Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

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  • Reconstruction of monocotelydoneousproto-chromosomes reveals faster evolutionin plants than in animalsJerome Salsea,1, Michael Abrouka, Stephanie Bolota, Nicolas Guilhota, Emmanuel Courcelleb, Thomas Farautc,Robbie Waughd, Timothy J. Closee, Joachim Messingf, and Catherine Feuilleta

    aInstitut National de la Recherche Agronomique, Unite Mixte de Recherche 1095, Genetique, Diversite et Ecophysiologie des Cereales, Universite BlaisePascal, 234 Avenue du Brezet, 63100 Clermont Ferrand, France; bInstitut National de la Recherche Agronomique, Centre National de la RechercheScientifique, Unite Mixte de Recherche 441/2594, Laboratoire des Interactions Plantes-Microorganismes, 31326 Castanet Tolosan, France; cInstitut Nationalde la Recherche Agronomique Unite Mixte de Recherche 444, BP 52627, 31326 Castanet Tolosan, France; dScottish Crop Research Institute, Invergowrie,Dundee, DD2 5DA, Scotland, United Kingdom; eDepartment of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside, CA92521-0124; and fThe Plant Genome Initiative at Rutgers, Waksman Institute, Piscataway, NJ 08854

    Edited by Eviatar Nevo, Institute of Evolution, Haifa, Israel, and approved June 30, 2009 (received for review March 5, 2009)

    Paleogenomics seeks to reconstruct ancestral genomes from thegenes of todays species. The characterization of paleo-duplicationsrepresented by 11,737 orthologs and 4,382 paralogs identified in fivespecies belonging to three of the agronomically most importantsubfamilies of grasses, that is, Ehrhartoideae (rice) Panicoideae (sor-ghum, maize), and Pooideae (wheat, barley), permitted us to proposea model for an ancestral genome with a minimal size of 33.6 Mbstructured in five proto-chromosomes containing at least 9,138 pre-dicted proto-genes. It appears that only four major evolutionaryshuffling events (, , , and ) explain the divergence of these fivecereal genomes during their evolution from a common paleo-ances-tor. Comparative analysis of ancestral gene function with rice as areference indicated that five categories of genes were preferentiallymodified during evolution. Furthermore, alignments between thefive grass proto-chromosomes and the recently identified seveneudicot proto-chromosomes indicated that additional very activeepisodes of genome rearrangements and gene mobility occurredduring angiosperm evolution. If one compares the pace of primateevolution of 90 million years (233 species) to 60 million years of thePoaceae (10,000 species), change in chromosome structure throughspeciation has accelerated significantly in plants.

    grasses paleogenomics

    Paleogenomics, the study of ancestral genome structures, allowsthe identification and characterization of mechanisms (e.g.,duplications, translocations, and inversions) that have shaped ge-nome species during their evolution and provides a framework tobetter integrate results from genetics, genomics, and comparativeanalyses. Studies of fossils and lower taxa organisms [Neanderthal(1), Echinoderms (2), Mammoth (3), Sponge (4), and Moss (5)]have yielded unprecedented information on the evolution of animalspecies and the relationships between them. When fossil DNA isnot available, paleogenomics can be performed through large-scale comparative analyses of actual species and through ancestormodeling.

    In silico colinearity studies and ancestral genome reconstructionin mammals have been facilitated by a generally moderate reshuf-fling of chromosomal segments since their divergence from acommon ancestor 130 million years ago (mya) (69). Recently,Nakatani et al. (10) provided an integrated view of vertebratepaleogenomics with an ancestor of 10 to 13 proto-chromosomes. Incontrast to mammals, paleogenomics has been poorly investigatedin plants as angiosperm species have undergone serial wholegenome or segmental duplications, diploidization, small-scale re-arrangements (translocations, gene conversions), and gene copyingevents that make comparative studies between and within themonocotyledon (mainly grasses) and eudicot families very chal-lenging. For the eudicots, two scenarios based on comparisons

