The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Külahoglu C, Bian C, et al. (2013)
Plant Cell 25(8): 2813-2830.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Cheng, Shifeng; van den Bergh, Erik; Zeng, Peng; Zhong, Xiao; Xu, Jiajia; Liu, Xin; Hofberger, Johannes; de Bruijn, Suzanne; Bhide, Amey S.; Külahoglu, Canan; Bian, Chao; Chen, Jing
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Abstract / Bemerkung
The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-alpha) that is independent of the Brassicaceae-specific duplication (At-alpha) and nested Brassica (Br-a) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.
Erscheinungsjahr
2013
Zeitschriftentitel
Plant Cell
Band
25
Ausgabe
8
Seite(n)
2813-2830
ISSN
1040-4651
Page URI
https://pub.uni-bielefeld.de/record/2915141

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Cheng S, van den Bergh E, Zeng P, et al. The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers. Plant Cell. 2013;25(8):2813-2830.
Cheng, S., van den Bergh, E., Zeng, P., Zhong, X., Xu, J., Liu, X., Hofberger, J., et al. (2013). The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers. Plant Cell, 25(8), 2813-2830. doi:10.1105/tpc.113.113480
Cheng, S., van den Bergh, E., Zeng, P., Zhong, X., Xu, J., Liu, X., Hofberger, J., de Bruijn, S., Bhide, A. S., Külahoglu, C., et al. (2013). The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers. Plant Cell 25, 2813-2830.
Cheng, S., et al., 2013. The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers. Plant Cell, 25(8), p 2813-2830.
S. Cheng, et al., “The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers”, Plant Cell, vol. 25, 2013, pp. 2813-2830.
Cheng, S., van den Bergh, E., Zeng, P., Zhong, X., Xu, J., Liu, X., Hofberger, J., de Bruijn, S., Bhide, A.S., Külahoglu, C., Bian, C., Chen, J., Fan, G., Kaufmann, K., Hall, J.C., Becker, A., Bräutigam, A., Weber, A.P.M., Shi, C., Zheng, Z., Li, W., Lv, M., Tao, Y., Wang, J., Zou, H., Quan, Z., Hibberd, J.M., Zhang, G., Zhu, X.-G., Xu, X., Schranz, M.E.: The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers. Plant Cell. 25, 2813-2830 (2013).
Cheng, Shifeng, van den Bergh, Erik, Zeng, Peng, Zhong, Xiao, Xu, Jiajia, Liu, Xin, Hofberger, Johannes, de Bruijn, Suzanne, Bhide, Amey S., Külahoglu, Canan, Bian, Chao, Chen, Jing, Fan, Guangyi, Kaufmann, Kerstin, Hall, Jocelyn C., Becker, Annette, Bräutigam, Andrea, Weber, Andreas P. M., Shi, Chengcheng, Zheng, Zhijun, Li, Wujiao, Lv, Mingju, Tao, Yimin, Wang, Junyi, Zou, Hongfeng, Quan, Zhiwu, Hibberd, Julian M., Zhang, Gengyun, Zhu, Xin-Guang, Xu, Xun, and Schranz, M. Eric. “The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers”. Plant Cell 25.8 (2013): 2813-2830.
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35 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.
Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH., Genome Biol 20(1), 2019
PMID: 30791939
Efficient inference of homologs in large eukaryotic pan-proteomes.
Sheikhizadeh Anari S, de Ridder D, Schranz ME, Smit S., BMC Bioinformatics 19(1), 2018
PMID: 30257640
PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity.
de Bruijn S, Zhao T, Muiño JM, Schranz EM, Angenent GC, Kaufmann K., BMC Plant Biol 18(1), 2018
PMID: 30577806
Network approaches for plant phylogenomic synteny analysis.
Zhao T, Schranz ME., Curr Opin Plant Biol 36(), 2017
PMID: 28327435
Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes.
Qiu Y, Liu SL, Adams KL., Plant Physiol 174(2), 2017
PMID: 28455403
Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana.
De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y., Plant Cell 29(11), 2017
PMID: 29070508
Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation.
