Comparative Genomics of Grasses: A Saccharinae-Centric View
Analysis of whole-genome sequences has revealed beyond doubt that all grasses are paleopolyploid, sharing at least one and probably two genome duplications since their divergence from eudicots. Comparative approaches that account for these events have beg
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Comparative Genomics of Grasses: A Saccharinae-Centric View Andrew H. Paterson, Xiyin Wang, Haibao Tang, and Changsoo Kim
Abstract Analysis of whole-genome sequences has revealed beyond doubt that all grasses are paleopolyploid, sharing at least one and probably two genome duplications since their divergence from eudicots. Comparative approaches that account for these events have begun to clarify grass–eudicot genome relationships, which were previously elusive. Within the grasses, the best-characterized clades (panicoid, oryzoid, and pooid) each include sequenced genomes that have not experienced further duplication and have evolved relatively conservatively, providing important models for many additional genomes that have experienced reduplication(s). Concerted evolution of duplicated genes is not uncommon in grass genomes and may be of remarkably long duration, particularly near the terminus of one pair of homoeologs tracing to the most recent of the pan-grass duplications. A general tendency to cyclic gain-loss of chromosome numbers, often in association with genome duplication, is evident in the Saccharinae and other cereals. Grass genomes, as well as those of eudicots are comprised of two qualitatively different “compartments,” classically referred to as euchromatin and heterochromatin based on differential staining in cytological preparations, but now known to vary in many ways from one another and perhaps to provide complementary “environments” facilitating different patterns of gene and genome evolution. A small percentage of genes appear to be grass-specific, being absent from eudicot models, and are a tantalizing target for A.H. Paterson (*) • H. Tang • C. Kim Plant Genome Mapping Laboratory and Departments of Crop and Soil Science, Plant Biology, and Genetics, University of Georgia, 111 Riverbend Road, Athens, GA 30602-6810, USA e-mail: [email protected] X. Wang Plant Genome Mapping Laboratory, Departments of Crop and Soil Science, Plant Biology, and Genetics, University of Georgia, 2091 South Milledge Ave, C67, Athens, GA 30602, USA Center for Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063009, China e-mail: [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_18, © Springer Science+Business Media New York 2013
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early functional analysis but caution is especially warranted in selecting such genes for study. Despite rapid progress in recent years, much of Saccharinae, and indeed Poaceae, diversity remains inadequately explored. A host of additional questions about the evolution of this clade are likely to become answerable with accelerating progress in genome analysis, both adding to fundamental knowledge of botanical diversity and further enhancing the contributions of members of the clade to production of food, feed, fiber, and fuel. Keywords Paleopolyploidy • Concerted evolution • Euchromatin • Heterochrom
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