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Plant genomics

Section edited by David Lightfoot and Keiichi Mochida

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 28 of 30

  1. Content type: Research article

    Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditio...

    Authors: Diana V Dugas, Marcela K Monaco, Andrew Olson, Robert R Klein, Sunita Kumari, Doreen Ware and Patricia E Klein

    Citation: BMC Genomics 2011 12:514

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  2. Content type: Methodology article

    Wheat is one of the most important cereal crops for human beings, with seeds being the tissue of highly economic value. Various morphogenetic and metabolic processes are exclusively associated with seed matura...

    Authors: Xinglu Yang, Hongliang Xu, Wenhui Li, Le Li, Jinyue Sun, Yaxuan Li, Yueming Yan and Yingkao Hu

    Citation: BMC Genomics 2011 12:513

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  3. Content type: Research article

    Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, dow...

    Authors: Falah As-sadi, Sébastien Carrere, Quentin Gascuel, Thibaut Hourlier, David Rengel, Marie-Christine Le Paslier, Amandine Bordat, Marie-Claude Boniface, Dominique Brunel, Jérôme Gouzy, Laurence Godiard and Patrick Vincourt

    Citation: BMC Genomics 2011 12:498

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  4. Content type: Research article

    Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these ca...

    Authors: Shengxin Chang, Tiantian Yang, Tongqing Du, Yongjuan Huang, Jianmei Chen, Jiyong Yan, Jianbo He and Rongzhan Guan

    Citation: BMC Genomics 2011 12:497

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  5. Content type: Research article

    Increasing the nutrient concentration of wheat grains is important to ameliorate nutritional deficiencies in many parts of the world. Proteins and nutrients in the wheat grain are largely derived from the remo...

    Authors: Dario Cantu, Stephen P Pearce, Assaf Distelfeld, Michael W Christiansen, Cristobal Uauy, Eduard Akhunov, Tzion Fahima and Jorge Dubcovsky

    Citation: BMC Genomics 2011 12:492

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  6. Content type: Research article

    Characterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore th...

    Authors: Jinquan Li, Ann-Katrin Lühmann, Knuth Weißleder and Benjamin Stich

    Citation: BMC Genomics 2011 12:484

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  7. Content type: Research article

    The mechanical properties of wood are largely determined by the orientation of cellulose microfibrils in secondary cell walls. Several genes and their allelic variants have previously been found to affect micr...

    Authors: Xinguo Li, Harry X Wu and Simon G Southerton

    Citation: BMC Genomics 2011 12:480

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  8. Content type: Research article

    WRKY proteins are a large family of transcriptional regulators in higher plant. They are involved in many biological processes, such as plant development, metabolism, and responses to biotic and abiotic stress...

    Authors: Jian Ling, Weijie Jiang, Ying Zhang, Hongjun Yu, Zhenchuan Mao, Xingfang Gu, Sanwen Huang and Bingyan Xie

    Citation: BMC Genomics 2011 12:471

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  9. Content type: Research article

    Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the ear...

    Authors: Pei Xu, Xiaohua Wu, Jie Luo, Baogen Wang, Yonghua Liu, Jeffrey D Ehlers, Sha Wang, Zhongfu Lu and Guojing Li

    Citation: BMC Genomics 2011 12:467

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  10. Content type: Research article

    Photoperiod-sensitive genic male sterile (PGMS) rice, Nongken 58S, was discovered in 1973. It has been widely used for the production of hybrid rice, and great achievements have been made in improving rice yie...

    Authors: Wei Wang, Zhenwei Liu, Zhibin Guo, Gaoyuan Song, Qin Cheng, Daiming Jiang, Yingguo Zhu and Daichang Yang

    Citation: BMC Genomics 2011 12:462

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  11. Content type: Research article

    Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes ...

    Authors: Shaogui Guo, Jingan Liu, Yi Zheng, Mingyun Huang, Haiying Zhang, Guoyi Gong, Hongju He, Yi Ren, Silin Zhong, Zhangjun Fei and Yong Xu

    Citation: BMC Genomics 2011 12:454

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  12. Content type: Research article

    Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In add...

    Authors: Wenliang Wei, Xiaoqiong Qi, Linhai Wang, Yanxin Zhang, Wei Hua, Donghua Li, Haixia Lv and Xiurong Zhang

    Citation: BMC Genomics 2011 12:451

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  13. Content type: Research article

    Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation be...

    Authors: Doug J Hinchliffe, Rickie B Turley, Marina Naoumkina, Hee Jin Kim, Yuhong Tang, Kathleen M Yeater, Ping Li and David D Fang

    Citation: BMC Genomics 2011 12:445

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  14. Content type: Research article

    Segmental duplications (SDs) are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as ot...

    Authors: Giuliana Giannuzzi, Pietro D'Addabbo, Marica Gasparro, Maurizio Martinelli, Francesco N Carelli, Donato Antonacci and Mario Ventura

    Citation: BMC Genomics 2011 12:436

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  15. Content type: Research article

    The highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to unde...