Chica C, Louis A, Roest Crollius H, Colot V, Roudier F., Genome Biol 18(1), 2017
PMID: 29084582
A Specific Transcriptome Signature for Guard Cells from the C4 Plant Gynandropsis gynandra.
Aubry S, Aresheva O, Reyna-Llorens I, Smith-Unna RD, Hibberd JM, Genty B., Plant Physiol 170(3), 2016
PMID: 26818731
Whole-genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms.
Hammoudi V, Vlachakis G, Schranz ME, van den Burg HA., New Phytol 211(1), 2016
PMID: 26934536
Biogeography and diversification of Brassicales: A 103million year tale.
Cardinal-McTeague WM, Sytsma KJ, Hall JC., Mol Phylogenet Evol 99(), 2016
PMID: 26993763
The evolutionary origin of CIPK16: A gene involved in enhanced salt tolerance.
Amarasinghe S, Watson-Haigh NS, Gilliham M, Roy S, Baumann U., Mol Phylogenet Evol 100(), 2016
PMID: 27044608
Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae.
Barker MS, Li Z, Kidder TI, Reardon CR, Lai Z, Oliveira LO, Scascitelli M, Rieseberg LH., Am J Bot 103(7), 2016
PMID: 27313199
A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants.
Nelson AD, Forsythe ES, Devisetty UK, Clausen DS, Haug-Batzell AK, Meldrum AM, Frank MR, Lyons E, Beilstein MA., G3 (Bethesda) 6(9), 2016
PMID: 27440919
Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism.
Liu Z, Tavares R, Forsythe ES, André F, Lugan R, Jonasson G, Boutet-Mercey S, Tohge T, Beilstein MA, Werck-Reichhart D, Renault H., Nat Commun 7(), 2016
PMID: 27713409
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data.
Rawat V, Abdelsamad A, Pietzenuk B, Seymour DK, Koenig D, Weigel D, Pecinka A, Schneeberger K., PLoS One 10(9), 2015
PMID: 26382944
Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.
Sun C, Wu J, Liang J, Schnable JC, Yang W, Cheng F, Wang X., Genome Biol Evol 7(11), 2015
PMID: 26527651
Drivers and dynamics of diversity in plant genomes.
Panaud O, Jackson SA, Wendel JF., New Phytol 202(1), 2014
PMID: 24571694
Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species.
Külahoglu C, Denton AK, Sommer M, Maß J, Schliesky S, Wrobel TJ, Berckmans B, Gongora-Castillo E, Buell CR, Simon R, De Veylder L, Bräutigam A, Weber AP., Plant Cell 26(8), 2014
PMID: 25122153
Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family.
Hofberger JA, Lyons E, Edger PP, Chris Pires J, Eric Schranz M., Genome Biol Evol 5(11), 2013
PMID: 24171911

90 References

Daten bereitgestellt von Europe PubMed Central.

The future of C4 research--maize, Flaveria or Cleome?
Brown NJ, Parsley K, Hibberd JM., Trends Plant Sci. 10(5), 2005
PMID: 15882653
PILER: identification and classification of genomic repeats.
Edgar RC, Myers EW., Bioinformatics 21 Suppl 1(), 2005
PMID: 15961452
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
Stanke M, Morgenstern B., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980513
FPC: a system for building contigs from restriction fingerprinted clones.
Soderlund C, Longden I, Mott R., Comput. Appl. Biosci. 13(5), 1997
PMID: 9367125
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D., Science 313(5793), 2006
PMID: 16973872
The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes.
Schranz ME, Lysak MA, Mitchell-Olds T., Trends Plant Sci. 11(11), 2006
PMID: 17029932
Elaboration of B gene function to include the identity of novel floral organs in the lower eudicot Aquilegia.
Kramer EM, Holappa L, Gould B, Jaramillo MA, Setnikov D, Santiago PM., Plant Cell 19(3), 2007
PMID: 17400892
The evolutionary significance of ancient genome duplications.
Van de Peer Y, Maere S, Meyer A., Nat. Rev. Genet. 10(10), 2009
PMID: 19652647
Pistillata--duplications as a mode for floral diversification in (Basal) asterids.