    between the grape, Arabidopsis thaliana, and poplar genome se-quences have been proposed recently. In the first one, the eudicotswere proposed to descend from a paleo-hexaploid ancestor withseven proto-chromosomes (11) whereas, in the second, they orig-inated from a paleo-tetraploid ancestor with seven proto-chromosomes (12). Comparative genomics studies in the monocotsand most particularly in grasses has been the subject of intenseresearch in the past decade (13, 14). Recently, we published anoriginal and robust method for the identification of orthologousregions between genomes as well as for the detection of duplicationswithin genomes based on integrative sequence alignment criteriacombined with a statistical validation (15). This approach has beenapplied to identify paleo-duplications between the rice, wheat,sorghum, and maize genomes and to propose a common ancestorfor the grasses with five proto-chromosomes (15). However, se-quence alignments were performed only between rice and wheat,and the relationships with the maize and sorghum genomes wereestablished using lower resolution, marker-based macrocolinearitystudies. Here, we were able to use a much higher resolution todelineate synteny blocks from sequences of the maize, rice, andsorghum genomes (16, 17), as well as from large sets of geneticallymapped genes in wheat and barley. This difference in resolution wascritical to estimate the size and gene content of the grass ancestralgenome as well as identify classes of genes that were particularlyaffected by rearrangements during the evolution of these species.Finally, comparison of the five monocot proto-chromosomes withthe seven eudicot proto-chromosomes demonstrated the fasterpace of changes in chromosomal structure in the plant versus theanimal kingdom, particularly in respect to conserved gene orderand mobility.

    ResultsCereal Genome Synteny and Duplication Pattern. By using alignmentparameters and statistical tests described in ref. 15 we analyzed thesyntenic relationships between the rice, maize, sorghum, wheat, andbarley genomes using various resources as described in SI Appendix.Using rice as a reference genome with 41,046 gene models, weidentified 4,454 maize orthologs (defining 30 syntenic blocks), 6,147sorghum orthologs (12 syntenic blocks), 827 wheat orthologs (13

    Author contributions: J.S. designed research; J.S., M.A., and S.B. performed research; N.G.,E.C., T.F., R.W., T.J.C., and J.M. contributed new reagents/analytic tools; J.S., M.A., and S.B.analyzed data; and J.S. and C.F. wrote the paper.

    The authors declare no conflict of interest.

    This article is a PNAS Direct Submission.

    1To whom correspondence should be addressed at: INRA/UBP UMR GDEC 1095, Domainede Crouelle, 234 Avenue du Brezet 63100 Clermont Ferrand, France. E-mail: jsalse@clermont.inra.fr.

    This article contains supporting information online at www.pnas.org/cgi/content/full/0902350106/DCSupplemental.

    1490814913 PNAS September 1, 2009 vol. 106 no. 35 www.pnas.orgcgidoi10.1073pnas.0902350106

    http://www.pnas.org/cgi/data/0902350106/DCSupplemental/Appendix_PDFhttp://www.pnas.org/cgi/content/full/0902350106/DCSupplementalhttp://www.pnas.org/cgi/content/full/0902350106/DCSupplemental

  • syntenic blocks), and 309 barley orthologs (13 syntenic blocks) (Fig.1A and Fig. S1 in SI Appendix). Thus, similar numbers of syntenicblocks were identified in genomes for which a complete sequenceis available and in those with limited sets of sequence data (e.g.,barley and wheat) thereby demonstrating the efficiency of themethod. In maize, the higher number of blocks reflects the recenttetraploidization of the genome. In total, 11,737 orthologous pairs(Table S1 in SI Appendix) and 68 synteny blocks that covered 99%,82%, 99%, 91%, and 84% of the rice, maize, sorghum, wheat, andbarley genomes, respectively, were observed. A recent comparisonof the sorghum genome with different numbers of gene models forrice and maize identified a set of 11,502 ancestral gene families (17),a number that is very close to ours, indicating the robustness ofsynteny alignments. This result complements and greatly refinesprevious marker-based and low resolution, sequence-based mac-rocolinearity studies [for review Salse and Feuillet (13)], therebyallowing us to better characterize the duplication patterns in thedifferent genomes.

    Two methods can be used for the in silico identification andcharacterization of genome duplications. The most robust anddirect approach, called intragenome duplication (ID), consists inaligning a genome sequence against itself with stringent alignmentcriteria and statistical validation. We have used it recently to initiatepaleogenomics studies in grasses (15). The second indirect ap-proach, called double synteny (DS) or doubly conserved syn-teny (DCS), is based on the identification of chromosomal dupli-cations through the detection of regions showing a high proportionof gene matches on two different chromosomes within a genomeand corresponding to two syntenic regions in another genome (forreview, see ref. 13). In this study, we reassessed duplications in the

    rice, maize, sorghum, wheat, and barley genomes through a com-bination of ID and DS approaches with the stringent alignmentparameters defined in Salse et al. (15) (SI Appendix). Ten (383paralogs), 17 (3,469 paralogs), 8 (390 paralogs), 10 (102 paralogs),and 9 (38 paralogs) intragenomic duplications were identified andcharacterized in the rice, maize, sorghum, wheat, and barley ge-nomes, respectively (Fig. 1B and Fig. S2 in SI Appendix). In total,54 interchromosomal duplications were characterized individuallyin the five cereal genomes, compared with the 31 previouslyidentified in the rice (18), sorghum (19), barley (2