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Genomics and evolution

Section edited by David Alvarez-Ponce and Z Jeffrey Chen 

This section considers studies in the evolution of plants as well as comparative genomics in relation to plant biology.

Page 7 of 7

  1. Natural hybridization is prevalent in ferns, and plays an important role in fern evolution and speciation. In the Indo West-Pacific region, the mangrove fern genus Acrostichum consists of two largely sympatric sp...

    Authors: Rongshu Zhang, Ting Liu, Wei Wu, Yunqin Li, Lifang Chao, Lishi Huang, Yelin Huang, Suhua Shi and Renchao Zhou

    Citation: BMC Plant Biology 2013 13:74

    Content type: Research article

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  2. Calmodulin (CaM) is a major calcium sensor in all eukaryotes. It binds calcium and modulates the activity of a wide range of downstream proteins in response to calcium signals. However, little is known about the

    Authors: Yuan Zhao, Wei Liu, You-Ping Xu, Jia-Yi Cao, Janet Braam and Xin-Zhong Cai

    Citation: BMC Plant Biology 2013 13:70

    Content type: Research article

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  3. Plant Glycogen Synthase Kinase 3/ SHAGGY-like kinases (GSKs) have been implicated in numerous biological processes ranging from embryonic, flower, stomata development to stress and wound responses. They are ke...

    Authors: Thomas Bittner, Sarah Campagne, Gunther Neuhaus, Stefan A Rensing and Christiane Fischer-Iglesias

    Citation: BMC Plant Biology 2013 13:64

    Content type: Research article

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  4. Natural selection acts on multiple traits in an organism, and the final outcome of adaptive evolution may be constrained by the interaction of physiological and functional integration of those traits. Fatty ac...

    Authors: Anushree Sanyal and Craig Randal Linder

    Citation: BMC Plant Biology 2013 13:63

    Content type: Research article

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  5. Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Various MITE families...

    Authors: Perumal Sampath, Sang-Choon Lee, Jonghoon Lee, Nur Kholilatul Izzah, Beom-Soon Choi, Mina Jin, Beom-Seok Park and Tae-Jin Yang

    Citation: BMC Plant Biology 2013 13:56

    Content type: Research article

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  6. The Phosphate transporter 1 (PHT1) gene family has crucial roles in phosphate uptake, translocation, remobilization, and optimization of metabolic processes using of Pi. Gene duplications expand the size of gene ...

    Authors: Chengming Fan, Xu Wang, Ruibo Hu, Yahui Wang, Chaowen Xiao, Ying Jiang, Xiaomei Zhang, Changying Zheng and Yong-Fu Fu

    Citation: BMC Plant Biology 2013 13:48

    Content type: Research article

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  7. The L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide o...

    Authors: Zefeng Yang, Yifan Wang, Yong Zhou, Qingsong Gao, Enying Zhang, Lei Zhu, Yunyun Hu and Chenwu Xu

    Citation: BMC Plant Biology 2013 13:34

    Content type: Research article

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  8. Long-lived trees can accumulate mutations throughout their lifetimes that may influence biotic and abiotic interactions. For example, some Eucalyptus trees display marked variation in herbivore defence within a s...

    Authors: Amanda Padovan, Andras Keszei, William J Foley and Carsten Külheim

    Citation: BMC Plant Biology 2013 13:29

    Content type: Research article

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    The Erratum to this article has been published in BMC Plant Biology 2013 13:57

  9. Plant parasitism represents an extraordinary interaction among flowering plants: parasitic plants use a specialized organ, the haustorium, to invade the host vascular system to deprive host plants of water and...

    Authors: Quy A Ngo, Huguette Albrecht, Takashi Tsuchimatsu and Ueli Grossniklaus

    Citation: BMC Plant Biology 2013 13:28

    Content type: Research article

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  10. Ginger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding...

    Authors: HyunJo Koo, Eric T McDowell, Xiaoqiang Ma, Kevin A Greer, Jeremy Kapteyn, Zhengzhi Xie, Anne Descour, HyeRan Kim, Yeisoo Yu, David Kudrna, Rod A Wing, Carol A Soderlund and David R Gang

    Citation: BMC Plant Biology 2013 13:27

    Content type: Research article

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  11. Previous studies in basal angiosperms have provided insight into the diversity within the angiosperm lineage and helped to polarize analyses of flowering plant evolution. However, there is still not an experim...

