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NM F SR W E V KL QX R W J O P F U N TS I J J OC B A F C A BM XH QXBLKV H F B XI N E C TB U B AO H D QXH B V VK B N I A A W RH R 110 Mb X W V S Q

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NM F SR W E V KL QX R W J O P F U N TS I J J OC B A F C A BM XH QXBLKV H F B XI N E C TB U B AO H D QXH B V VK B N I A A W RH R 110 Mb X W V S Q
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  NATURE GENETICS   VOLUME 43 | NUMBER 10 | OCTOBER 2011 1035 LETTERS Brassica nigra  (B genome) and B. oleracea  (C genome) having formed the amphidiploid species B. juncea  (A and B genomes), B. napus  (A and C genomes) and B. carinata  (B and C genomes) by hybridiza-tion. Comparative physical mapping studies have confirmed genome triplication in a common ancestor of B. oleracea 11  and B. rapa 12  since its divergence from the  A. thaliana  lineage at least 13–17 MYA 6,7,13 .Using 72× coverage of paired short read sequences generated by Illumina GA II technology and stringent assembly parameters, we assembled the genome of the B. rapa  ssp.  pekinensis  line Chiifu-401-42 and analyzed the assembly (Online Methods and Supplementary Note ). The final assembly statistics are summarized in Table 1 . The assembled sequence of 283.8 Mb was estimated to cover >98% of the gene space ( Supplementary Table 1 ) and is greater than the previous estimated size of the euchromatic space, 220 Mb 14 . The assembly showed excellent agreement with the previously reported chromosome A03 (ref. 15) and with 647 bacterial artificial chromosomes (BACs) 14  (Online Methods) sequenced by Sanger technology. Integration with 199,452 BAC-end sequences produced 159 super scaffolds representing 90% of the assem-bled sequences, with an N50 scaffold (N50 scaffold is a weighted median statistic indicating that 50% of the entire assembly is contained in scaf-folds equal to or larger than this value) size of 1.97 Mb. Genetic mapping of 1,427 markers in B. rapa  allowed us to produce ten pseudo chromo-somes that included 90% of the assembly ( Supplementary Table 2 ).We found the difference in the physical sizes of the  A. thaliana  and B. rapa  genomes to be largely because of transposable elements ( Supplementary Table 3 ). Although widely dispersed throughout the genome, as shown in Figure 1 , the transposon-related sequences were most abundant in the vicinity of the centromeres. We estimated that transposon-related sequences occupy 39.5% of the genome, with the proportions of retrotransposons (with long terminal repeats), DNA transposons and long interspersed elements being 27.1%, 3.2% and 2.8%, respectively ( Supplementary Tables 4  and 5 ).We modeled and analyzed protein coding genes (described in the Online Methods and the Supplementary Note ). We identified 41,174 protein coding genes, distributed as shown in  Figure 1 . The gene models have an average transcript length of 2,015 bp, a coding length of 1,172 bp and a mean of 5.03 exons per gene, both similar to that observed in  A. thaliana 16 . A total of 95.8% of gene models have a match in at least one of the public protein databases and 99.3% are represented among the public EST collections or de novo  Illumina mRNA-Seq data. Among the total 16,917 B. rapa  gene families, only 1,003 (5.9%) appear to be lineage specific, with 15,725 (93.0%) shared with  A. thaliana 16  and 9,909 (58.6%) also shared by Carica papaya 17  and Vitis vinifera 18  ( Fig. 2 ). The genome of the mesopolyploid crop species Brassica rapa The Brassica rapa  Genome Sequencing Project Consortium We report the annotation and analysis of the draft genome sequence of Brassica rapa  accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa  genome, which has undergone genome triplication. We used  Arabidopsis thaliana  as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica  species. The B. rapa  genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica  oil and vegetable crops. Model species have provided valuable insights into angiosperm (flowering plant) genome structure, function and evolution. For example,  A. thaliana  has experienced two genome duplications since its divergence from Carica , with rapid DNA sequence divergence, extensive gene loss and fractionation of ancestral gene order eroding the resemblance of  A. thaliana  to ancestral Brassicales 1 . Compared with an ancestor at just a few million years ago,  A. thaliana  has undergone a ~30% reduction in genome size 2  and 9–10 chromosomal rearrangements 3,4  that differentiate it from its sister species  Arabidopsis lyrata . Whole-genome duplication has been observed in all plant genomes sequenced to date.  