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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 26 of 34

  1. The Polima (pol) system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rfp have been used in hybrid breeding in Brassica napus, which has greatly improved the yield of rapeseed. However, t...

    Authors: Hong An, Zonghui Yang, Bin Yi, Jing Wen, Jinxiong Shen, Jinxing Tu, Chaozhi Ma and Tingdong Fu

    Citation: BMC Genomics 2014 15:258

    Content type: Research article

    Published on:

  2. MicroRNAs (miRNAs) are small, non-coding RNAs of 20 to 24 nucleotides that regulate gene expression and responses to biotic and abiotic stress. Till now, no reports have previously been published concerning mi...

    Authors: Meng-Yao Li, Feng Wang, Zhi-Sheng Xu, Qian Jiang, Jing Ma, Guo-Fei Tan and Ai-Sheng Xiong

    Citation: BMC Genomics 2014 15:242

    Content type: Research article

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  3. The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. Some members of the gene family have been show...

    Authors: Hala Badr Khalil, Sabrina C Brunetti, Uyen Minh Pham, Deborah Maret, André Laroche and Patrick J Gulick

    Citation: BMC Genomics 2014 15:239

    Content type: Research article

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  4. The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.

    Authors: Louise Brousseau, Alexandra Tinaut, Caroline Duret, Tiange Lang, Pauline Garnier-Gere and Ivan Scotti

    Citation: BMC Genomics 2014 15:238

    Content type: Research article

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  5. The rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world’s natural rubber, a strategic raw material for a variety of products. One of the major ...

    Authors: Leonardo Rippel Salgado, Daniela Martins Koop, Daniel Guariz Pinheiro, Ronan Rivallan, Vincent Le Guen, Marisa Fabiana Nicolás, Luiz Gonzaga Paula de Almeida, Viviani Ribeiro Rocha, Milena Magalhães, Alexandra Lehmkuhl Gerber, Antonio Figueira, Júlio Cézar de Mattos Cascardo, AnaTereza Ribeiro de Vasconcelos, Wilson Araújo Silva Jr, Luiz Lehmann Coutinho and Dominique Garcia

    Citation: BMC Genomics 2014 15:236

    Content type: Research article

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  6. Highly adapted plant species are able to alter their root architecture to improve nutrient uptake and thrive in environments with limited nutrient supply. Cluster roots (CRs) are specialised structures of dens...

    Authors: David Secco, Huixia Shou, James Whelan and Oliver Berkowitz

    Citation: BMC Genomics 2014 15:230

    Content type: Research article

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  7. Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves...

    Authors: Eric J Belfield, Carly Brown, Xiangchao Gan, Caifu Jiang, Dilair Baban, Aziz Mithani, Richard Mott, Jiannis Ragoussis and Nicholas P Harberd

    Citation: BMC Genomics 2014 15:224

    Content type: Methodology article

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  8. Tomato (Solanum lycopersicum) establishes a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The formation of the mycorrhizal association in the roots leads to plant-wide modulation of gene expression...

    Authors: Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi and Paola Bonfante

    Citation: BMC Genomics 2014 15:221

    Content type: Research article

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  9. Canola (Brassica napus L.) is one of the most important oil-producing crops in China and worldwide. The yield and quality of canola is frequently threatened by environmental stresses including drought, cold and h...

    Authors: Hanfeng Zhang, Wu-Zhen Liu, Yupeng Zhang, Min Deng, Fangfang Niu, Bo Yang, Xiaoling Wang, Boya Wang, Wanwan Liang, Michael K Deyholos and Yuan-Qing Jiang

    Citation: BMC Genomics 2014 15:211

    Content type: Research article

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  10. Lilium lancifolium, a very important cold-resistant wild flower for lily cold resistance breeding, is widely distributed in southwestern and northeastern China. To gain a better understanding of the cold signalin...

    Authors: Jingmao Wang, Yang Yang, Xiaohua Liu, Jie Huang, Qing Wang, Jiahui Gu and Yingmin Lu

    Citation: BMC Genomics 2014 15:203

    Content type: Research article

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  11. Algae are important non-vascular plants that have many research applications, including high species diversity, biofuel sources, and adsorption of heavy metals and, following processing, are used as ingredient...

    Authors: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Bo-Kai Justin Hsu, Tsung-Lin Liu, Ching-Nen Nathan Chen and Wen-Chi Chang

    Citation: BMC Genomics 2014 15:196

    Content type: Database

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  12. Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilita...

    Authors: Malleswari Gelli, Yongchao Duo, Anji Reddy Konda, Chi Zhang, David Holding and Ismail Dweikat

    Citation: BMC Genomics 2014 15:179

    Content type: Research article

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  13. The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been devel...

    Authors: Christophe Plomion, Emilie Chancerel, Jeffrey Endelman, Jean-Baptiste Lamy, Eric Mandrou, Isabelle Lesur, François Ehrenmann, Fikret Isik, Marco CAM Bink, Joost van Heerwaarden and Laurent Bouffier

    Citation: BMC Genomics 2014 15:171

    Content type: Research article

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  14. Transcriptional activator-like (TAL) effectors, formerly known as the AvrBs3/PthA protein family, are DNA-binding effectors broadly found in Xanthomonas spp. that transactivate host genes upon injection via the b...

    Authors: Andre LA Pereira, Marcelo F Carazzolle, Valeria Y Abe, Maria LP de Oliveira, Mariane N Domingues, Jaqueline C Silva, Raul A Cernadas and Celso E Benedetti

    Citation: BMC Genomics 2014 15:157

    Content type: Research article

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  15. Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition...

