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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 29 of 31

  1. Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptom...

    Authors: Jörg Toepel, Stefan P Albaum, Samuel Arvidsson, Alexander Goesmann, Marco la Russa, Kristin Rogge and Olaf Kruse

    Citation: BMC Genomics 2011 12:579

    Content type: Methodology article

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  2. The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced usi...

    Authors: Riaz Ahmad, Dan E Parfitt, Joseph Fass, Ebenezer Ogundiwin, Amit Dhingra, Thomas M Gradziel, Dawei Lin, Nikhil A Joshi, Pedro J Martinez-Garcia and Carlos H Crisosto

    Citation: BMC Genomics 2011 12:569

    Content type: Database

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  3. Bald cypress (Taxodium distichum var. distichum) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias,...

    Authors: Wenxuan Liu, Supaphan Thummasuwan, Sunish K Sehgal, Philippe Chouvarine and Daniel G Peterson

    Citation: BMC Genomics 2011 12:553

    Content type: Research article

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  4. Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The ...

    Authors: Chun Sui, Jie Zhang, Jianhe Wei, Shilin Chen, Ying Li, Jiesen Xu, Yue Jin, Caixiang Xie, Zhihui Gao, Hongjiang Chen, Chengmin Yang, Zheng Zhang and Yanhong Xu

    Citation: BMC Genomics 2011 12:539

    Content type: Research article

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  5. In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantat...

    Authors: Emilie Villar, Christophe Klopp, Céline Noirot, Evandro Novaes, Matias Kirst, Christophe Plomion and Jean-Marc Gion

    Citation: BMC Genomics 2011 12:538

    Content type: Research article

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  6. Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT), which exhibits clinical e...

    Authors: Yongzhen Sun, Hongmei Luo, Ying Li, Chao Sun, Jingyuan Song, Yunyun Niu, Yingjie Zhu, Liang Dong, Aiping Lv, Enzo Tramontano and Shilin Chen

    Citation: BMC Genomics 2011 12:533

    Content type: Research article

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  7. Soybean is a valuable crop that provides protein and oil. Soybean requires a large amount of nitrogen (N) to accumulate high levels of N in the seed. The yield and protein content of soybean seeds are directly...

    Authors: Qing N Hao, Xin A Zhou, Ai H Sha, Cheng Wang, Rong Zhou and Shui L Chen

    Citation: BMC Genomics 2011 12:525

    Content type: Research article

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  8. Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. R...

    Authors: Ling-Ling Gao, James K Hane, Lars G Kamphuis, Rhonda Foley, Bu-Jun Shi, Craig A Atkins and Karam B Singh

    Citation: BMC Genomics 2011 12:521

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Methodology article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Research article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Database

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

    Published on:

  44. 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

    Content type: Research article

    Published on:

  45. 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

    Content type: Research article

    Published on:

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