A. thaliana  has undergone three paleo-polyploidy events 5 : a paleohexaploidy ( γ  ) event shared with most dicots (asterids and rosids) and two paleotetraploidy events ( β  then α ) shared with other members of the order Brassicales. B. rapa  shares this complex history but with the addition of a whole-genome triplication (WGT) thought to have occurred between 13 and 17 million years ago (MYA) 6,7 , making ‘mesohexaploidy’ a characteristic of the Brassiceae tribe of the Brassicaceae 8 . Brassica  crops are used for human nutrition and provide opportuni-ties for the study of genome evolution. These crops include important  vegetables ( B. rapa  (Chinese cabbage, pak choi and turnip) and Brassica oleracea  (broccoli, cabbage and cauliflower)) as well as oilseed crops ( Brassica napus , B. rapa , Brassica juncea  and Brassica carinata ), which provide collectively 12% of the world’s edible vegetable oil production 9 . The six widely cultivated Brassica  species are also a classical example of the importance of polyploidy in botanical evolution, described by ‘U’s triangle’ 10 , with the three diploid species B. rapa  (A genome), A full list of members appears at the end of the paper.Received 7 March 2011; accepted 3 August 2011; published online 28 August 2011; doi:10.1038/ng.919  1036 VOLUME 43 | NUMBER 10 | OCTOBER 2011 NATURE GENETICS LETTERS We analyzed the organization and evolution of the genome (as described in the Online Methods and the Supplementary Note ). B. rapa ’s close relationship to  A. thaliana  allows  Arabidopsis  to be used as an outgroup for investigating the adaptation of the Brassica  lineage to the triplicated state. In total, 108.6 Mb (90.01%) of the  A. thaliana  genome and 259.6 Mb (91.13%) of the B. rapa  genome assembly were contained within collinear blocks. We confirmed the almost complete triplication of the B. rapa  genome relative to  A. thaliana  ( Fig. 3 ) and (by inference) to the postulated Brassicaceae ancestral genome ( n  = 8). The gene paralogues anchored in the triplicated segments ( Supplementary Fig. 1 ) and their orthologs ( Supplementary Table 6 ) dated the meso-hexaploidy event to between 5 and 9 MYA ( Supplementary Fig. 2 ), which is more recent than has been reported previously  13 .The Brassica  mesohexaploidy offers an opportunity to study gene retention in triplicated genomes. Assuming an initial count of protein coding genes similar to that of  A. thaliana  (around 30,000), the newly formed hexaploid would have about 90,000 genes, of which we can now identify only 41,174. This is typical of the substantial gene loss that occurs following polyploid formation in eukaryotes 19–21 . We identified each of the orthologous blocks in the B. rapa  genome corresponding to ancestral blocks using collinearity between orthologs on the genomes of B. rapa  and  A. thaliana  and found significant disparity in gene loss across the triplicated blocks ( Supplementary Fig. 3 ). Of the 21 regions of conserved synteny, 20 showed significant deviations from equivalent gene frequen-cies ( P   < 0.05) ( Supplementary Fig. 4 ). To illustrate this variation, we concatenated the least fractionated blocks (LF), the medium fractionated blocks (MF1) and the most fractionated blocks (MF2) and calculated the proportions of genes retained in each of these sub-genomes relative to  A. thaliana . The LF sub-genome retains 70% of the genes found in  A. thaliana , whereas the MF1 and MF2 sub-genomes retain substantially lower proportions of    retained genes (46% and 36%, respectively; Fig. 