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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 27 of 34

  1. Brassica juncea is an economically important vegetable crop in China, oil crop in India, condiment crop in Europe and selected for canola quality recently in Canada and Australia. B. juncea (2n = 36, AABB) is an ...

    Authors: Jinghua Yang, Ning Song, Xuan Zhao, Xiaohua Qi, Zhongyuan Hu and Mingfang Zhang

    Citation: BMC Genomics 2014 15:107

    Content type: Research article

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  2. The immature fiber (im) mutant of Gossypium hirsutum L. is a special cotton fiber mutant with non-fluffy fibers. It has low dry weight and fineness of fibers due to developmental defects in fiber secondary cell w...

    Authors: Cheng Wang, Yuanda Lv, Wentin Xu, Tianzhen Zhang and Wangzhen Guo

    Citation: BMC Genomics 2014 15:94

    Content type: Research article

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  3. Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxta...

    Authors: Shuo Zhang, Chanjuan Tang, Qiang Zhao, Jing Li, Lifang Yang, Lufeng Qie, Xingke Fan, Lin Li, Ning Zhang, Meicheng Zhao, Xiaotong Liu, Yang Chai, Xue Zhang, Hailong Wang, Yingtao Li, Wen Li…

    Citation: BMC Genomics 2014 15:78

    Content type: Research article

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  4. Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cult...

    Authors: Yong-Mei Bi, Ann Meyer, Gregory S Downs, Xuejiang Shi, Ashraf El-kereamy, Lewis Lukens and Steven J Rothstein

    Citation: BMC Genomics 2014 15:77

    Content type: Research article

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  5. Plant natural products have been co-opted for millennia by humans for various uses such as flavor, fragrances, and medicines. These compounds often are only produced in relatively low amounts and are difficult...

    Authors: Wei Gao, Hai-Xi Sun, Hongbin Xiao, Guanghong Cui, Matthew L Hillwig, Alana Jackson, Xiao Wang, Ye Shen, Nan Zhao, Liangxiao Zhang, Xiu-Jie Wang, Reuben J Peters and Luqi Huang

    Citation: BMC Genomics 2014 15:73

    Content type: Research article

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  6. Wheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological proper...

    Authors: Andrzej K Noyszewski, Farhad Ghavami, Loai M Alnemer, Ali Soltani, Yong Q Gu, Naxin Huo, Steven Meinhardt, Penny MA Kianian and Shahryar F Kianian

    Citation: BMC Genomics 2014 15:67

    Content type: Research article

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  7. A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense res...

    Authors: Danielle C Cardoso, Juliana C Martinati, Poliana F Giachetto, Ramon O Vidal, Marcelo F Carazzolle, Lilian Padilha, Oliveiro Guerreiro-Filho and Mirian P Maluf

    Citation: BMC Genomics 2014 15:66

    Content type: Research article

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  8. The gynoecium is one of the most complex organs of angiosperms specialized for seed production and dispersal, but only several genes important for ovule or embryo sac development were identified by using femal...

    Authors: Wen-qin Fu, Zhi-gang Zhao, Xian-hong Ge, Li Ding and Zai-yun Li

    Citation: BMC Genomics 2014 15:61

    Content type: Research article

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  9. The purpose of this study was to sequence and assemble the tobacco mitochondrial transcriptome and obtain a genomic-level view of steady-state RNA abundance. Plant mitochondrial genomes have a small number of ...

    Authors: Benjamin T Grimes, Awa K Sisay, Hyrum D Carroll and A Bruce Cahoon

    Citation: BMC Genomics 2014 15:31

    Content type: Research article

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  10. The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The p...

    Authors: Anuradha Singh, Shrikant Mantri, Monica Sharma, Ashok Chaudhury, Rakesh Tuli and Joy Roy

    Citation: BMC Genomics 2014 15:29

    Content type: Research article

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  11. In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elemen...