    Authors: William Hintz, Michael Pinchback, Paul de la Bastide, Steven Burgess, Volker Jacobi, Richard Hamelin, Colette Breuil and Louis Bernier

    Citation: BMC Genomics 2011 12:431

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  16. Content type: Research article

    The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and g...

    Authors: Luis Rodríguez-Moreno, Víctor M González, Andrej Benjak, M Carmen Martí, Pere Puigdomènech, Miguel A Aranda and Jordi Garcia-Mas

    Citation: BMC Genomics 2011 12:424

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  17. Content type: Research article

    Phloem-feeding aphids deprive plants of assimilates, but mostly manage to avoid causing the mechanical tissue damage inflicted by chewing insects. Nevertheless, jasmonate signalling that is induced by infestat...

    Authors: Anna Kuśnierczyk, Diem HT Tran, Per Winge, Tommy S Jørstad, John C Reese, Joanna Troczyńska and Atle M Bones

    Citation: BMC Genomics 2011 12:423

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  18. Content type: Research article

    The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2....

    Authors: Christopher A Saski, Frank A Feltus, Margaret E Staton, Barbara P Blackmon, Stephen P Ficklin, David N Kuhn, Raymond J Schnell, Howard Shapiro and Juan Carlos Motamayor

    Citation: BMC Genomics 2011 12:413

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  19. Content type: Research article

    Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged ...

    Authors: Dawei Li, Hugo E Cuevas, Luming Yang, Yuhong Li, Jordi Garcia-Mas, Juan Zalapa, Jack E Staub, Feishi Luan, Umesh Reddy, Xiaoming He, Zhenhui Gong and Yiqun Weng

    Citation: BMC Genomics 2011 12:396

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  20. Content type: Research article

    Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the ...

    Authors: Daniel Gonzalez-Ibeas, José Blanca, Livia Donaire, Montserrat Saladié, Albert Mascarell-Creus, Ana Cano-Delgado, Jordi Garcia-Mas, Cesar Llave and Miguel A Aranda

    Citation: BMC Genomics 2011 12:393

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  21. Content type: Research article

    In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is una...

    Authors: Yoan Coudert, Martine Bès, Thi Van Anh Le, Martial Pré, Emmanuel Guiderdoni and Pascal Gantet

    Citation: BMC Genomics 2011 12:387

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  22. Content type: Research article

    The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, mole...

    Authors: Pablo F Cavagnaro, Sang-Min Chung, Sylvie Manin, Mehtap Yildiz, Aamir Ali, Maria S Alessandro, Massimo Iorizzo, Douglas A Senalik and Philipp W Simon

    Citation: BMC Genomics 2011 12:386

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  23. Content type: Research article

    Fluctuations in temperature occur naturally during plant growth and reproduction. However, in the hot summers this variation may become stressful and damaging for the molecular mechanisms involved in proper ce...

    Authors: Craita E Bita, Sara Zenoni, Wim H Vriezen, Celestina Mariani, Mario Pezzotti and Tom Gerats

    Citation: BMC Genomics 2011 12:384

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  24. Content type: Research article

    The R locus controls the color of pigmented soybean (Glycine max) seeds. However information about its control over seed coat biochemistry and gene expressions remains limited. The seed coats of nearly-isogenic b...

    Authors: Nik Kovinich, Ammar Saleem, John T Arnason and Brian Miki

    Citation: BMC Genomics 2011 12:381

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  25. Content type: Research article

    Triticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches a...

    Authors: Katharina V Alheit, Jochen C Reif, Hans Peter Maurer, Volker Hahn, Elmar A Weissmann, Thomas Miedaner and Tobias Würschum

    Citation: BMC Genomics 2011 12:380

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  26. Content type: Research article

    BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and ...

    Authors: Frank A Feltus, Christopher A Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E Staton, Stephen P Ficklin, Barbara P Blackmon, Chun-Huai Cheng, Raymond J Schnell, David N Kuhn and Juan-Carlos Motamayor

    Citation: BMC Genomics 2011 12:379

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  27. Content type: Research article

    The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources f...

    Authors: Nicolas Blavet, Delphine Charif, Christine Oger-Desfeux, Gabriel AB Marais and Alex Widmer

    Citation: BMC Genomics 2011 12:376

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  28. Content type: Research article

    Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence pheno...

    Authors: Ping Yu, Caihong Wang, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Shengxiang Tang and Xinghua Wei

    Citation: BMC Genomics 2011 12:372

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  29. Content type: Research article

    Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many a...

    Authors: Prabin Bajgain, Bryce A Richardson, Jared C Price, Richard C Cronn and Joshua A Udall

    Citation: BMC Genomics 2011 12:370

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  30. Content type: Research article

    Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock t...

    Authors: Christopher A Saski, Zhigang Li, Frank A Feltus and Hong Luo

    Citation: BMC Genomics 2011 12:369

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  31. Content type: Research article

    Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single re...

