Genomics / Proteomics
Zhengqiu, Cai , Kim, Hyi-Gyung , Ruck, Elizabeth , Guisinger-Bellian, Mary M. , McMurtry, Vanity , Boore, Jeffrey L. , Jansen, Robert K. .
Extensive rearrangements in the plastid genome of Trifolium subterraneum (Fabaceae) are associated with numerous repeated sequences and novel DNA insertions.
Organization of the plastid genome of Trifolium subterraneum is very divergent compared to those of other flowering plants. The complete genome sequence of Trifolium subterraneum is 144,762 bp, about 20 kb longer than closely related legumes with one copy of the inverted repeat. One of the most unusual features of this genome is the large number of dispersed repeats. Comparative analyses with other angiosperm plastid genomes indicate that these repeats comprise 19.5% of the Trifolium genome (versus about 4% for other angiosperms) and account for the increase in genome size. Several genes have been duplicated partially or completely. psbN has been duplicated twice, and the duplicate copies differ by a single base-pair insertion compared with to the complete, functional copy. rpl23 is the most highly duplicated gene, with six copies, five of which include a duplication of an identical portion of rpl23. BLAST analyses of the sequences flanking the rpl23 repeats show no sequence similarity to other plastid genome sequences, suggesting that this novel DNA may represent lateral transfer. Comparisons of the Trifolium plastid genome with databases of repeated sequences of plant nuclear genomes did not identify any significant sequence similarity to transposable elements, suggesting that the high incidence of dispersed repeats is not the result of transposition. The Trifolium plastid genome has also experienced extensive genomic rearrangements, including gene (accD, ccsA, infA, rpl22, rps16, rps18, ycf1) and intron (clpP, rps12) losses and gene order changes. Comparison of the Trifolium genome with Nicotiana reveals that it is composed of 19 clusters of genes, with genes within each cluster in the same order as Nicotiana but the clusters are highly rearranged. Furthermore, all endpoints of these rearranged gene clusters are flanked by repeated sequences or tRNAs. These unusual features provide important clues for developing models of plastid genome evolution in Trifolium.
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1 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA
2 - University of Texas at Austin, Section of Integrative Biology, Austin, TX, 78712, USA
3 - The University of Texas M.D. Anderson Cancer Center, Department of Experimental Therapeutics, Houston, TX, 77030, USA
4 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA
Presentation Type: Oral Paper:Papers for Topics
Location: Boulevard A/Hilton
Date: Wednesday, July 11th, 2007
Time: 3:45 PM