Viaene T, Vekemans D, Irish VF, Geeraerts A, Huysmans S, Janssens S, Smets E, Geuten K., Mol. Biol. Evol. 26(11), 2009
PMID: 19679752
Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae).
Couvreur TL, Franzke A, Al-Shehbaz IA, Bakker FT, Koch MA, Mummenhoff K., Mol. Biol. Evol. 27(1), 2010
PMID: 19744998
A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development.
Colombo M, Brambilla V, Marcheselli R, Caporali E, Kater MM, Colombo L., Dev. Biol. 337(2), 2009
PMID: 19900437
De novo assembly of human genomes with massively parallel short read sequencing.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J., Genome Res. 20(2), 2009
PMID: 20019144
The ABC model and the diversification of floral organ identity.
Litt A, Kramer EM., Semin. Cell Dev. Biol. 21(1), 2009
PMID: 19948236
The development of Arabidopsis as a model plant.
Koornneef M, Meinke D., Plant J. 61(6), 2010
PMID: 20409266
Transcriptional regulation of the CRK/DUF26 group of receptor-like protein kinases by ozone and plant hormones in Arabidopsis.
Wrzaczek M, Brosche M, Salojarvi J, Kangasjarvi S, Idanheimo N, Mersmann S, Robatzek S, Karpinski S, Karpinska B, Kangasjarvi J., BMC Plant Biol. 10(), 2010
PMID: 20500828
Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana.
Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S., Proc. Natl. Acad. Sci. U.S.A. 107(43), 2010
PMID: 20921408
Aligning short sequencing reads with Bowtie.
Langmead B., Curr Protoc Bioinformatics Chapter 11(), 2010
PMID: 21154709
Cabbage family affairs: the evolutionary history of Brassicaceae.
Franzke A, Lysak MA, Al-Shehbaz IA, Koch MA, Mummenhoff K., Trends Plant Sci. 16(2), 2010
PMID: 21177137
Sequence-based physical mapping of complex genomes by whole genome profiling.
van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJ, Prins M., Genome Res. 21(4), 2011
PMID: 21324881
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL., Nat. Genet. 43(5), 2011
PMID: 21478890
Ancestral polyploidy in seed plants and angiosperms.
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW., Nature 473(7345), 2011
PMID: 21478875
Screening synteny blocks in pairwise genome comparisons through integer programming.
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M., BMC Bioinformatics 12(), 2011
PMID: 21501495
The genome of the extremophile crucifer Thellungiella parvula.
Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK, Bohnert HJ, Cheeseman JM., Nat. Genet. 43(9), 2011
PMID: 21822265
The genome of the mesopolyploid crop species Brassica rapa.
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium, Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Chris Pires J, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z., Nat. Genet. 43(10), 2011
PMID: 21873998
Evolution of the S-locus region in Arabidopsis relatives.
Guo YL, Zhao X, Lanz C, Weigel D., Plant Physiol. 157(2), 2011
PMID: 21810962
The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22127870
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K., Nucleic Acids Res. 40(2), 2011
PMID: 22102584
Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
Smaczniak C, Immink RG, Muino JM, Blanvillain R, Busscher M, Busscher-Lange J, Dinh QD, Liu S, Westphal AH, Boeren S, Parcy F, Xu L, Carles CC, Angenent GC, Kaufmann K., Proc. Natl. Acad. Sci. U.S.A. 109(5), 2012
PMID: 22238427
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L., Nat Protoc 7(3), 2012
PMID: 22383036
Corolla monosymmetry: evolution of a morphological novelty in the Brassicaceae family.
Busch A, Horn S, Muhlhausen A, Mummenhoff K, Zachgo S., Mol. Biol. Evol. 29(4), 2011
PMID: 22135189
Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model.