    Authors: Hongjun Liu, Cheng Qin, Zhe Chen, Tao Zuo, Xuerong Yang, Huangkai Zhou, Meng Xu, Shiliang Cao, Yaou Shen, Haijian Lin, Xiujing He, Yinchao Zhang, Lujiang Li, Haiping Ding, Thomas Lübberstedt, Zhiming Zhang…

    Citation: BMC Genomics 2014 15:25

    Content type: Research article

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  12. Regulatory function of small non-coding RNAs (sRNA) in response to environmental and developmental cues has been established. Additionally, sRNA, also plays an important role in maintaining the heterochromatin...

    Authors: Rishi Aryal, Guru Jagadeeswaran, Yun Zheng, Qingyi Yu, Ramanjulu Sunkar and Ray Ming

    Citation: BMC Genomics 2014 15:20

    Content type: Research article

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  13. Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually ...

    Authors: Feng Lin, Meixia Zhao, Douglas D Baumann, Jieqing Ping, Lianjun Sun, Yunfeng Liu, Biao Zhang, Zongxiang Tang, Elisa Hughes, Rebecca W Doerge, Teresa J Hughes and Jianxin Ma

    Citation: BMC Genomics 2014 15:18

    Content type: Research article

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  14. Degradation is essential for RNA maturation, turnover, and quality control. RNA degradome sequencing that integrates a modified 5′-rapid amplification of cDNA ends protocol with next-generation sequencing tech...

    Authors: Cheng-Yu Hou, Ming-Tsung Wu, Shin-Hua Lu, Yue-Ie Hsing and Ho-Ming Chen

    Citation: BMC Genomics 2014 15:15

    Content type: Research article

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  15. GSL1 and GSL2, Gibberellin Stimulated-Like proteins (also known as Snakin-1 and Snakin-2), are cysteine-rich peptides from potato (Solanum tuberosum L.) with antimicrobial properties. Similar peptides in other sp...

    Authors: Sathiyamoorthy Meiyalaghan, Susan J Thomson, Mark WEJ Fiers, Philippa J Barrell, Julie M Latimer, Sara Mohan, E Eirian Jones, Anthony J Conner and Jeanne ME Jacobs

    Citation: BMC Genomics 2014 15:2

    Content type: Research article

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  16. Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the g...

    Authors: Eun-Young Hwang, Qijian Song, Gaofeng Jia, James E Specht, David L Hyten, Jose Costa and Perry B Cregan

    Citation: BMC Genomics 2014 15:1

    Content type: Research article

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  17. Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions th...

    Authors: Zlatko Satovic, Carmen M Avila, Serafin Cruz-Izquierdo, Ramón Díaz-Ruíz, Gloria M García-Ruíz, Carmen Palomino, Natalia Gutiérrez, Stefania Vitale, Sara Ocaña-Moral, María Victoria Gutiérrez, José I Cubero and Ana M Torres

    Citation: BMC Genomics 2013 14:932

    Content type: Research article

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  18. Microalgae are gaining importance as sustainable production hosts in the fields of biotechnology and bioenergy. A robust biomass accumulating strain of the genus Monoraphidium (SAG 48.87) was investigated in this...

    Authors: Christian Bogen, Arwa Al-Dilaimi, Andreas Albersmeier, Julian Wichmann, Michael Grundmann, Oliver Rupp, Kyle J Lauersen, Olga Blifernez-Klassen, Jörn Kalinowski, Alexander Goesmann, Jan H Mussgnug and Olaf Kruse

    Citation: BMC Genomics 2013 14:926

    Content type: Research article

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  19. Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism. The identificat...

    Authors: Niharika Sharma, Prem L Bhalla and Mohan B Singh

    Citation: BMC Genomics 2013 14:915

    Content type: Research article

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  20. Wheat gluten is important for the industrial quality of bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L.). Gluten proteins are also the source of immunogenic peptides that can trigger a T cell r...

