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Plant genomics

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

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  1. Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new techno...

    Authors: Nicholas P. Howard, Michela Troggio, Charles-Eric Durel, Hélène Muranty, Caroline Denancé, Luca Bianco, John Tillman and Eric van de Weg

    Citation: BMC Genomics 2021 22:246

    Content type: Research article

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  2. Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pe...

    Authors: Yun Dai, Xiao Sun, Chenggang Wang, Fei Li, Shifan Zhang, Hui Zhang, Guoliang Li, Lingyun Yuan, Guohu Chen, Rifei Sun and Shujiang Zhang

    Citation: BMC Genomics 2021 22:236

    Content type: Research article

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  3. Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased t...

    Authors: Jorge A. Ramírez-Tejero, Jaime Jiménez-Ruiz, Alicia Serrano, Angjelina Belaj, Lorenzo León, Raúl de la Rosa, Jesús Mercado-Blanco and Francisco Luque

    Citation: BMC Genomics 2021 22:229

    Content type: Research article

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  4. Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of ...

    Authors: Peter Civáň, Konstantina Drosou, David Armisen-Gimenez, Wandrille Duchemin, Jérôme Salse and Terence A. Brown

    Citation: BMC Genomics 2021 22:227

    Content type: Research article

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  5. B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryz...

    Authors: Xiuming Zhang, Li Zhang, Miaomiao Ji, Yifei Wu, Songlin Zhang, Yanxun Zhu, Jin Yao, Zhi Li, Hua Gao and Xiping Wang

    Citation: BMC Genomics 2021 22:221

    Content type: Research article

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  6. Persimmon (Diospyros kaki Thunb.) has various labile sex types, and studying its sex differentiation can improve breeding efficiency. However, studies on sexual regulation patterns in persimmon have focused mainl...

    Authors: Huawei Li, Liyuan Wang, Yini Mai, Weijuan Han, Yujing Suo, Songfeng Diao, Peng Sun and Jianmin Fu

    Citation: BMC Genomics 2021 22:203

    Content type: Research article

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  7. Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkalo...

    Authors: Alex Rajewski, Derreck Carter-House, Jason Stajich and Amy Litt

    Citation: BMC Genomics 2021 22:201

    Content type: Research article

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  8. Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important ec...

    Authors: Shoubo Tian, Panling Lu, Zhaohui Zhang, Jian Qiang Wu, Hui Zhang and Haibin Shen

    Citation: BMC Genomics 2021 22:194

    Content type: Research article

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  9. The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia),...

    Authors: Junjie Cui, Jiazhu Peng, Jiaowen Cheng and Kailin Hu

    Citation: BMC Genomics 2021 22:190

    Content type: Research article

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  10. Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cyc...

    Authors: Zena J. Rawandoozi, Timothy P. Hartmann, Silvia Carpenedo, Ksenija Gasic, Cassia da Silva Linge, Lichun Cai, Eric Van de Weg and David H. Byrne

    Citation: BMC Genomics 2021 22:187

    Content type: Research article

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  11. Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of...

    Authors: Maricel Podio, Carolina Colono, Lorena Siena, Juan Pablo A. Ortiz and Silvina Claudia Pessino

    Citation: BMC Genomics 2021 22:185

    Content type: Research article

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  12. Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few la...

    Authors: Ying Wang, Hui-Liang Li, Yong-Kai Zhou, Dong Guo, Jia-Hong Zhu and Shi-Qing Peng

    Citation: BMC Genomics 2021 22:183

    Content type: Research article

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  13. Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season perennial forage grasses that is widely cultivated in the world and is highly tolerant to stressful conditions. However, little is kno...

    Authors: Zhongfu Yang, Gang Nie, Guangyan Feng, Jiating Han, Linkai Huang and Xinquan Zhang

    Citation: BMC Genomics 2021 22:178

    Content type: Research article

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  14. Finger millet (Eleusine coracana 2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, b...

    Authors: Nathan D. Hall, Jinesh D. Patel, J. Scott McElroy and Leslie R. Goertzen

    Citation: BMC Genomics 2021 22:175

    Content type: Research article

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  15. Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake r...

    Authors: Mengjiao Yang, Cairong Wang, Muhammad Adeel Hassan, Faji Li, Xianchun Xia, Shubing Shi, Yonggui Xiao and Zhonghu He

    Citation: BMC Genomics 2021 22:174

    Content type: Research article

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  16. The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent econom...

    Authors: Dingding Cao, Zhongyuan Lin, Longyu Huang, Rebecca Njeri Damaris and Pingfang Yang

    Citation: BMC Genomics 2021 22:171

    Content type: Research article

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  17. Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific...