    Authors: Barbara J Bliss, Stefan Wanke, Abdelali Barakat, Saravanaraj Ayyampalayam, Norman Wickett, P Kerr Wall, Yuannian Jiao, Lena Landherr, Paula E Ralph, Yi Hu, Christoph Neinhuis, Jim Leebens-Mack, Kathiravetpilla Arumuganathan, Sandra W Clifton, Siela N Maximova, Hong Ma…

    Citation: BMC Plant Biology 2013 13:13

    Content type: Research article

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  12. Bitter acids (e.g. humulone) are prenylated polyketides synthesized in lupulin glands of the hop plant (Humulus lupulus) which are important contributors to the bitter flavour and stability of beer. Bitter acids ...

    Authors: Shawn M Clark, Vinidhra Vaitheeswaran, Stephen J Ambrose, Randy W Purves and Jonathan E Page

    Citation: BMC Plant Biology 2013 13:12

    Content type: Research article

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  13. Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the fol...

    Authors: Huriye Yanik, Mine Turktas, Ekrem Dundar, Pilar Hernandez, Gabriel Dorado and Turgay Unver

    Citation: BMC Plant Biology 2013 13:10

    Content type: Research article

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  14. Expansins are plant cell wall loosening proteins encoded by a large superfamily of genes, consisting of four families named EXPA, EXPB, EXLA, and EXLB. The evolution of the expansin superfamily is well underst...

    Authors: Robert E Carey, Nathan K Hepler and Daniel J Cosgrove

    Citation: BMC Plant Biology 2013 13:4

    Content type: Research article

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  15. Plant cell walls are complex multicomponent structures that have evolved to fulfil an essential function in providing strength and protection to cells. Hemicelluloses constitute a key component of the cell wal...

    Authors: Emma Hörnblad, Mikael Ulfstedt, Hans Ronne and Alan Marchant

    Citation: BMC Plant Biology 2013 13:3

    Content type: Research article

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  16. Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little ...

    Authors: João Paulo Fabi, Graham B Seymour, Neil S Graham, Martin R Broadley, Sean T May, Franco Maria Lajolo, Beatriz Rosana Cordenunsi and João Roberto Oliveira do Nascimento

    Citation: BMC Plant Biology 2012 12:242

    Content type: Research article

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  17. Endo-(1,4)-β-glucanase (cellulase) glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modificatio...

    Authors: Margaret Buchanan, Rachel A Burton, Kanwarpal S Dhugga, Antoni J Rafalski, Scott V Tingey, Neil J Shirley and Geoffrey B Fincher

    Citation: BMC Plant Biology 2012 12:235

    Content type: Research article

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  18. Receptor-like kinases (RLKs) play key roles during development and in responses to the environment. Despite the relevance of the RLK family and the completion of the tomato genome sequencing, the tomato RLK fa...

    Authors: Tetsu Sakamoto, Michihito Deguchi, Otávio JB Brustolini, Anésia A Santos, Fabyano F Silva and Elizabeth PB Fontes

    Citation: BMC Plant Biology 2012 12:229

    Content type: Research article

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  19. Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved ‘Rossmann-fold’ structure, members of the SDR superfamily exhibi...

    Authors: Hanane Moummou, Yvonne Kallberg, Libert Brice Tonfack, Bengt Persson and Benoît van der Rest

    Citation: BMC Plant Biology 2012 12:219

    Content type: Research article

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  20. MicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs...

    Authors: Bumjin Kim, Hee-Ju Yu, Sin-Gi Park, Ja Young Shin, Mijin Oh, Namshin Kim and Jeong-Hwan Mun

    Citation: BMC Plant Biology 2012 12:218

    Content type: Research article

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  21. Transcription factors (TFs) are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that ...

    Authors: Sara Hernando-Amado, Virginia González-Calle, Pilar Carbonero and Cristina Barrero-Sicilia

    Citation: BMC Plant Biology 2012 12:202

    Content type: Research article

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  22. Epigenetic marks superimposed on the DNA sequence of eukaryote chromosomes provide agility and plasticity in terms of modulating gene expression, ontology, and response to the environment. Modulating the methy...

    Authors: Stephen Amoah, Smita Kurup, Carlos Marcelino Rodriguez Lopez, Sue J Welham, Stephen J Powers, Clare J Hopkins, Michael J Wilkinson and Graham J King

    Citation: BMC Plant Biology 2012 12:193

    Content type: Research article

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  23. Seed germination is of immense significance for agriculture and has been studied for centuries. Yet, our understanding of the molecular mechanisms underlying regulation of dormancy and germination is still in ...

    Authors: Petra Stamm, Pratibha Ravindran, Bijayalaxmi Mohanty, Ee Ling Tan, Hao Yu and Prakash P Kumar

    Citation: BMC Plant Biology 2012 12:179

    Content type: Research article

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  24. The Arabidopsis microRNA156 (miR156) regulates 11 members of the SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) family by base pairing to complementary target mRNAs. Each SPL gene further regulates a set of other g...

