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Plant Physiology 138:1205-1215 (2005) © 2005 American Society of Plant Biologists Complex Organization and Evolution of the Tomato Pericentromeric Region at the FER Gene Locus1,[w]Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland (R.G., E.S., B.K., H.-Q.L.); and Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China (X.C., Y.S., Z.C., H.-Q.L.)
Tomato (Lycopersicon esculentum) is a model species for molecular biology research and a candidate for large-scale genome sequencing. Pericentromeric heterochromatin constitutes a large portion of the tomato chromosomes. However, the knowledge of the structure, organization, and evolution of such regions remains very limited. Here, we report the analysis of a 198-kb sequence near the FER gene, located in a distal part of pericentromeric heterochromatin on the long arm of tomato chromosome 6. Nine genes, one pseudogene, and 55 transposable elements (TEs) were identified, showing a low gene density (19.8 kb/gene) and a high content of transposable elements (>45% of the sequence). Six genes (56B23_g3, g5, g7, g8, g9, and g10) have perfect matches (>98% identity) with tomato expressed sequence tags. Two genes (56B23_g1 and g6), which share <98% sequence identity with expressed sequence tags, were confirmed for transcriptional activity by reverse transcription-PCR. The genes were not uniformly distributed along the sequence and grouped into gene islands separated by stretches of retrotransposons, forming a pattern similar to that found in the gene-rich regions of the large genomes of maize (Zea mays) and Triticeae. Long terminal repeat retrotransposons account for 60% of the TE sequence length. Sixteen of 55 TEs were completely new and remain unclassified. Surprisingly, five of the seven identified DNA transposons were closely associated with coding regions. The action of transposable elements and DNA rearrangements form the molecular basis of the dynamic genome evolution at the FER locus. Multiple rounds of genome duplication in Arabidopsis (Arabidopsis thaliana) and subsequent gene loss have generated a mosaic pattern of conservation between tomato and Arabidopsis orthologous sequences. Our data show that the distal parts of pericentromeric heterochromatin may contain many valuable genes and that these regions form an evolutionary active part of the tomato genome.
1 This work was supported by the Chinese Ministry of Science and Technology (grant nos. 2004AA222061 to H.-Q.L. and 2002AA225011 to Z.C.), by the Chinese National Science Foundation (Talented Young Scientist grant no. 30225029 to H.-Q.L. and no. 30325008 to Z.C.), and by the Swiss National Science Foundation (grant nos. 3100–65114 to B.K. and 31–55288.98. to H.-Q.L.). 2 These authors contributed equally to the paper. [w] The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.104.058099. * Corresponding author; e-mail hqling{at}genetics.ac.cn; fax 86–10–64860377. Received December 11, 2004; returned for revision April 12, 2005; accepted April 13, 2005. This article has been cited by other articles:
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