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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 5 of 7

  1. The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epi...

    Authors: Anna Venetsky, Adva Levy-Zamir, Vadim Khasdan, Katherine Domb and Khalil Kashkush

    Citation: BMC Plant Biology 2015 15:200

    Content type: Research article

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  2. Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism and occurs in both eukaryotes and prokaryotes. Yet, to date, no trans...

    Authors: Alice Louise Burgess, Rakesh David and Iain Robert Searle

    Citation: BMC Plant Biology 2015 15:199

    Content type: Research article

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  3. Pineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the...

    Authors: R. M. Redwan, A. Saidin and S. V. Kumar

    Citation: BMC Plant Biology 2015 15:196

    Content type: Research article

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    The Erratum to this article has been published in BMC Plant Biology 2015 15:294

  4. Tea plants (Camellia sinensis) are used to produce one of the most important beverages worldwide. The nutritional value and healthful properties of tea are closely related to the large amounts of three major char...

    Authors: Yuling Tai, Chaoling Wei, Hua Yang, Liang Zhang, Qi Chen, Weiwei Deng, Shu Wei, Jing Zhang, Congbing Fang, Chitang Ho and Xiaochun Wan

    Citation: BMC Plant Biology 2015 15:190

    Content type: Research article

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  5. Calcium ions, the most versatile secondary messenger found in plants, are involved in the regulation of diverse arrays of plant growth and development, as well as biotic and abiotic stress responses. The calci...

    Authors: Tapan Kumar Mohanta, Nibedita Mohanta, Yugal Kishore Mohanta, Pratap Parida and Hanhong Bae

    Citation: BMC Plant Biology 2015 15:189

    Content type: Research article

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  6. Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation seq...

    Authors: Joseph L. Cotton, William P. Wysocki, Lynn G. Clark, Scot A. Kelchner, J Chris Pires, Patrick P. Edger, Dustin Mayfield-Jones and Melvin R. Duvall

    Citation: BMC Plant Biology 2015 15:178

    Content type: Research article

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  7. Leaf red coloration is an important characteristic in many plant species, including cultivars of ornamental peach (Prunus persica). Peach leaf color is controlled by a single Gr gene on linkage group 6, with a re...

    Authors: Ying Zhou, Hui Zhou, Kui Lin-Wang, Sornkanok Vimolmangkang, Richard V Espley, Lu Wang, Andrew C Allan and Yuepeng Han

    Citation: BMC Plant Biology 2014 14:388

    Content type: Research article

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  8. Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to ...

    Authors: Rick E Masonbrink, Joseph P Gallagher, Josef J Jareczek, Simon Renny-Byfield, Corrinne E Grover, Lei Gong and Jonathan F Wendel

    Citation: BMC Plant Biology 2014 14:383

    Content type: Research article

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  9. Western white pine (WWP, Pinus monticola Douglas ex D. Don) is of high interest in forest breeding and conservation because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused...

    Authors: Jun-Jun Liu, Richard A Sniezko, Rona N Sturrock and Hao Chen

    Citation: BMC Plant Biology 2014 14:380

    Content type: Research article

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  10. GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese c...

    Authors: Ningning Wu, Yan Zhu, Wanlu Song, Yaxuan Li, Yueming Yan and Yingkao Hu

    Citation: BMC Plant Biology 2014 14:373

    Content type: Research article

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  11. Availability of the draft nuclear genome sequences of small-seeded desi-type legume crop Cicer arietinum has provided an opportunity for investigating unique chickpea genomic features and evaluation of their biol...

    Authors: Gopal Misra, Piyush Priya, Nitesh Bandhiwal, Neha Bareja, Mukesh Jain, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K Tyagi and Gitanjali Yadav

    Citation: BMC Plant Biology 2014 14:315

    Content type: Software

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  12. Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small ...

    Authors: Thomas Nussbaumer, Karl G Kugler, Wolfgang Schweiger, Kai C Bader, Heidrun Gundlach, Manuel Spannagl, Naser Poursarebani, Matthias Pfeifer and Klaus FX Mayer

    Citation: BMC Plant Biology 2014 14:348

    Content type: Database

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  13. Mitogen-activated protein kinase (MAPK) cascades play a crucial role in plant growth and development as well as biotic and abiotic stress responses. Knowledge about the MAPK gene family in cotton is limited, a...

    Authors: Xueying Zhang, Liman Wang, Xiaoyang Xu, Caiping Cai and Wangzhen Guo

    Citation: BMC Plant Biology 2014 14:345

    Content type: Research article

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  14. For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis...

