The Sorghum Genome Sequence: A Core Resource for Saccharinae Genomics
As a taxon noted for large and complex polyploid genomes, a facile genomic model is of especially great importance to the Saccharinae. The genome of Sorghum bicolor (sorghum) offers numerous advantages as such a model, with a physical size (about 730 mbp)
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The Sorghum Genome Sequence: A Core Resource for Saccharinae Genomics Andrew H. Paterson
Abstract As a taxon noted for large and complex polyploid genomes, a facile genomic model is of especially great importance to the Saccharinae. The genome of Sorghum bicolor (sorghum) offers numerous advantages as such a model, with a physical size (about 730 mbp) that is only moderately larger than that of rice, and enjoying the same low level of gene duplication as rice by virtue of a lack of genome duplication for 70 million years. Saccharinae, especially sugarcane, researchers have long exploited comparative genomics to leverage the small and well-mapped sorghum genome in the study and improvement of more complex genomes. The sequencing of the sorghum genome further enhances such leveraging opportunities, also providing insights into genes and genomic features that may contribute to distinguishing features of the Saccharinae. A host of postgenomic tools for sorghum, many described elsewhere in this volume, provide the foundation for use of sorghum as a Saccharinae functional genomics model. Here, we revisit the sequencing and initial analysis of the sorghum genome, providing more detail than could be included in the primary description of the genome and also highlighting planned efforts to increase knowledge of sequence diversity in the species and the genus. Keywords Whole-genome shotgun sequence • Repetitive DNA • Gene repertoire • Recombination • Genome duplication • Sequence diversity • Single-nucleotide polymorphism
A.H. Paterson (*) Plant Genome Mapping Laboratory, Departments of Crop and Soil Science, Plant Biology, and Genetics, University of Georgia, Athens, GA, USA e-mail: [email protected]; [email protected] A.H. Paterson (ed.), Genomics of the Saccharinae, Plant Genetics and Genomics: Crops and Models 11, DOI 10.1007/978-1-4419-5947-8_5, © Springer Science+Business Media New York 2013
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Rationale for Sorghum as a Saccharinae Botanical and Genomic Model
The small genome of sorghum has long been an attractive model for advancing understanding of the structure, function, and evolution of grass genomes. Sorghum is representative of many grasses of tropical origin in that it has “C4” photosynthesis, using complex biochemical and morphological specializations to improve carbon assimilation at high temperatures. By contrast, rice, the first grass genome to be sequenced, is more representative of temperate grasses, using “C3” photosynthesis. Sorghum and rice each share the distinction, as does Brachypodium (Initiative 2010) of a lack of genome duplication since an event in a common ancestor of the three about 70 mya (Paterson et al. 2004b). The resulting low levels of gene duplication make these three taxa attractive models for functional genomics. However, sorghum is much more closely related than rice to several major crops with complex genomes and high levels of gene duplication. Sorghum and Zea (maize, the leading US crop with a farm-gate value of $15–20 billion/year, in the Andr
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