    Authors: Elma MJ Salentijn, Danny G Esselink, Svetlana V Goryunova, Ingrid M van der Meer, Luud JWJ Gilissen and Marinus JM Smulders

    Citation: BMC Genomics 2013 14:905

    Content type: Research article

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  21. Hybridization is a major driver of evolution in plants. In a number of plant species, the process of hybridization has been revealed to be accompanied by wide-ranging genetic and epigenetic alterations, some o...

    Authors: Haibin Wang, Jiafu Jiang, Sumei Chen, Weimin Fang, Zhiyong Guan, Yuan Liao and Fadi Chen

    Citation: BMC Genomics 2013 14:902

    Content type: Research article

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  22. Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in ...

    Authors: Vaibhav Srivastava, Ogonna Obudulu, Joakim Bygdell, Tommy Löfstedt, Patrik Rydén, Robert Nilsson, Maria Ahnlund, Annika Johansson, Pär Jonsson, Eva Freyhult, Johanna Qvarnström, Jan Karlsson, Michael Melzer, Thomas Moritz, Johan Trygg, Torgeir R Hvidsten…

    Citation: BMC Genomics 2013 14:893

    Content type: Research article

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  23. Cotton fiber maturity is an important factor for determining the commercial value of cotton. How fiber cell wall development affects fiber maturity is not well understood. A comparison of fiber cross-sections ...

    Authors: Hee Jin Kim, Yuhong Tang, Hong S Moon, Christopher D Delhom and David D Fang

    Citation: BMC Genomics 2013 14:889

    Content type: Research article

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  24. Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as ‘junk’ DNA, microsatellites are rece...

    Authors: Zhimin Gao, Jie Wu, Zheng’an Liu, Liangsheng Wang, Hongxu Ren and Qingyan Shu

    Citation: BMC Genomics 2013 14:886

    Content type: Research article

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  25. Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem ac...

    Authors: Juha Immanen, Kaisa Nieminen, Héctor Duchens Silva, Fernanda Rodríguez Rojas, Lee A Meisel, Herman Silva, Victor A Albert, Torgeir R Hvidsten and Ykä Helariutta

    Citation: BMC Genomics 2013 14:885

    Content type: Research article

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  26. Five-needle pines are important forest species that have been devastated by white pine blister rust (WPBR, caused by Cronartium ribicola) across North America. Currently little transcriptomic and genomic data are...

    Authors: Jun-Jun Liu, Rona N Sturrock and Ross Benton

    Citation: BMC Genomics 2013 14:884

    Content type: Research article

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  27. Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerou...

    Authors: Nepolean Thirunavukkarasu, Firoz Hossain, Kaliyugam Shiriga, Swati Mittal, Kanika Arora, Abhishek Rathore, Sweta Mohan, Trushar Shah, Rinku Sharma, Pottekatt Mohanlal Namratha, Amitha SV Mithra, Trilochan Mohapatra and Hari Shankar Gupta

    Citation: BMC Genomics 2013 14:877

    Content type: Research article

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  28. Alloplasmic lines provide a unique tool to study nuclear-cytoplasmic interactions. Three alloplasmic lines, with nuclear genomes from Triticum aestivum and harboring cytoplasm from Aegilops uniaristata, Aegilops ...

    Authors: Cristina Crosatti, Lydia Quansah, Caterina Maré, Lorenzo Giusti, Enrica Roncaglia, Sergio G Atienza, Luigi Cattivelli and Aaron Fait

    Citation: BMC Genomics 2013 14:868

    Content type: Research article

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  29. In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full rip...

    Authors: Ruben Parra, Miguel A Paredes, Isabel M Sanchez-Calle and Maria C Gomez-Jimenez

    Citation: BMC Genomics 2013 14:866

    Content type: Research article

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  30. The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and...