    Authors: Shu Wei, Margaret Y Gruber, Bianyun Yu, Ming-Jun Gao, George G Khachatourians, Dwayne D Hegedus, Isobel AP Parkin and Abdelali Hannoufa

    Citation: BMC Plant Biology 2012 12:169

    Content type: Research article

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  25. Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major l...

    Authors: Sheila MC Gordo, Daniel G Pinheiro, Edith CO Moreira, Simone M Rodrigues, Marli C Poltronieri, Oriel F de Lemos, Israel Tojal da Silva, Rommel TJ Ramos, Artur Silva, Horacio Schneider, Wilson A Silva Jr, Iracilda Sampaio and Sylvain Darnet

    Citation: BMC Plant Biology 2012 12:168

    Content type: Research article

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  26. The intrinsically unstructured state of some proteins, observed in all living organisms, is essential for basic cellular functions. In this field the available information from plants is limited but it has bee...

    Authors: Inmaculada Yruela and Bruno Contreras-Moreira

    Citation: BMC Plant Biology 2012 12:165

    Content type: Research article

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  27. Olive (Olea europaea L.) fruits contain numerous secondary metabolites, primarily phenolics, terpenes and sterols, some of which are particularly interesting for their nutraceutical properties. This study will at...

    Authors: Fiammetta Alagna, Roberto Mariotti, Francesco Panara, Silvia Caporali, Stefania Urbani, Gianluca Veneziani, Sonia Esposto, Agnese Taticchi, Adolfo Rosati, Rosa Rao, Gaetano Perrotta, Maurizio Servili and Luciana Baldoni

    Citation: BMC Plant Biology 2012 12:162

    Content type: Research article

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  28. Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functi...

    Authors: Jan Bartoš, Čestmír Vlček, Frédéric Choulet, Mária Džunková, Kateřina Cviková, Jan Šafář, Hana Šimková, Jan Pačes, Hynek Strnad, Pierre Sourdille, Hélène Bergès, Federica Cattonaro, Catherine Feuillet and Jaroslav Doležel

    Citation: BMC Plant Biology 2012 12:155

    Content type: Research article

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  29. Histone acetyltransferases (HATs) play an important role in eukaryotic transcription. Eight HATs identified in rice (OsHATs) can be organized into four families, namely the CBP (OsHAC701, OsHAC703, and OsHAC70...

    Authors: Xia Liu, Ming Luo, Wei Zhang, Jinhui Zhao, Jianxia Zhang, Keqiang Wu, Lining Tian and Jun Duan

    Citation: BMC Plant Biology 2012 12:145

    Content type: Research article

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  30. R genes are a key component of genetic interactions between plants and biotrophic bacteria and are known to regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-bindi...

    Authors: Yang Jae Kang, Kil Hyun Kim, Sangrea Shim, Min Young Yoon, Suli Sun, Moon Young Kim, Kyujung Van and Suk-Ha Lee

    Citation: BMC Plant Biology 2012 12:139

    Content type: Research article

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  31. Identification of the novel genes relevant to plant cell-wall (PCW) synthesis represents a highly important and challenging problem. Although substantial efforts have been invested into studying this problem, ...

    Authors: Shan Wang, Yanbin Yin, Qin Ma, Xiaojia Tang, Dongyun Hao and Ying Xu

    Citation: BMC Plant Biology 2012 12:138

    Content type: Research article

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  32. Plant stilbenes are a small group of phenylpropanoids, which have been detected in at least 72 unrelated plant species and accumulate in response to biotic and abiotic stresses such as infection, wounding, UV-...

    Authors: Alessandro Vannozzi, Ian B Dry, Marianna Fasoli, Sara Zenoni and Margherita Lucchin

    Citation: BMC Plant Biology 2012 12:130

    Content type: Research article

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  33. The MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Nevertheless, their functions appear to be highly diverse and remain rather unclear. To date, no ge...

    Authors: Hai Du, Si-Si Yang, Zhe Liang, Bo-Run Feng, Lei Liu, Yu-Bi Huang and Yi-Xiong Tang

    Citation: BMC Plant Biology 2012 12:106

    Content type: Research article

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  34. In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the h...

    Authors: Sònia Garcia, Lucie Crhák Khaitová and Aleš Kovařík

    Citation: BMC Plant Biology 2012 12:95

    Content type: Research article

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  35. Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effe...