    Authors: Yan Cheng, Xiaoxue He, S. V. G. N. Priyadarshani, Yu Wang, Li Ye, Chao Shi, Kangzhuo Ye, Qiao Zhou, Ziqiang Luo, Fang Deng, Ling Cao, Ping Zheng, Mohammad Aslam and Yuan Qin

    Citation: BMC Genomics 2021 22:167

    Content type: Research article

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  18. Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Ps...

    Authors: Thomas M. Adams, Tjelvar S. G. Olsson, Ricardo H. Ramírez-González, Ruth Bryant, Rosie Bryson, Pablo Eduardo Campos, Paul Fenwick, David Feuerhelm, Charlotte Hayes, Tina Henriksson, Amelia Hubbard, Radivoje Jevtić, Christopher Judge, Matthew Kerton, Jacob Lage, Clare M. Lewis…

    Citation: BMC Genomics 2021 22:166

    Content type: Database

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  19. Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration tr...

    Authors: Pawel Sega, Katarzyna Kruszka, Dawid Bielewicz, Wojciech Karlowski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska and Andrzej Pacak

    Citation: BMC Genomics 2021 22:165

    Content type: Research article

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  20. Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triter...

    Authors: Feng Wen, Xiaozhu Wu, Tongjian Li, Mingliang Jia, Xinsheng Liu and Liang Liao

    Citation: BMC Genomics 2021 22:161

    Content type: Research article

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  21. Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollinat...

    Authors: Ningthaipuilu Longmei, Gurjit Kaur Gill, Pervez Haider Zaidi, Ramesh Kumar, Sudha Krishnan Nair, Vermuri Hindu, Madhumal Thayil Vinayan and Yogesh Vikal

    Citation: BMC Genomics 2021 22:154

    Content type: Research article

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  22. Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its ...

    Authors: Tao-Xiong Shi, Rui-Yuan Li, Ran Zheng, Qing-Fu Chen, Hong-You Li, Juan Huang, Li-Wei Zhu and Cheng-Gang Liang

    Citation: BMC Genomics 2021 22:142

    Content type: Research article

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  23. Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant...

    Authors: Fuyun Hou, Taifeng Du, Zhen Qin, Tao Xu, Aixian Li, Shunxu Dong, Daifu Ma, Zongyun Li, Qingmei Wang and Liming Zhang

    Citation: BMC Genomics 2021 22:140

    Content type: Research article

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  24. Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grape...

    Authors: Xiangjing Yin, Yu Gao, Shiren Song, Danial Hassani and Jiang Lu

    Citation: BMC Genomics 2021 22:136

    Content type: Research article

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  25. The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative...

    Authors: Huatao Chen, Giriraj Kumawat, Yongliang Yan, Baojie Fan and Donghe Xu

    Citation: BMC Genomics 2021 22:132

    Content type: Research article

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  26. 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different develo...

    Authors: Shuo Wei, Wen Zhang, Rao Fu and Yang Zhang

    Citation: BMC Genomics 2021 22:126

    Content type: Research article

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  27. Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid bre...

    Authors: Xiaoli Geng, Yujie Qu, Yinhua Jia, Shoupu He, Zhaoe Pan, Liru Wang and Xiongming Du

    Citation: BMC Genomics 2021 22:123

    Content type: Research article

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  28. Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay ...

    Authors: Huan Wang, Zhaotang Ding, Mengjie Gou, Jianhui Hu, Yu Wang, Lu Wang, Yuchun Wang, Taimei Di, Xinfu Zhang, Xinyuan Hao, Xinchao Wang, Yajun Yang and Wenjun Qian

    Citation: BMC Genomics 2021 22:121

    Content type: Research article

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  29. Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses ...

    Authors: Daniel Restrepo-Montoya, Phillip E. McClean and Juan M. Osorno

    Citation: BMC Genomics 2021 22:113

    Content type: Research article

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  30. Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very li...

    Authors: Wei Wang, Lei Wang, Ling Wang, Meilian Tan, Collins O. Ogutu, Ziyan Yin, Jian Zhou, Jiaomei Wang, Lijun Wang and Xingchu Yan

    Citation: BMC Genomics 2021 22:109

    Content type: Research article

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  31. Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the uni...

    Authors: Yiheng Wang, Sheng Wang, Yanlei Liu, Qingjun Yuan, Jiahui Sun and Lanping Guo

    Citation: BMC Genomics 2021 22:103

    Content type: Research article

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  32. Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with h...