4 ). Based on the analysis of synonymous base substitution rates ( K  s  values), the pairwise divergences between the three sub-genomes are indistin-guishable from each other ( Supplementary Table 7 ). Our observation of differentially fractionated sub-genomes is consistent with the hypothesis that the sub-genomes MF1 and MF2 underwent substantial fractiona-tion in a tetraploid nucleus before fractionation commenced in the LF genome in a more recently formed hexaploid. However, biased fractiona-tion following tetraploidy (albeit less extreme than we observed) has been reported in  A. thaliana 22  and maize 23 , where it was hypothesized to be the result of differential epigenetic marking of the parent genomes (resulting in differential gene silencing and consequential fraction), rep-resenting an alternative hypothesis.The retention of extensive collinear genome blocks provides a potential opportunity for ectopic DNA recombination. By finding and comparing homologous gene quartets, including two α  or β  duplicates in Brassica  and their respective orthologs in  Arabidopsis , we noted that, respectively, 25% and 30% of Brassica  and  Arabidopsis  duplicates are more similar to their intragenomic paralog than to their intergenomic ortholog, suggesting appreciable gene conversion since the divergence of these lineages ( Supplementary Note ). The sizes of the affected regions  vary from 10 bp to >2 kb, with a majority of these apparent conversion events occurring in parallel in both species. Genes proximal to telo-meres tend to have lower nucleotide substitution rates than distal genes ( P   = 0.0004), which is likely to be a result of higher conversion rates in the former and is consistent with prior findings in grasses 24,25 .The gene dosage hypothesis 26  predicts that gene functional categor-ies encoding products that interact with one another or in networks Table 1 Summary of the final assembly statistics Contig sizeContig numberScaffold sizeScaffold numberN905,59310,564357,979159N8010,9847,292773,703104N7015,9475,3081,257,65377N6021,2293,8741,452,35556N5027,2942,7781,971,13739Total size264,110,991283,823,632Total number (>100 bp)60,52140,549Total number (>2 kb)14,207794 A01A02A03A04A05A06A07A08A09A100M 10M 20M 30MRetrotransposonsDNA transposonsGenes (introns)Genes (exons) Figure 1  Chromosomal distribution of the main B. rapa   genome features. Area charts quantify retrotransposons, genes (exons and introns) and DNA transposons. The x   axis denotes the physical position along the B. rapa   chromosomes in units of million (M) bases. C. papaya 19,09313,533  A. thaliana 29,13916,985 B. rapa 32,54316,9178213,660721,2281,0439,90971708912491,1131181,41248 V. vinifera 22,60813,8101,003 Figure 2  Venn diagram showing unique and shared gene families between and among four sequenced dicotyledonous species ( B. rapa  , A. thaliana  , C. papaya   and V. vinifera  ).  NATURE GENETICS   VOLUME 43 | NUMBER 10 | OCTOBER 2011 1037 LETTERS should be over retained and genes with products that do not interact with other gene products should be under retained. In accordance with this hypothesis, we found B. rapa  transcription factors with a detectable ortholog in  A. thaliana  to be significantly over retained ( Supplementary Table 8  and Supplementary Note ). We obtained similarly consistent results for genes encoding known protein subunits of cytoplasmic ribosomes and for genes known to be involved with the proteosome. We found under retention of genes encoding products with few interactions, specifically those associated with DNA repair, nuclease activity, binding and the chloroplast ( Supplementary Table 9 ). The Gene Ontology annotation classes of over retained genes sug-gests that genome triplication may have expanded gene families that underlie environmental adaptability, as observed in other polyploid species 27 . Genes with Gene Ontology terms associated with response to important environmental factors, including salt, cold, osmotic stress, light, wounding, pathogen (broad spectrum) defense and both cadmium and zinc ions, were over retained ( Fig. 5 ). Genes