
Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors

Long Mao,1 Todd C. Wood,1 Yeisoo Yu,1 Muhammad A. Budiman,1,3 Jeff Tomkins,1 Sung-sick Woo,1,4 Maciek Sasinowski,1,5 Gernot Presting,1 David Frisch,1 Steve Goff,2 Ralph A. Dean,1,6 and Rod A. Wing1,7

1 Clemson University Genomics Institute, Clemson, South Carolina 29634 USA; 2 Novartis Agricultural Discovery Institute, San Diego, California 92121 USA

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.

Present addresses: 3Orion Genomics, St. Louis, Missouri 63108 USA; 4Department of Agronomy, Konkuk University, Seoul, South Korea 143-701, Korea; 5Institute for Computational Genomics, 110 Clemson, South Carolina 29631 USA; 6Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27606 USA.

7 Corresponding author.

10:982-990 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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