Mao L, 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
Clemson University Genomics Institute, South Carolina 29634 USA.
Genome Res. 2000 Jul;10(7):982-90. doi: 10.1101/gr.10.7.982.
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.
作为水稻基因组测序国际合作项目的一部分，克莱姆森大学基因组学研究所正在构建一个序列标签连接体（STC）框架。该框架包括构建来自粳稻品种日本晴的高覆盖度细菌人工染色体（BAC）文库，以及对BAC克隆基因组DNA插入片段的两端进行测序。在此，我们报告了对超过73,000个STC中的转座元件（TE）的调查结果。通过将STC与从GenBank获得的1358个TE蛋白序列进行FASTX搜索，共发现6848个STC与已知TE序列区域同源（E<10^(-5)）。在这些含有TE的STC（TE-STC）中，88%（6027个）与反转录元件相关，其余的是转座酶同源物。几乎所有先前在植物中已知的DNA转座子都存在于STC中，包括玉米的Ac/Ds、En/Spm、Mutator和类水手元件。此外，发现2746个STC含有与已知微型反向重复转座元件（MITE）同源的区域。通过将EST与含有MITE的STC进行比较，证实了这些MITE在基因附近区域的分布，并且我们的结果表明，MITE与已知EST转录本的关联因MITE类型而异。与玉米中反转录元件的偏向分布不同，当我们将TE-STC与CUGI BAC文库的物理图谱相关联时，没有发现基因岛存在的证据。对近50 Mb水稻基因组DNA中TE的这些分析为水稻基因组提供了有趣且信息丰富的预览。