Schranz ME, Mohammadin S, Edger PP., Curr. Opin. Plant Biol. 15(2), 2012
PMID: 22480429
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP., Syst. Biol. 61(3), 2012
PMID: 22357727
The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium, Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, Xu X, Pan S, Cheng S, Liu X, Ren Y, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels RM, Bombarely A, Gosselin JR, Huang M, Leto JA, Menda N, Strickler S, Mao L, Gao S, Tecle IY, York T, Zheng Y, Vrebalov JT, Lee J, Zhong S, Mueller LA, Stiekema WJ, Ribeca P, Alioto T, Yang W, Huang S, Du Y, Zhang Z, Gao J, Guo Y, Wang X, Li Y, He J, Li C, Cheng Z, Zuo J, Ren J, Zhao J, Yan L, Jiang H, Wang B, Li H, Li Z, Fu F, Chen B, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, McCombie WR, Lippman ZB, Chia JM, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson LK, Chang SB, Royer SM, Shearer LA, Stack SM, Rose JK, Xu Y, Eannetta N, Matas AJ, McQuinn R, Tanksley SD, Camara F, Guigo R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang C, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia Z, Zhang J, Ye Z, Bishop GJ, Butcher S, Lopez-Cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal JK, Pandit A, Singh PK, Mahato AK, Gaikwad VD, Sharma RR, Mohapatra T, Singh NK, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latche A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Pericard P, Osorio S, Fernandez del Carmen A, Monforte A, Granell A, Fernandez-Munoz R, Conte M, Lichtenstein G, Carrari F, De Bellis G, Fuligni F, Peano C, Grandillo S, Termolino P, Pietrella M, Fantini E, Falcone G, Fiore A, Giuliano G, Lopez L, Facella P, Perotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek MG, Feron RM, van Oeveren J, de Heer P, daPonte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk MJ, Janssen A, van Haaren MJ, Jungeun Kim SH, Kwon SY, Kim S, Koo DH, Lee S, Hur CG, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jocker A, Warfsmann J, Gobel U, Kawamura S, Yano K, Sherman JD, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen EG, van de Belt J, van Haarst JC, Peters SA, van Staveren MA, Henkens MH, Mooyman PJ, Hesselink T, van Ham RC, Jiang G, Droege M, Choi D, Kang BC, Kim BD, Park M, Kim S, Yeom SI, Lee YH, Choi YD, Li G, Gao J, Liu Y, Huang S, Fernandez-Pedrosa V, Collado C, Zuniga S, Wang G, Cade R, Dietrich RA, Rogers J, Knapp S, Fei Z, White RA, Thannhauser TW, Giovannoni JJ, Botella MA, Gilbert L, Gonzalez R, Goicoechea JL, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Meyers BC, Gurazada AB, Green PJ, Vyas SM, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi AK, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk WB, Li J, Guo H, Lee TH, Wang Y, Zhang D, Paterson AH, Wang X, Tang H, Barone A, Chiusano ML, Ercolano MR, D'Agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour GB, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe BA, Vezzi A, D'Angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson DR, De Paoli E, Szinay D, de Jong HH, Bai Y, Visser RG, Klein R, Beasley H, McLaren K, Nicholson C, Riddle C, Gianese G., Nature 485(7400), 2012
PMID: 22660326
Insights into salt tolerance from the genome of Thellungiella salsuginea.
Wu HJ, Zhang Z, Wang JY, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R, Wu Y, Wang YN, Yang Z, Liu Y, Zhang W, Zhang H, Chu J, Yan C, Fang S, Zhang J, Wang Y, Zhang F, Wang G, Lee SY, Cheeseman JM, Yang B, Li B, Min J, Yang L, Wang J, Chu C, Chen SY, Bohnert HJ, Zhu JK, Wang XJ, Xie Q., Proc. Natl. Acad. Sci. U.S.A. 109(30), 2012
PMID: 22778405
Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification.
Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K., Mol. Biol. Evol. 29(12), 2012
PMID: 22821009
The Capsella rubella genome and the genomic consequences of rapid mating system evolution.
Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandakova T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI., Nat. Genet. 45(7), 2013
PMID: 23749190
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandakova T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M., Nat. Genet. 45(8), 2013
PMID: 23817568
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
Development of floral organ identity: stories from the MADS house.
Theissen G., Curr. Opin. Plant Biol. 4(1), 2001
PMID: 11163172
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M., Nucleic Acids Res. 31(1), 2003
PMID: 12520024
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.
Bowers JE, Chapman BA, Rong J, Paterson AH., Nature 422(6930), 2003
PMID: 12660784
Locating sequence on FPC maps and selecting a minimal tiling path.