respond-ing to plant hormones (jasmonic acid, auxin, salicylic acid, ethylene, brassinosteroid, cytokinin and abscisic acid) were also over retained.Under selection, Brassica  species have a remarkable propensity for the development of morphological variants 28 ; we analyzed factors poten-tially involved in this development ( Supplementary Note ). One factor may be a general acceleration of nucleotide substitution rates. For 2,275 orthologous groups of genes in B. rapa ,  A. thaliana , papaya and grape ( Supplementary Table 10 ), the nucleotide substitution rates in B. rapa  were greater than in the other plants, with average K  s  ( K  s  is the ratio of the number of synonymous substitutions per synonymous site) and K  a ( K  a is the ratio of the number of non-synonymous substitutions per non- synonymous site) values 69% and 24%, respectively, greater than papaya and 1% and 7%, respectively, greater than  A. thaliana  ( Supplementary Table 11 ). The much slower evolutionary rate in papaya may be explained by its longer generation time as a perennial. Another factor may be expan-sion of auxin-related gene families, as auxin controls many plant growth and morphological developmental processes 29–31 . We identified 347 B. rapa  genes related to auxin synthesis, transportation, signal transduc-tion and inactivation, in contrast to 187 such genes present in  A. thaliana  ( Supplementary Tables 12 and 13  and Supplementary Figs. 5 – 14 ). The TCP gene family is important in the evolution and specification of plant morphology  32 . This family has been amplified in B. rapa , which contains 39 TCP genes, which is more than  A. thaliana  (24), grape (19) or papaya (21) ( Supplementary Fig. 15 ). The regulation of flowering is key to many Brassica  morphotypes. Mesohexaploidy has had contrasting effects on the genes involved. FLC   ( FLOWERING LOCUS C  ) 33  has three orthologs in B. rapa  as a consequence of the WGT ( Supplementary Fig. 16 ). Likewise, five of six B. rapa VRN1  ( VERNALIZATION1 ) genes 34   U    C   H   R   5   C   H   R   4   C   H   R   3   C   H   R   2   C   H   R   1   9   0   M   b   7   0   M   b   5   0   M   b   3   0   M   b   1   0   M   b 10 Mb   A   0  1  A   0   2  A   0   3  A   0  4  A   0   5  A   0   6  A   0   7  A   0   8  A   0   9  A  1   0 30 Mb50 Mb70 Mb90 Mb110 Mb130 Mb150 Mb170 Mb190 Mb210 Mb230 Mb250 Mb    1   1   0   M   b TNMDWFSRWEVKLQXRWJPFUNIJJABFCABMXHQXBLKVHFBXNECTBUBAOOTSOCIQXHHDBVKVBNIAAWRHRXWVSQRUTPONMLFJIHGKEDCBA Figure 3  Segmental collinearity of the genomes of B. rapa   and A. thaliana  . Conserved collinear blocks of gene models are shown between the ten chromosomes of the B. rapa   genome (horizontal axis) and the five chromosomes of the A. thaliana   genome (vertical axis). These blocks are labeled A to X and are color coded by inferred ancestral chromosome following established convention. 100LFMF1 and MF28060    P  e  r  c  e  n   t  o   f  o  r   t   h  o   l  o  g  s  r  e   t  a   i  n  e   d 40200020Chr1Chr2Chr3Chr4Chr54060  A. thaliana  chromosome (Mb)80100120 Figure 4  The density of orthologous genes in three subgenomes (LF, MF1 and MF2) of B. rapa   compared to A. thaliana.  The x   axis denotes the physical position of each A. thaliana   gene locus. The  y   axis denotes the percentage of retained orthologous genes in B. rapa   subgenomes around each A. thaliana   gene, where 500 genes flanking each side of a certain gene locus were analyzed, giving a total window size of 1,001 genes.  1038 VOLUME 43 | NUMBER 10 | OCTOBER 2011 NATURE GENETICS LETTERS  produced by the WGT have been preserved ( Supplementary Fig. 17 ). However, GI   ( GIGANTEA ) genes 35  have been limited to only one copy ( Supplementary Fig. 18 ), as have the SVP   ( SHORT VEGETATIVE PHASE ) genes 36  ( Supplementary Fig. 19 ) and each of the three COL  ( CONSTANS-LIKE ) genes 37  ( Supplementary Fig. 20 ).The comparison of the genomes of B. rapa  and  A. thaliana , as for pre- vious comparisons of the cereals sorghum and rice 38 , sheds new light on the evolution of genome evolution in plants important for human nutri-tion. Our growing understanding of the processes shaping the triplicated genome of the mesopolyploid B. rapa  is of relevance not only for closely related crops species, such as B. oleracea  and B. napus , but also for other important crops with triplicated genomes, such as bread wheat. URLs.   