    Authors: David Amar, Itziar Frades, Agnieszka Danek, Tatyana Goldberg, Sanjeev K Sharma, Pete E Hedley, Estelle Proux-Wera, Erik Andreasson, Ron Shamir, Oren Tzfadia and Erik Alexandersson

    Citation: BMC Plant Biology 2014 14:329

    Content type: Research article

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  15. Banana is one of the most important crop plants grown in the tropics and sub-tropics. It is a climacteric fruit and undergoes ethylene dependent ripening. Once ripening is initiated, it proceeds at a fast rate...

    Authors: Mehar Hasan Asif, Deepika Lakhwani, Sumya Pathak, Parul Gupta, Sumit K Bag, Pravendra Nath and Prabodh Kumar Trivedi

    Citation: BMC Plant Biology 2014 14:316

    Content type: Research article

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  16. Hybrids of larch (Larix kaempferi × Larix olgensis) are important afforestation species in northeastern China. They are routinely propagated via rooted stem cuttings. Despite the importance of rooting, little is ...

    Authors: Hua Han, Xiaomei Sun, Yunhui Xie, Jian Feng and Shougong Zhang

    Citation: BMC Plant Biology 2014 14:305

    Content type: Research article

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  17. The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II,...

    Authors: Zhihua Wu, Songtao Gui, Zhiwu Quan, Lei Pan, Shuzhen Wang, Weidong Ke, Dequan Liang and Yi Ding

    Citation: BMC Plant Biology 2014 14:289

    Content type: Research article

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  18. In the co-evolution between insects and plants, the establishment of floral monosymmetry was an important step in angiosperm development as it facilitated the interaction with insect pollinators and, by that, ...

    Authors: Andrea Busch, Stefanie Horn and Sabine Zachgo

    Citation: BMC Plant Biology 2014 14:285

    Content type: Research article

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  19. The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid ...

    Authors: Olga P Yurchenko, Sunjung Park, Daniel C Ilut, Jay J Inmon, Jon C Millhollon, Zach Liechty, Justin T Page, Matthew A Jenks, Kent D Chapman, Joshua A Udall, Michael A Gore and John M Dyer

    Citation: BMC Plant Biology 2014 14:312

    Content type: Research article

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  20. Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. Most resistance genes were identified by linkage mapping using genetic populations. We extensively examin...

    Authors: Caihong Wang, Yaolong Yang, Xiaoping Yuan, Qun Xu, Yue Feng, Hanyong Yu, Yiping Wang and Xinghua Wei

    Citation: BMC Plant Biology 2014 14:311

    Content type: Research article

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  21. Xylogen, a chimeric arabinogalactan protein containing a non-specific lipid transfer protein domain, can promote xylem cell differentiation. No comprehensive study has been carried out on the XYLP gene family in ...

    Authors: Tengfei Ma, Haoli Ma, Heming Zhao, Huandong Qi and Jie Zhao

    Citation: BMC Plant Biology 2014 14:299

    Content type: Research article

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  22. Plant glandular trichomes are chemical factories with specialized metabolic capabilities to produce diverse compounds. Aromatic mint plants produce valuable essential oil in specialised glandular trichomes kno...

    Authors: Jingjing Jin, Deepa Panicker, Qian Wang, Mi Jung Kim, Jun Liu, Jun-Lin Yin, Limsoon Wong, In-Cheol Jang, Nam-Hai Chua and Rajani Sarojam

    Citation: BMC Plant Biology 2014 14:292

    Content type: Research article

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  23. Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Com...

    Authors: Naama Menda, Susan R Strickler, Jeremy D Edwards, Aureliano Bombarely, Diane M Dunham, Gregory B Martin, Luis Mejia, Samuel F Hutton, Michael J Havey, Douglas P Maxwell and Lukas A Mueller

    Citation: BMC Plant Biology 2014 14:287

    Content type: Research article

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  24. In plant, non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that have been reported to be involved in numerous biological processes such as transfer of phospholipids, reproductive develop...

    Authors: Kaifa Wei and Xiaojun Zhong

    Citation: BMC Plant Biology 2014 14:281

    Content type: Research article

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  25. Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem ...

    Authors: Guillaume Bauchet, Stéphane Munos, Christopher Sauvage, Julien Bonnet, Laurent Grivet and Mathilde Causse

    Citation: BMC Plant Biology 2014 14:279

    Content type: Research article

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  26. An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome "shock" and instability occur dur...