    Authors: Emilie Chancerel, Camille Lepoittevin, Grégoire Le Provost, Yao-Cheng Lin, Juan Pablo Jaramillo-Correa, Andrew J Eckert, Jill L Wegrzyn, Diana Zelenika, Anne Boland, Jean-Marc Frigerio, Philippe Chaumeil, Pauline Garnier-Géré, Christophe Boury, Delphine Grivet, Santiago C González-Martínez, Pierre Rouzé…

    Citation: BMC Genomics 2011 12:368

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  32. Content type: Research article

    MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in development and stress response in plants by negatively affecting gene expression post-transcriptionally. Identification of...

    Authors: Tianzuo Wang, Lei Chen, Mingui Zhao, Qiuying Tian and Wen-Hao Zhang

    Citation: BMC Genomics 2011 12:367

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  33. Content type: Database

    Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the ...

    Authors: Noé Fernández-Pozo, Javier Canales, Darío Guerrero-Fernández, David P Villalobos, Sara M Díaz-Moreno, Rocío Bautista, Arantxa Flores-Monterroso, M Ángeles Guevara, Pedro Perdiguero, Carmen Collada, M Teresa Cervera, Álvaro Soto, Ricardo Ordás, Francisco R Cantón, Concepción Avila, Francisco M Cánovas…

    Citation: BMC Genomics 2011 12:366

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  34. Content type: Research article

    Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a ...

    Authors: John P Délano-Frier, Hamlet Avilés-Arnaut, Kena Casarrubias-Castillo, Gabriela Casique-Arroyo, Paula A Castrillón-Arbeláez, Luis Herrera-Estrella, Julio Massange-Sánchez, Norma A Martínez-Gallardo, Fannie I Parra-Cota, Erandi Vargas-Ortiz and María G Estrada-Hernández

    Citation: BMC Genomics 2011 12:363

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  35. Content type: Research article

    Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economic...

    Authors: Yu-Yun Hsiao, Yun-Wen Chen, Shi-Ching Huang, Zhao-Jun Pan, Chih-Hsiung Fu, Wen-Huei Chen, Wen-Chieh Tsai and Hong-Hwa Chen

    Citation: BMC Genomics 2011 12:360

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  36. Content type: Research article

    Eight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for...

    Authors: James C Nelson, Shichen Wang, Yuye Wu, Xianran Li, Ginny Antony, Frank F White and Jianming Yu

    Citation: BMC Genomics 2011 12:352

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  37. Content type: Research article

    Single nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analys...

    Authors: Yuanhong Han, Yun Kang, Ivone Torres-Jerez, Foo Cheung, Christopher D Town, Patrick X Zhao, Michael K Udvardi and Maria J Monteros

    Citation: BMC Genomics 2011 12:350

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  38. Content type: Research article

    Siraitia grosvenorii (Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chi...

    Authors: Qi Tang, Xiaojun Ma, Changming Mo, Iain W Wilson, Cai Song, Huan Zhao, Yanfang Yang, Wei Fu and Deyou Qiu

    Citation: BMC Genomics 2011 12:343

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  39. Content type: Research article

    Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree ...

    Authors: Melissa ML Wong, Charles H Cannon and Ratnam Wickneswari

    Citation: BMC Genomics 2011 12:342

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  40. Content type: Research article

    Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-ac...

    Authors: Beth Holloway, Stanley Luck, Mary Beatty, J-Antoni Rafalski and Bailin Li

    Citation: BMC Genomics 2011 12:336

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  41. Content type: Research article

    Colletotrichum truncatum is a haploid, hemibiotrophic, ascomycete fungal pathogen that causes anthracnose disease on many economically important leguminous crops. This pathogen exploits sequential biotrophic- and...

    Authors: Vijai Bhadauria, Sabine Banniza, Albert Vandenberg, Gopalan Selvaraj and Yangdou Wei

    Citation: BMC Genomics 2011 12:327

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  42. Content type: Research article

    In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics...

    Authors: BP Mallikarjuna Swamy, Prashant Vikram, Shalabh Dixit, HU Ahmed and Arvind Kumar

    Citation: BMC Genomics 2011 12:319

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  43. Content type: Research article

    Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs...

    Authors: Franceli R Kulcheski, Luiz FV de Oliveira, Lorrayne G Molina, Maurício P Almerão, Fabiana A Rodrigues, Juliana Marcolino, Joice F Barbosa, Renata Stolf-Moreira, Alexandre L Nepomuceno, Francismar C Marcelino-Guimarães, Ricardo V Abdelnoor, Leandro C Nascimento, Marcelo F Carazzolle, Gonçalo AG Pereira and Rogério Margis

    Citation: BMC Genomics 2011 12:307

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  44. Content type: Research article

    The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on th...

    Authors: Lorenzo Barchi, Sergio Lanteri, Ezio Portis, Alberto Acquadro, Giampiero Valè, Laura Toppino and Giuseppe Leonardo Rotino

    Citation: BMC Genomics 2011 12:304

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  45. Content type: Research article

    Current breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequen...

    Authors: John P Hamilton, Candice N Hansey, Brett R Whitty, Kevin Stoffel, Alicia N Massa, Allen Van Deynze, Walter S De Jong, David S Douches and C Robin Buell

    Citation: BMC Genomics 2011 12:302

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