Brassica  info, http://www.brassica.info/; GenoScope database, http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/; Hawaii Papaya Genome Project, http://asgpb.mhpcc.hawaii.edu/papaya/;  Arabidopsis  Information Resource, http://www.arabidopsis.org/. METHODS Methods and any associated references are available in the online  version of the paper at http://www.nature.com/naturegenetics/. Accession codes.  This whole-genome shotgun project has been depos-ited at DDBJ/EMBL/GenBank under the accession AENI00000000. The  version described in this paper is the first version, AENI01000000. Full annotation is available at http://brassicadb.org/. Note: Supplementary information is available on the Nature Genetics website. ACKNOWLEDGMENTS This work was primarily funded by the Chinese Ministry of Science and Technology, Ministry of Agriculture, Ministry of Finance, the National Natural Science Foundation of China. Other funding sources included: Core Research Budget of the Non-profit Governmental Research Institution; the European Union 7th Framework Project; funds from Shenzhen Municipal Government of China; the Danish Natural Science Research Council; National Academy of Agricultural Science and the Next-Generation Biogreen21 Program, Rural Development Administration, Korea; the Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Korea; United Kingdom’s Biotechnology and Biological Sciences Research Council; Institute National de la Recherche Agronomique, France; Japanese Kazusa DNA Research Institute Foundation; National Science Foundation, USA; Bielefeld University, Germany; the Australian Research Council; the Australian Grains Research and Development Corporation; Agriculture and Agri-Food Canada; and the National Research Council of Canada’s Plant Biotechnology Institute. See the Supplementary Note  for a full list of support and acknowledgments. AUTHOR CONTRIBUTIONS Principal investigators:  Xiaowu Wang, J. Wu, S.L., Y.B., J.-H.M. and I.B. DNA and transcriptome sequencing:  Bo Wang (group leader), Xiaowu Wang (group leader), B.C. (group leader), Jun Wang (BGI), K.W., J. Wu, S.L., W.H., B.-S.P., I.B., D.E., I.A.P.P., J.-H.M., H.A., Bernd Weisshaar, Shusei Sato, H.H., S.T., A.G.S., Y. Lim, G.B., J.B., C.L., C.G., J.P., S.-J.K., J.A.K., M.T., F.F., E.S., M.G.L., C.K., K.H., Y.N., P.J.B. and C.D. Sequence assembly:  Junyi Wang (group leader), Jun Wang (BGI), D.M., Y. Li, X.X., Bo Liu, Silong Sun, Z.Z., Z.L., Binghang Liu, Q.C., Shu Zhang, Y.B., Zhiwen Wang, X.Z., C.S., J.Y. and J.J. Anchoring to linkage maps:  J. Wu (group leader), W.H. (group leader), G.J.K., Y. Lim, B.-S.P., I.B., J.B., D.E., Yan Wang, Bo Liu, Silong Sun, Jun Wang (Rothamsted), I.A.P.P., J. Meng, Hui Wang, J.D., Y. Liao, Y.B., Haiping Wang, M.J., J.-S.K., S.-R.C., N.R. and A.H. Annotation:  Y.B. (group leader), S.L. (group leader), R.L., W.F., Q.H., F.C., Bo Liu, D.E., J. Min, Jianwen Li, C.P., H.Z., Shunmou Huang, B.C., J.J., H.B., G.L., N.D. and M.T. Stabilizing the genome of a polyploidy dicotyledonous species:  F.C. (group leader), Sanwen Huang (group leader), Y.B., Xiaowu Wang, B. Li, S.C., Y.Y., J.X. and C.T. Comparative genomics:  Xiaowu Wang (group leader), J.C.P. (group leader), Xiyin Wang (group leader), I.B., F.C., H.T., G.C., H.G., T.-H.L., Jinpeng Wang and Zhenyi Wang. Retention of genes duplicated by polyploidy:  M.F. (group leader), A.H.P. (group leader), F.C., H.T., Bo Liu, Silong Sun, L.F., Z.X., M.Z., Jingping Li, H.J. and X.T. Characteristics of a crop genome:  J. Wu (group leader), X.L. (group leader), R.S., Hanzhong Wang, Y.D., Xiaowu Wang, Hui Wang, J.D., D.S., Y.Q., Shujiang Zhang, F.L., L.W. and Yupeng Wang. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. Published online at http://www.nature.com/naturegenetics/. Reprints and permissions information is available online at http://www.nature.com/ reprints/index.html. 1. Tang, H. et al.  Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res.   18 , 1944–1954 (2008).2. Johnston, J.S. et al.  Evolution of genome size in Brassicaceae. Ann. Bot.   95 , 229–235 (2005).3. Koch, M.A. & Kiefer, M. Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species— Capsella rubella  , Arabidopsis    lyrata   subsp Petraea, and A. thaliana  . Am. J. Bot.   92 , 761–767 (2005).4. Yogeeswaran, K. et al.  Comparative genome analyses of Arabidopsis   spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana  . Genome Res.   15 , 505–515 (2005).5. Bowers, J.E., Chapman, B.A., Rong, J. & Paterson, A.H. 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Genome analysis in Brassica   with special reference to the experimental formation of B. napus   and peculiar mode of fertilization. Jap. J. Bot.   7 , 389–452 (1935).11. O’Neill, C.M. & Bancroft, I. Comparative physical mapping of segments of the genome of Brassica oleracea   var. alboglabra   that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana  . Plant J.   23 , 233–243 (2000).12. Park, J.Y. et al.  Physical mapping and microsynteny of Brassica rapa   ssp. pekinensis   genome corresponding to a 222 kbp gene-rich region of Arabidopsis   chromosome 4 and partially duplicated on chromosome 5. Mol. Genet. Genomics    274 , 579–588 (2005).13. Beilstein, M.A., Nagalingum, N.S., Clements, M.D., Manchester, S.R. & Mathews, S. Dated molecular phylogenies indicate a Miocene srcin for Arabidopsis    thaliana  . Proc. Natl. Acad. Sci. USA   107 , 18724–18728 (2010). 1.0 a b       1 ,      0      2      1      5      3      5      2      9      8      1      8      1      3      0      4      7      9      6      3      8      5      1 ,      0      7      1      1      8      7      1      5 ,      9      7      6      2 ,      3      4      6 0.80.60.4       R     a      t      i     o 0.20   4 .   7  8     ×    1  0   –  2  1    R   E  1 .  0  1     ×    1  0   –  1  8    R   H   5 .  2  4     ×    1  0   –  2  0    T   F  3 .   5  2     ×    1  0   –  2  0   C   R GO category   3 .  2  9     ×    1  0   –  1   5   C   W  /    T  o   t  a   l One- or two-copy genesThree-copy genes1.0       4      9      2      2      4      7      8      2      7      4      6      9      8      9      8      3      1      1      1      1      8      3      4      7      7      1      8      9      9 ,      2      9      3      9 ,      0      2      9 0.80.60.4       R     a      t      i     o 0.20   1 .  9  6     ×    1  0   –  2  1    R   E  6 .  4  6     ×    1  0   –  1  8    R   H  4 .  8  2     ×    1  0   –  3  1    T   F  1 .   7  0     ×    1  0   –  1  2   C   R GO category   1 .  6  1     ×    1  0   –  1  1   C   W  /    T  o   t  a   l One-copy genesTwo- or three-copy genes Figure 5  The over retention genes in B. rapa   showing strong bias. The x   axis denotes the gene category. The  y   axis denotes the ratio of different copies in each category. The number of B. rapa   orthologs of each class is indicated above each bar. RE, response to environment; RH, response to hormone; TF, transcription factor; CR, cytosolic ribosome; CW, cell wall. ( a ) The orange bar is the ratio of one- or two-copy orthologs, and the light green bar is the ratio of three copies. ( b ) The yellow bar is the ratio of one-copy orthologs, and the dark green bar is the ratio of two- or three-copy orthologs. The last category is the total sets of all orthologs listed as a control. The P   value of each category is indicated under the bars. GO, Gene Ontology.  NATURE GENETICS   VOLUME 43 | NUMBER 10 | OCTOBER 2011 1039 LETTERS 14. Mun, J.H. et al.  Genome-wide comparative analysis of the Brassica rapa   gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol.   10 , R111 (2009).15. 