    Authors: Muhammad Awais Ghani, Junxing Li, Linli Rao, Muhammad Ammar Raza, Liwen Cao, Ningning Yu, Xiaoxia Zou and Liping Chen

    Citation: BMC Plant Biology 2014 14:272

    Content type: Research article

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  27. Evolutionary theory suggests that males and females may evolve sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximi...

    Authors: Kathryn M Robinson, Nicolas Delhomme, Niklas Mähler, Bastian Schiffthaler, Jenny Önskog, Benedicte R Albrectsen, Pär K Ingvarsson, Torgeir R Hvidsten, Stefan Jansson and Nathaniel R Street

    Citation: BMC Plant Biology 2014 14:276

    Content type: Research article

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  28. Tea is a popular natural non-alcoholic beverage consumed worldwide due to its bioactive ingredients, particularly catechins (flavan-3-ols). Catechins not only contribute to tea quality but also serve important...

    Authors: Zhi-Jun Wu, Xing-Hui Li, Zhi-Wei Liu, Zhi-Sheng Xu and Jing Zhuang

    Citation: BMC Plant Biology 2014 14:277

    Content type: Research article

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  29. Members of the ancient land-plant-specific transcription factor AT-Hook Motif Nuclear Localized (AHL) gene family regulate various biological processes. However, the relationships among the AHL genes, as well as ...

    Authors: Jianfei Zhao, David S Favero, Jiwen Qiu, Eric H Roalson and Michael M Neff

    Citation: BMC Plant Biology 2014 14:266

    Content type: Research article

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  30. New SNP marker platforms offer the opportunity to investigate the relationships between wheat cultivars from different regions and assess the mechanism and processes that have led to adaptation to particular p...

    Authors: Yuri Shavrukov, Radoslaw Suchecki, Serik Eliby, Aigul Abugalieva, Serik Kenebayev and Peter Langridge

    Citation: BMC Plant Biology 2014 14:258

    Content type: Research article

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  31. Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultiv...

    Authors: Ying-Hui Li, Jochen C Reif, Scott A Jackson, Yan-Song Ma, Ru-Zhen Chang and Li-Juan Qiu

    Citation: BMC Plant Biology 2014 14:251

    Content type: Research article

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  32. The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Alth...

    Authors: Ralf Stracke, Daniela Holtgräwe, Jessica Schneider, Boas Pucker, Thomas Rosleff Sörensen and Bernd Weisshaar

    Citation: BMC Plant Biology 2014 14:249

    Content type: Research article

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  33. Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of ...

    Authors: Marta Bencke-Malato, Caroline Cabreira, Beatriz Wiebke-Strohm, Lauro Bücker-Neto, Estefania Mancini, Marina B Osorio, Milena S Homrich, Andreia Carina Turchetto-Zolet, Mayra CCG De Carvalho, Renata Stolf, Ricardo LM Weber, Gastón Westergaard, Atílio P Castagnaro, Ricardo V Abdelnoor, Francismar C Marcelino-Guimarães, Márcia Margis-Pinheiro…

    Citation: BMC Plant Biology 2014 14:236

    Content type: Research article

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  34. In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinife...

    Authors: Sandrine Picq, Sylvain Santoni, Thierry Lacombe, Muriel Latreille, Audrey Weber, Morgane Ardisson, Sarah Ivorra, David Maghradze, Rosa Arroyo-Garcia, Philippe Chatelet, Patrice This, Jean-Frédéric Terral and Roberto Bacilieri

    Citation: BMC Plant Biology 2014 14:229

    Content type: Research article

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  35. MicroRNAs (miRNAs) are a new class of endogenous regulators of a broad range of physiological processes, which act by regulating gene expression post-transcriptionally. The brassica vegetable, broccoli (Brassica ...

    Authors: Yunhong Tian, Yunming Tian, Xiaojun Luo, Tao Zhou, Zuoping Huang, Ying Liu, Yihan Qiu, Bing Hou, Dan Sun, Hongyu Deng, Shen Qian and Kaitai Yao

    Citation: BMC Plant Biology 2014 14:226

    Content type: Research article

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  36. Mitogen-activated protein kinase kinase kinases (MAPKKKs; MAP3Ks) are important components of MAPK cascades, which are highly conserved signal transduction pathways in animals, yeast and plants, play important...

