Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

Florent Murat 1 Rongzhi Zhang 1 Sébastien Guizard 2 Haris Gavranovic 3 Raphael Flores 4 Delphine Steinbach 4 Hadi Quesneville 4 Eric Tannier 5, 6 Jérôme Salse 1
2 PCSV
LPC - Laboratoire de Physique Corpusculaire - Clermont-Ferrand
5 BEAGLE - Artificial Evolution and Computational Biology
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558, Inria Grenoble - Rhône-Alpes, LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information
Abstract : We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, “DicotSyntenyViewer” (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.
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Submitted on : Friday, March 20, 2015 - 3:59:32 PM
Last modification on : Thursday, February 20, 2020 - 7:22:26 PM

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Florent Murat, Rongzhi Zhang, Sébastien Guizard, Haris Gavranovic, Raphael Flores, et al.. Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩. ⟨hal-01133906⟩

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