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Xiaowu Wang 1 , Hanzhong Wang 2 , Jun Wang 3,4 , Rifei Sun 1 , Jian Wu 1 , Shengyi Liu 2 , Yinqi Bai 3 , Jeong-Hwan Mun 5 , Ian Bancroft 6 , Feng Cheng 1 , Sanwen Huang 1 , Xixiang Li 1 , Wei Hua 2 , Junyi Wang 3 , Xiyin Wang 7–9 , Michael Freeling 10 , J Chris Pires 11 , Andrew H Paterson 9 , Boulos Chalhoub 12 , Bo Wang 3 , Alice Hayward 13,14 , Andrew G Sharpe 15 , Beom-Seok Park  5 , Bernd Weisshaar 16 , Binghang Liu 3 , Bo Li 3 , Bo Liu 1 , Chaobo Tong 2 , Chi Song 3 , Christopher Duran 13,17 , Chunfang Peng 3 , Chunyu Geng 3 , Chushin Koh 15 , Chuyu Lin 3 , David Edwards 13,17 , Desheng Mu 3 , Di Shen 1 , Eleni Soumpourou 6 , Fei Li 1 , Fiona Fraser 6 , Gavin Conant 18 , Gilles Lassalle 19 , Graham J King 20 , Guusje Bonnema 21 , Haibao Tang 10 , Haiping Wang 1 , Harry Belcram 12 , Heling Zhou 3 , Hideki Hirakawa 22 , Hiroshi Abe 23 , Hui Guo 9 , Hui Wang 1 , Huizhe Jin 9 , Isobel A P Parkin 24 , Jacqueline Batley  13,14 , Jeong-Sun Kim 5 , Jérémy Just 12 , Jianwen Li 3 , Jiaohui Xu 3 , Jie Deng 1 , Jin A Kim 5 , Jingping Li 9 , Jingyin Yu 2 , Jinling Meng 25 , Jinpeng Wang 7,8 , Jiumeng Min 3 , Julie Poulain 26 , Jun Wang 20 , Katsunori Hatakeyama 27 , Kui Wu 3 , Li Wang 7,8 , Lu Fang 1 , Martin Trick  6 , Matthew G Links 24 , Meixia Zhao 2 , Mina Jin 5 , Nirala Ramchiary  28 , Nizar Drou 6 , Paul J Berkman 13,17 , Qingle Cai 3 , Quanfei Huang 3 , Ruiqiang Li 3 , Satoshi Tabata 22 , Shifeng Cheng 3 , Shu Zhang 3 , Shujiang Zhang 1 , Shunmou Huang 2 , Shusei Sato 22 , Silong Sun 1 , Soo-Jin Kwon 5 , Su-Ryun Choi 28 , Tae-Ho Lee 9 , Wei Fan 3 , Xiang Zhao 3 , Xu Tan 9 , Xun Xu 3 , Yan Wang 1 , Yang Qiu 1 , Ye Yin 3 , Yingrui Li 3 , Yongchen Du 1 , Yongcui Liao 1 , Yongpyo Lim 28 , Yoshihiro Narusaka 29 , Yupeng Wang 8 , Zhenyi Wang 7,8 , Zhenyu Li 3 , Zhiwen Wang 3 , Zhiyong Xiong 11  & Zhonghua Zhang 1 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China. 2 Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China. 3 BGI-Shenzhen, Shenzhen, China. 4 Department of Biology, University of Copenhagen, Copenhagen, Denmark. 5 Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea. 6 John Innes Centre, Norwich Research Park, Colney, Norwich, UK. 7 Center for Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei, China. 8 School of Sciences, Hebei United University, Tangshan, Hebei, China. 9 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA. 10 Department of Plant and Microbial Biology, University of California, Berkeley, California, USA. 11 Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA. 12 Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherché 1165, (Inland Northwest Research Alliance-Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry, France. 13 University of Queensland, School of Agriculture and Food Sciences, Brisbane, Queensland, Australia. 14 Australian Research Council Centre of Excellence for Integrative Legume Research, Brisbane, Queensland, Australia. 15 National Research Council-Plant Biotechnology Institute, Saskatoon, Saskatchewan, Canada. 16 Center for Biotechnology, Bielefeld University, Bielefeld, Germany. 17 Australian Centre for Plant Functional Genomics, Brisbane, Queensland, Australia. 18 Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA. 19 Inland Northwest Research Alliance-Agrocampus Rennes–University of Rennes 1, Unité Mixte de Recherché 118 Amélioration des Plantes et Biotechnologies Végétales, Le Rheu Cedex, France. 20 Centre for Crop Genetic Improvement, Rothamsted Research, West Common, Harpenden, UK. 21 Droevendaalsesteeg 1, Wageningen University, Wageningen, The Netherlands. 22 Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, Japan. 23 Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Japan. 24 Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada. 25 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. 26 Genoscope, Institut de Génomique du Commissariat à l’Energie Atomique, 2 rue Gaston Crémieux, Evry, France. 27 National Institute of Vegetable and Tea Science, Tsu, Japan. 28 Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea. 29 Research Institute for Biological Sciences, Okayama, Japan. Correspondence should be addressed to Xiaowu Wang (wangxw@mail.caas.net.cn), Jun Wang (wangj@genomics.org.cn), Hanzhong Wang (wanghz@oilcrops.cn) or R.S. (rifei.sun@caas.net.cn).
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