    Authors: Gang Wang, Arianna Lovato, Annalisa Polverari, Min Wang, Ying-Hai Liang, Yuan-Chun Ma and Zong-Ming Cheng

    Citation: BMC Plant Biology 2014 14:219

    Content type: Research article

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  37. Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and m...

    Authors: Sonali Sachin Ranade, Yao-Cheng Lin, Andrea Zuccolo, Yves Van de Peer and María del Rosario García-Gil

    Citation: BMC Plant Biology 2014 14:220

    Content type: Research article

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  38. The paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is also commonly utilized in traditional medicine in China and other Asian countries. To identify ...

    Authors: Xianjun Peng, Yucheng Wang, Ruiping He, Meiling Zhao and Shihua Shen

    Citation: BMC Plant Biology 2014 14:194

    Content type: Research article

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  39. Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species.

    Authors: Yu-Duan Ding, Ji-Wei Chang, Jing Guo, DiJun Chen, Sen Li, Qiang Xu, Xiu-Xin Deng, Yun-Jiang Cheng and Ling-Ling Chen

    Citation: BMC Plant Biology 2014 14:213

    Content type: Research article

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  40. The Maternally expressed gene (Meg) family is a locally-duplicated gene family of maize which encodes cysteine-rich proteins (CRPs). The founding member of the family, Meg1, is required for normal development of ...

    Authors: Yuqing Xiong, Wenbin Mei, Eun-Deok Kim, Krishanu Mukherjee, Hatem Hassanein, William Brad Barbazuk, Sibum Sung, Bryan Kolaczkowski and Byung-Ho Kang

    Citation: BMC Plant Biology 2014 14:204

    Content type: Research article

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  41. The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the geno...

    Authors: Karen S Aitken, Meredith D McNeil, Paul J Berkman, Scott Hermann, Andrzej Kilian, Peter C Bundock and Jingchuan Li

    Citation: BMC Plant Biology 2014 14:190

    Content type: Research article

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  42. Taxodium is renowned for its strong tolerance to waterlogging stress, thus it has great ecological and economic potential. However, the scant genomic resources in genus Taxodium have greatly hindered further expl...

    Authors: Baiyan Qi, Ying Yang, Yunlong Yin, Meng Xu and Huogen Li

    Citation: BMC Plant Biology 2014 14:201

    Content type: Research article

    Published on:

  43. In angiosperms, the endosperm plays a crucial placenta-like role in that not only is it necessary for nurturing the embryo, but also regulating embryogenesis through complicated genetic and epigenetic interact...

    Authors: Mingming Xin, Ruolin Yang, Yingyin Yao, Chuang Ma, Huiru Peng, Qixin Sun, Xiangfeng Wang and Zhongfu Ni

    Citation: BMC Plant Biology 2014 14:192

    Content type: Research article

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  44. Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene cop...

    Authors: Raviraj M Kalunke, Alberto Cenci, Chiara Volpi, Donal M O’Sullivan, Luca Sella, Francesco Favaron, Felice Cervone, Giulia De Lorenzo and Renato D’Ovidio

    Citation: BMC Plant Biology 2014 14:189

    Content type: Research article

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  45. Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. In vitro somatic embryogenesis (SE) of cacao is a propagation system useful for rapid mass-multiplication to accelerat...

    Authors: Siela N Maximova, Sergio Florez, Xiangling Shen, Nicolas Niemenak, Yufan Zhang, Wayne Curtis and Mark J Guiltinan

    Citation: BMC Plant Biology 2014 14:185

    Content type: Research article

    Published on:

  46. The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world’s most economically important fruit crops. With increasing volumes of transcriptomics dat...

    Authors: Darren CJ Wong, Crystal Sweetman and Christopher M Ford

    Citation: BMC Plant Biology 2014 14:186

    Content type: Research article

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  47. Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA ...

    Authors: Ningning Wang, Di Zhang, Zhenhui Wang, Hongwei Xun, Jian Ma, Hui Wang, Wei Huang, Ying Liu, Xiuyun Lin, Ning Li, Xiufang Ou, Chunyu Zhang, Ming-Bo Wang and Bao Liu

    Citation: BMC Plant Biology 2014 14:177

    Content type: Research article

    Published on:

  48. Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model...

    Authors: Lei Wang, Chenlong Cao, Qibin Ma, Qiaoying Zeng, Haifeng Wang, Zhihao Cheng, Genfeng Zhu, Ji Qi, Hong Ma, Hai Nian and Yingxiang Wang

    Citation: BMC Plant Biology 2014 14:169

    Content type: Research article

    Published on:

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