    Authors: Peipei Wang, Fanrui Meng, Bethany M. Moore and Shin-Han Shiu

    Citation: BMC Genomics 2021 22:99

    Content type: Research article

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  33. Paeonia lactiflora ‘Hangshao’ is widely cultivated in China as a traditional Chinese medicine ‘Radix Paeoniae Alba’. Due to the abundant unsaturated fatty acids in its seed, it can also be regarded as a new oilse...

    Authors: Jia-Song Meng, Yu-Han Tang, Jing Sun, Da-Qiu Zhao, Ke-Liang Zhang and Jun Tao

    Citation: BMC Genomics 2021 22:94

    Content type: Research article

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  34. The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miR...

    Authors: Lan Yu, Rongkai Guo, Yeqin Jiang, Xinghuo Ye, Zhihong Yang, Yijun Meng and Chaogang Shao

    Citation: BMC Genomics 2021 22:93

    Content type: Research article

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  35. Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main trans...

    Authors: Wei Li, Ziwen Geng, Cuiping Zhang, Kuiling Wang and Xinqiang Jiang

    Citation: BMC Genomics 2021 22:90

    Content type: Research article

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  36. Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real...

    Authors: Jianqing Chen, Jinyu Zhou, Yanhong Hong, Zekun Li, Xiangyu Cheng, Aiying Zheng, Yilin Zhang, Juanjuan Song, Guifeng Xie, Changmei Chen, Meng Yuan, Tengyun Wang and Qingxi Chen

    Citation: BMC Genomics 2021 22:88

    Content type: Research article

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  37. The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total...

    Authors: Hua Zhong, Shuai Liu, Xiaoxi Meng, Tong Sun, Yujuan Deng, Weilong Kong, Zhaohua Peng and Yangsheng Li

    Citation: BMC Genomics 2021 22:86

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:206

  38. Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have ...

    Authors: Lingling Dou, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Haihong Shang, Hongbin Li and Guanghui Xiao

    Citation: BMC Genomics 2021 22:85

    Content type: Research article

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  39. Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here...

    Authors: Pan Zhang, Tianqi Duo, Fengdan Wang, Xunzhong Zhang, Zouzhuan Yang and Guofu Hu

    Citation: BMC Genomics 2021 22:82

    Content type: Research article

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  40. The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic st...

    Authors: Mirosław Tyrka, Monika Mokrzycka, Beata Bakera, Dorota Tyrka, Magdalena Szeliga, Stefan Stojałowski, Przemysław Matysik, Michał Rokicki, Monika Rakoczy-Trojanowska and Paweł Krajewski

    Citation: BMC Genomics 2021 22:81

    Content type: Research article

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  41. Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberelli...

    Authors: Rongfa Chen, Yegeng Fan, Huiwen Zhou, Shanping Mo, Zhongfeng Zhou, Haifeng Yan, Ting Luo, Xing Huang, Mengling Weng, Prakash Lakshmanan, Yangrui Li, Lihang Qiu and Jianming Wu

    Citation: BMC Genomics 2021 22:79

    Content type: Research article

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  42. Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia argut...

    Authors: Miaomiao Lin, Shihang Sun, Jinbao Fang, Xiujuan Qi, Leiming Sun, Yunpeng Zhong, Yanxiang Sun, Gu Hong, Ran Wang and Yukuo Li

    Citation: BMC Genomics 2021 22:72

    Content type: Research article

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  43. Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activatio...

    Authors: Ambika Dudhate, Harshraj Shinde, Pei Yu, Daisuke Tsugama, Shashi Kumar Gupta, Shenkui Liu and Tetsuo Takano

    Citation: BMC Genomics 2021 22:70

    Content type: Research article

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  44. The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang,...

    Authors: Songyue Chai, Qin Yao, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Lina Sha, Houyang Kang, Haiqin Zhang, Jun Li, Yonghong Zhou and Yi Wang

    Citation: BMC Genomics 2021 22:63

    Content type: Research article

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  45. We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker–free MucoRice-CTB line 51A, which ha...

    Authors: Ai Sasou, Yoshikazu Yuki, Ayaka Honma, Kotomi Sugiura, Koji Kashima, Hiroko Kozuka-Hata, Masanori Nojima, Masaaki Oyama, Shiho Kurokawa, Shinichi Maruyama, Masaharu Kuroda, Shinjiro Tanoue, Narushi Takamatsu, Kohtaro Fujihashi, Eiji Goto and Hiroshi Kiyono

    Citation: BMC Genomics 2021 22:59

    Content type: Research article

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