    Authors: Adam Barling, Kankshita Swaminathan, Therese Mitros, Brandon T James, Juliette Morris, Ornella Ngamboma, Megan C Hall, Jessica Kirkpatrick, Magdy Alabady, Ashley K Spence, Matthew E Hudson, Daniel S Rokhsar and Stephen P Moose

    Citation: BMC Genomics 2013 14:864

    Content type: Research article

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  31. In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the...

    Authors: Sidi Boubacar Ould Estaghvirou, Joseph O Ogutu, Torben Schulz-Streeck, Carsten Knaak, Milena Ouzunova, Andres Gordillo and Hans-Peter Piepho

    Citation: BMC Genomics 2013 14:860

    Content type: Research article

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  32. Septoria tritici blotch is an important leaf disease of European winter wheat. In our survey, we analyzed Septoria tritici blotch resistance in field trials with a large population of 1,055 elite hybrids and t...

    Authors: Thomas Miedaner, Yusheng Zhao, Manje Gowda, C Friedrich H Longin, Viktor Korzun, Erhard Ebmeyer, Ebrahim Kazman and Jochen C Reif

    Citation: BMC Genomics 2013 14:858

    Content type: Research article

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  33. Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective i...

    Authors: Junfeng Chen, Xin Dong, Qing Li, Xun Zhou, Shouhong Gao, Ruibing Chen, Lianna Sun, Lei Zhang and Wansheng Chen

    Citation: BMC Genomics 2013 14:857

    Content type: Research article

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  34. Cavendish, the most widely grown banana cultivar, is relatively resistant to Race 1 of Fusarium oxysporum f. sp. cubense (Foc1) which caused widespread Panama disease during the first half of the 20th century but...

    Authors: Chunqiang Li, Jiaofang Shao, Yejun Wang, Wenbin Li, Dianjing Guo, Bin Yan, Yiji Xia and Ming Peng

    Citation: BMC Genomics 2013 14:851

    Content type: Research article

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  35. Abscisic acid (ABA) can regulate the expressions of many stress-responsive genes in plants. However, in defense responses to pathogens, mounting evidence suggests that ABA plays variable roles. Little informat...

    Authors: Yan Wang, Xiang Tao, Xiao-Mei Tang, Liang Xiao, Jiao-long Sun, Xue-Feng Yan, Dan Li, Hong-Yuan Deng and Xin-Rong Ma

    Citation: BMC Genomics 2013 14:841

    Content type: Research article

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  36. Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporal...

    Authors: Ram Kumar Basnet, Natalia Moreno-Pachon, Ke Lin, Johan Bucher, Richard G F Visser, Chris Maliepaard and Guusje Bonnema

    Citation: BMC Genomics 2013 14:840

    Content type: Research article

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  37. Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about ...

    Authors: Yan Wang, Yan Pan, Zhe Liu, Xianwen Zhu, Lulu Zhai, Liang Xu, Rugang Yu, Yiqin Gong and Liwang Liu

    Citation: BMC Genomics 2013 14:836

    Content type: Research article

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  38. The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop ha...

    Authors: Giandomenico Corrado, Pietro Piffanelli, Martina Caramante, Mariangela Coppola and Rosa Rao

    Citation: BMC Genomics 2013 14:835

    Content type: Research article

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  39. Anthurium andraeanum is one of the most popular tropical flowers. In temperate and cold zones, a much greater risk of cold stress occurs in the supply of Anthurium plants. Unlike the freeze-tolerant model plants,...

    Authors: Dan-Qing Tian, Xiao-Yun Pan, Yong-Ming Yu, Wei-Yong Wang, Fei Zhang, Ya-Ying Ge, Xiao-Lan Shen, Fu-Quan Shen and Xiao-Jing Liu

    Citation: BMC Genomics 2013 14:827

    Content type: Research article

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  40. Pear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Combining the Solexa/Illumina RNA-seq high-throughput sequencing approach (RNA-seq) with Digital...