    Authors: Claudia T Guimaraes, Christiano C Simoes, Maria Marta Pastina, Lyza G Maron, Jurandir V Magalhaes, Renato CC Vasconcellos, Lauro JM Guimaraes, Ubiraci GP Lana, Carlos FS Tinoco, Roberto W Noda, Silvia N Jardim-Belicuas, Leon V Kochian, Vera MC Alves and Sidney N Parentoni

    Citation: BMC Genomics 2014 15:153

    Content type: Research article

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  16. Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids betw...

    Authors: Karen S Aitken, Meredith D McNeil, Scott Hermann, Peter C Bundock, Andrzej Kilian, Katarzyna Heller-Uszynska, Robert J Henry and Jingchuan Li

    Citation: BMC Genomics 2014 15:152

    Content type: Research article

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  17. microRNAs (miRNAs) are endogenous, noncoding, small RNAs that have essential regulatory functions in plant growth, development, and stress response processes. However, limited information is available about th...

    Authors: Jianxia Jiang, Meiling Lv, Ying Liang, Zhiming Ma and Jiashu Cao

    Citation: BMC Genomics 2014 15:146

    Content type: Research article

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  18. The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we...

    Authors: Luis A Martínez-López, Neftalí Ochoa-Alejo and Octavio Martínez

    Citation: BMC Genomics 2014 15:143

    Content type: Research article

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  19. Even in the age of next-generation sequencing (NGS), it has been unclear whether or not cells within a single organism have systematically distinctive genomes. Resolving this question, one of the most basic biolo...

    Authors: Deepti Diwan, Shun Komazaki, Miho Suzuki, Naoto Nemoto, Takuyo Aita, Akiko Satake and Koichi Nishigaki

    Citation: BMC Genomics 2014 15:142

    Content type: Methodology article

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  20. Arabidopsis thaliana, a member of the Brassicaceae family is the dominant genetic model plant. However, while the flowers within the Brassicaceae members are rather uniform, mainly radially symmetrical, mostly wh...

    Authors: Amey Bhide, Simon Schliesky, Marlis Reich, Andreas PM Weber and Annette Becker

    Citation: BMC Genomics 2014 15:140

    Content type: Research article

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  21. Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Ca...

    Authors: Maria Raffaella Ercolano, Adriana Sacco, Francesca Ferriello, Raffaella D’Alessandro, Paola Tononi, Alessandra Traini, Amalia Barone, Elisa Zago, Maria Luisa Chiusano, Genny Buson, Massimo Delledonne and Luigi Frusciante

    Citation: BMC Genomics 2014 15:138

    Content type: Research article

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  22. Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and us...

    Authors: Jorge Duarte, Nathalie Rivière, Alain Baranger, Grégoire Aubert, Judith Burstin, Laurent Cornet, Clément Lavaud, Isabelle Lejeune-Hénaut, Jean-Pierre Martinant, Jean-Philippe Pichon, Marie-Laure Pilet-Nayel and Gilles Boutet

    Citation: BMC Genomics 2014 15:126

    Content type: Research article

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  23. Leaf pigment content is an important trait involved in environmental interactions. In order to determine its impact on drought tolerance in wheat, we characterized a pale-green durum wheat mutant (Triticum turgid...

    Authors: Ariadna Peremarti, Caterina Marè, Alessio Aprile, Enrica Roncaglia, Luigi Cattivelli, Dolors Villegas and Conxita Royo

    Citation: BMC Genomics 2014 15:125

    Content type: Research article

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  24. In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP an...

    Authors: Chao Liang, Xuan Liu, Yuzhe Sun, Siu-Ming Yiu and Boon Leong Lim

    Citation: BMC Genomics 2014 15:116

    Content type: Research article

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  25. The persimmon Diospyros kaki Thunb. is an important commercial and deciduous fruit tree. The fruits have proanthocyanidin (PA) content of >25% of the dry weight and are astringent. PAs cause astringency that is o...

    Authors: Chun Luo, Qinglin Zhang and Zhengrong Luo

    Citation: BMC Genomics 2014 15:112

    Content type: Research article

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  26. MicroRNAs (miRNAs), involving in various biological and metabolic processes, have been discovered and analyzed in quite a number of plants species, such as Arabidopsis, rice and other plants. However, there have ...

    Authors: Jian Han, Jinggui Fang, Chen Wang, Yanlei Yin, Xin Sun, Xiangpeng Leng and Changnian Song

    Citation: BMC Genomics 2014 15:111

    Content type: Research article

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  27. 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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  28. Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regu...

    Authors: Sergiu Netotea, David Sundell, Nathaniel R Street and Torgeir R Hvidsten

    Citation: BMC Genomics 2014 15:106

    Content type: Research article

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  29. We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed c...

    Authors: Hui Liu, Micha Bayer, Arnis Druka, Joanne R Russell, Christine A Hackett, Jesse Poland, Luke Ramsay, Pete E Hedley and Robbie Waugh

    Citation: BMC Genomics 2014 15:104

    Content type: Research article

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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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

    Published on:

  40. 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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  41. 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

    Published on:

  42. 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

    Published on:

  43. 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

    Published on:

  44. 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

    Published on:

  45. 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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  46. 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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  47. 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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  48. 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

    Published on:

  49. 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

    Published on:

  50. 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

    Published on:

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