    Authors: Daniel Fonceka, Hodo-Abalo Tossim, Ronan Rivallan, Hélène Vignes, Issa Faye, Ousmane Ndoye, Márcio C Moretzsohn, David J Bertioli, Jean-Christophe Glaszmann, Brigitte Courtois and Jean-François Rami

    Citation: BMC Plant Biology 2012 12:26

    Content type: Research article

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  36. Previous studies on the reproductive biology of ferns showed that mating strategies vary among species, and that polyploid species often show higher capacity for self-fertilization than diploid species. Howeve...

    Authors: G Arjen de Groot, Betty Verduyn, ER Jasper Wubs, Roy HJ Erkens and Heinjo J During

    Citation: BMC Plant Biology 2012 12:3

    Content type: Research article

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  37. Eukaryotic cilia are complex, highly conserved microtubule-based organelles with a broad phylogenetic distribution. Cilia were present in the last eukaryotic common ancestor and many proteins involved in cilia...

    Authors: Matthew E Hodges, Bill Wickstead, Keith Gull and Jane A Langdale

    Citation: BMC Plant Biology 2011 11:185

    Content type: Research article

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  38. Sesame (Sesamum indicum) is one of the most important oilseed crops with high oil contents and rich nutrient value. However, genetic improvement efforts in sesame could not get benefit from molecular biology tech...

    Authors: Tao Ke, Caihua Dong, Han Mao, Yingzhong Zhao, Hong Chen, Hongyan Liu, Xuyan Dong, Chaobo Tong and Shengyi Liu

    Citation: BMC Plant Biology 2011 11:180

    Content type: Research article

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  39. Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to de...

    Authors: Matthew W Blair, Andrea C Fernandez, Manabu Ishitani, Danilo Moreta, Motoaki Seki, Sarah Ayling and Kazuo Shinozaki

    Citation: BMC Plant Biology 2011 11:171

    Content type: Research article

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  40. Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not ...

    Authors: Ana M Fortes, Patricia Agudelo-Romero, Marta S Silva, Kashif Ali, Lisete Sousa, Federica Maltese, Young H Choi, Jerome Grimplet, José M Martinez- Zapater, Robert Verpoorte and Maria S Pais

    Citation: BMC Plant Biology 2011 11:149

    Content type: Research article

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  41. Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous...

    Authors: Feng Cheng, Shengyi Liu, Jian Wu, Lu Fang, Silong Sun, Bo Liu, Pingxia Li, Wei Hua and Xiaowu Wang

    Citation: BMC Plant Biology 2011 11:136

    Content type: Database

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  42. The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementat...

    Authors: Grit Haseneyer, Thomas Schmutzer, Michael Seidel, Ruonan Zhou, Martin Mascher, Chris-Carolin Schön, Stefan Taudien, Uwe Scholz, Nils Stein, Klaus FX Mayer and Eva Bauer

    Citation: BMC Plant Biology 2011 11:131

    Content type: Research article

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  43. Streptophyte green algae share several characteristics of cell growth and cell wall formation with their relatives, the embryophytic land plants. The multilobed cell wall of Micrasterias denticulata that rebuilds...

    Authors: Katrijn Vannerum, Marie JJ Huysman, Riet De Rycke, Marnik Vuylsteke, Frederik Leliaert, Jacob Pollier, Ursula Lütz-Meindl, Jeroen Gillard, Lieven De Veylder, Alain Goossens, Dirk Inzé and Wim Vyverman

    Citation: BMC Plant Biology 2011 11:128

    Content type: Research article

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  44. Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identif...

    Authors: Peter C McKeown, Sylvia Laouielle-Duprat, Pjotr Prins, Philip Wolff, Marc W Schmid, Mark TA Donoghue, Antoine Fort, Dorota Duszynska, Aurélie Comte, Nga Thi Lao, Trevor J Wennblom, Geert Smant, Claudia Köhler, Ueli Grossniklaus and Charles Spillane

    Citation: BMC Plant Biology 2011 11:113

    Content type: Research article

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  45. The carnivorous plant Utricularia gibba (bladderwort) is remarkable in having a minute genome, which at ca. 80 megabases is approximately half that of Arabidopsis. Bladderworts show an incredible diversity of for...

    Authors: Enrique Ibarra-Laclette, Victor A Albert, Claudia A Pérez-Torres, Flor Zamudio-Hernández, María de J Ortega-Estrada, Alfredo Herrera-Estrella and Luis Herrera-Estrella

    Citation: BMC Plant Biology 2011 11:101

    Content type: Research article

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  46. Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, lim...

    Authors: Guillaume Besnard, Pilar Hernández, Bouchaib Khadari, Gabriel Dorado and Vincent Savolainen

    Citation: BMC Plant Biology 2011 11:80

    Content type: Methodology article

    Published on:

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