    Authors: Min Xie, Ying Huang, Yanping Zhang, Xin Wang, Hua Yang, Oliver Yu, Wenhao Dai and Congbing Fang

    Citation: BMC Genomics 2013 14:823

    Content type: Research article

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  41. Durum wheat often faces water scarcity and high temperatures, two events that usually occur simultaneously in the fields. Here we report on the stress responsive strategy of two durum wheat cultivars, characte...

    Authors: Alessio Aprile, Lenka Havlickova, Riccardo Panna, Caterina Marè, Grazia M Borrelli, Daniela Marone, Carla Perrotta, Patrizia Rampino, Luigi De Bellis, Vladislav Curn, Anna M Mastrangelo, Fulvia Rizza and Luigi Cattivelli

    Citation: BMC Genomics 2013 14:821

    Content type: Research article

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  42. Freezing provokes severe yield losses to different fall-sown annual legumes. Understanding the molecular bases of freezing tolerance is of great interest for breeding programs. Medicago truncatula Gaertn. is an a...

    Authors: Nadim Tayeh, Nasser Bahrman, Hélène Sellier, Aurélie Bluteau, Christelle Blassiau, Joëlle Fourment, Arnaud Bellec, Frédéric Debellé, Isabelle Lejeune-Hénaut and Bruno Delbreil

    Citation: BMC Genomics 2013 14:814

    Content type: Research article

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  43. Stem cells located in the centre of the shoot apical meristem are required for the repetitive formation of new organs such as leaves, branches and flowers. In Arabidopsis thaliana, the ZWILLE/PINHEAD/AGO10 (ZLL) ...

    Authors: Matthew R Tucker, Farshad Roodbarkelari, Elisabeth Truernit, Nikolai M Adamski, Annika Hinze, Barbara Lohmüller, Tobias Würschum and Thomas Laux

    Citation: BMC Genomics 2013 14:809

    Content type: Research article

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  44. The phytohormone auxin mediates a stunning array of plant development through the functions of AUXIN RESPONSE FACTORs (ARFs), which belong to transcription factors and are present as a protein family comprisin...

    Authors: Qian Zhu, Baoyan Li, Shuyuan Mu, Bing Han, Runzhi Cui, Manyu Xu, Zhenzhen You and Hansong Dong

    Citation: BMC Genomics 2013 14:806

    Content type: Research article

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  45. Lycium chinense is well known in traditional Chinese herbal medicine for its medicinal value and composition, which have been widely studied for decades. However, further research on Lycium chinense is limited du...

    Authors: Shicheng Zhao, Pham Anh Tuan, Xiaohua Li, Yeon Bok Kim, HyeRan Kim, Chun Geon Park, Jingli Yang, Cheng Hao Li and Sang Un Park

    Citation: BMC Genomics 2013 14:802

    Content type: Research article

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  46. Plant microRNAs are short (~21 nt) non-coding molecules that regulate gene expression by targeting the mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cel...

    Authors: Anna Lukasik, Halina Pietrykowska, Leszek Paczek, Zofia Szweykowska-Kulinska and Piotr Zielenkiewicz

    Citation: BMC Genomics 2013 14:801

    Content type: Research article

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  47. One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow ...

    Authors: Mathilde Causse, Nelly Desplat, Laura Pascual, Marie-Christine Le Paslier, Christopher Sauvage, Guillaume Bauchet, Aurélie Bérard, Rémi Bounon, Maria Tchoumakov, Dominique Brunel and Jean-Paul Bouchet

    Citation: BMC Genomics 2013 14:791

    Content type: Research article

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  48. Ribosomes are essential ribonucleoprotein complexes that are engaged in translation and thus indispensable for growth. Arabidopsis thaliana ribosomes are composed of 80 distinct ribosomal proteins (RPs), each of ...

    Authors: Jinyan Wang, Ping Lan, Huimin Gao, Lu Zheng, Wenfeng Li and Wolfgang Schmidt

    Citation: BMC Genomics 2013 14:783

    Content type: Research article

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