Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors
| العنوان: | Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors |
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| المؤلفون: | Maciek Sasinowski, Steve Goff, Sung Sick Woo, Long Mao, Ralph A. Dean, Muhammad A. Budiman, Todd C. Wood, Jeff Tomkins, Gernot G. Presting, David Frisch, Yeisoo Yu, Rod A. Wing |
| المصدر: | Genome Research. 10:982-990 |
| بيانات النشر: | Cold Spring Harbor Laboratory, 2000. |
| سنة النشر: | 2000 |
| مصطلحات موضوعية: | Letter, DNA, Plant, Population, Arabidopsis, Transposases, Genomics, Retrotransposon, Biology, Genes, Plant, Genome, Plant Viruses, Capsid, Sequence Homology, Nucleic Acid, Tobacco, Genetics, education, Genome size, Genetics (clinical), Gene Library, Plant Proteins, Repetitive Sequences, Nucleic Acid, Sequence Tagged Sites, Synteny, Whole genome sequencing, education.field_of_study, Oryza sativa, food and beverages, Oryza, Chromosomes, Bacterial, Physical Chromosome Mapping, DNA-Binding Proteins, Plants, Toxic, Multigene Family, DNA Transposable Elements, Carrier Proteins, Genome, Plant |
| الوصف: | Transposable elements (TEs) are ubiquitous in all organisms (Burge and Howe 1989; Xiong and Eickbush 1990). In plants, TEs are classified into two main classes (Flavell et al. 1994). Retrotransposons comprise Class I and transpose via an RNA intermediate. Class I TEs include retrotransposons with long terminal repeats (LTRs) such as Ty1/Copia-like and Ty3/Gypsy-like, as well as non-LTR retrotransposons. The class II TEs transpose via a DNA intermediate and in plants have been found mainly in maize. Class II TEs include Ac/Ds, En/Spm, and Mutator (Federoff 1989). MITEs, that is, miniature inverted-repeat transposable elements, such as maize Tourist and Stowaway, fall into a newly described third class of TEs (Bureau and Wessler 1992, 1994a,b, 1996). The mechanism of transposition of MITEs is still unclear, although they have received considerable attention recently due to their high copy numbers and tendency to be associated with genes in maize (Wessler et al. 1995; Zhang et al. 2000). Rice (Oryza sativa) is the main staple food for more than half of the world's population and is of great economic importance. Among the cereal grasses, rice has the smallest genome size (430 Mb) and, as revealed by comparative mapping, has substantial conservation of synteny with other cereal crops such as maize, sorghum, and wheat (Gale and Devos 1998). Consequently, rice is an ideal representative for cereal genomics studies and is the focus of an international effort to completely sequence its genome. Although numerous TEs have been reported in rice, no comprehensive investigation has been carried out on a genome-wide scale, because the majority of rice TEs were uncovered by chance or by limited assays using conserved regions such as reverse transcriptase of retrotransposons (Hirochika et al. 1992; Motohashi et al. 1996; Kumekawa et al. 1999). As part of the International Rice Genome Sequencing Project (IRGSP), a rice BAC library was constructed from a partial HindIII digest of the genome of the rice variety Nipponbare (Budiman 1999), and the ends of BAC clone inserts have been sequenced. BAC end sequences will serve as sequence-tagged-connectors (STCs) for selecting minimum overlapping clones for genome sequencing (Venter et al. 1996). The generation of >73,000 Nipponbare STCs also provides an opportunity to preview TE content and distribution in rice genome. The current STC library contains ∼48 Mb of rice genomic DNA after vector removal, with an average sequence read of 707 nucleotides. With an average insert of 128.5 kb, the CUGI rice BAC library is expected to cover ∼10 rice genome equivalents. Preliminary efforts to confirm the coverage of the library based strictly on sequence comparison of the STCs to finished rice BACs have shown that the estimated coverage is ∼10.4 genome equivalents (data not shown). Assuming that the HindIII sites are evenly distributed, our 73,000 STCs should be distributed one STC every 9 kb across the 430-Mb rice genome. TEs are one of the major sources of repetitive sequences in cereal plants and have been a concern of the IRGSP as a potential source of problems in completing the rice genome sequence. Here, we report the TE content of the STC database and show that the rice genome probably contains a small fraction of TEs in comparison with other cereal genomes, such as maize. The small amount of TEs confirms rice as a well-chosen model crop genome. We note the discovery of several potentially novel TEs, and we investigate the location of TE–STCs on the current physical map of the CUGI rice BAC library. We find that the TEs appear to be randomly distributed with respect to potential genes, identified by similarity to rice ESTs. |
| تدمد: | 1549-5469 1088-9051 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cee56088cdf123f0443f04e6057815c6 https://doi.org/10.1101/gr.10.7.982 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....cee56088cdf123f0443f04e6057815c6 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15495469 10889051 |
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