Engler FW, Hatfield J, Nelson W, Soderlund CA., Genome Res. 13(9), 2003
PMID: 12915486
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li L, Stoeckert CJ Jr, Roos DS., Genome Res. 13(9), 2003
PMID: 12952885
GeneWise and Genomewise.
Birney E, Clamp M, Durbin R., Genome Res. 14(5), 2004
PMID: 15123596
Four DEF-like MADS box genes displayed distinct floral morphogenetic roles in Phalaenopsis orchid.
Tsai WC, Kuoh CS, Chuang MH, Chen WH, Chen HH., Plant Cell Physiol. 45(7), 2004
PMID: 15295066
A superfamily of S locus-related sequences in Arabidopsis: diverse structures and expression patterns.
Dwyer KG, Kandasamy MK, Mahosky DI, Acciai J, Kudish BI, Miller JE, Nasrallah ME, Nasrallah JB., Plant Cell 6(12), 1994
PMID: 7866027
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS., Science 317(5834), 2007
PMID: 17615350
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
Xu Z, Wang H., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17485477
Cleome, a genus closely related to Arabidopsis, contains species spanning a developmental progression from C(3) to C(4) photosynthesis.
Marshall DM, Muhaidat R, Brown NJ, Liu Z, Stanley S, Griffiths H, Sage RF, Hibberd JM., Plant J. 51(5), 2007
PMID: 17692080
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization., Nature 449(7161), 2007
PMID: 17721507
The 2R hypothesis: an update.
Kasahara M., Curr. Opin. Immunol. 19(5), 2007
PMID: 17707623
Control of corolla monosymmetry in the Brassicaceae Iberis amara.
Busch A, Zachgo S., Proc. Natl. Acad. Sci. U.S.A. 104(42), 2007
PMID: 17940055
B-class MADS-box genes in trioecious papaya: two paleoAP3 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI.
Ackerman CM, Yu Q, Kim S, Paull RE, Moore PH, Ming R., Planta 227(4), 2007
PMID: 17985156
Using RepeatMasker to identify repetitive elements in genomic sequences.
Chen N., Curr Protoc Bioinformatics Chapter 4(), 2004
PMID: 18428725
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M., Nature 452(7190), 2008
PMID: 18432245
Interactions of B-class complex proteins involved in tepal development in Phalaenopsis orchid.
Tsai WC, Pan ZJ, Hsiao YY, Jeng MF, Wu TF, Chen WH, Chen HH., Plant Cell Physiol. 49(5), 2008
PMID: 18390881
Analyzing real-time PCR data by the comparative C(T) method.
Schmittgen TD, Livak KJ., Nat Protoc 3(6), 2008
PMID: 18546601
Automatically extracting functionally equivalent proteins from SwissProt.
McMillan LE, Martin AC., BMC Bioinformatics 9(), 2008
PMID: 18838004
InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18940856
Assessing the gene space in draft genomes.
Parra G, Bradnam K, Ning Z, Keane T, Korf I., Nucleic Acids Res. 37(1), 2008
PMID: 19042974
Evolution of floral symmetry: a state of the art.
Jabbour F, Nadot S, Damerval C., C. R. Biol. 332(2-3), 2008
PMID: 19281953
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT., Clin. Chem. 55(4), 2009
PMID: 19246619
TopHat: discovering splice junctions with RNA-Seq.
Trapnell C, Pachter L, Salzberg SL., Bioinformatics 25(9), 2009
PMID: 19289445
Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR., Bioinformatics 25(10), 2009
PMID: 19307242
Gene duplication and evolutionary novelty in plants.
Flagel LE, Wendel JF., New Phytol. 183(3), 2009
PMID: 19555435
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
Majoros WH, Pertea M, Salzberg SL., Bioinformatics 20(16), 2004
PMID: 15145805
Natural variation in expression of self-incompatibility in Arabidopsis thaliana: implications for the evolution of selfing.
Nasrallah ME, Liu P, Sherman-Broyles S, Boggs NA, Nasrallah JB., Proc. Natl. Acad. Sci. U.S.A. 101(45), 2004
PMID: 15505209
A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., Nat. Genet. 37(5), 2005
PMID: 15806101

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