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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 4 of 7

  1. Content type: Research article

    It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetical...

    Authors: Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jiankun Xie and Shan Gao

    Citation: BMC Plant Biology 2016 16:103

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  2. Content type: Research article

    The ability to grow in phosphorus-depleted soils is an important trait for rice cultivation in many world regions, especially in the tropics. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been identifie...

    Authors: Cynthia C. Vigueira, Linda L. Small and Kenneth M. Olsen

    Citation: BMC Plant Biology 2016 16:101

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  3. Content type: Research article

    CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly depende...

    Authors: Yi Wang, Xianju Liu, Chong Ren, Gan-Yuan Zhong, Long Yang, Shaohua Li and Zhenchang Liang

    Citation: BMC Plant Biology 2016 16:96

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  4. Content type: Research article

    Glyoxalase pathway consists of two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII) which detoxifies a highly cytotoxic metabolite methylglyoxal (MG) to its non-toxic form. MG may form advanced glycation...

    Authors: Ajit Ghosh and Tahmina Islam

    Citation: BMC Plant Biology 2016 16:87

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  5. Content type: Research article

    Dove tree (Davidia involucrata Baill.) is a rare and endangered species. Natural reproduction of dove tree is extremely difficult due to its low fecundity. Serious seed abortion is one of the key factors restrain...

    Authors: Meng Li, Xujie Dong, Jiqing Peng, Wen Xu, Rui Ren, Jane Liu, Fuxiang Cao and Zhiming Liu

    Citation: BMC Plant Biology 2016 16:82

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  6. Content type: Research article

    Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, d...

    Authors: Fulai Zhou, Yong Guo and Li-Juan Qiu

    Citation: BMC Plant Biology 2016 16:58

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  7. Content type: Research article

    MicroRNAs (miRNAs) are important regulatory elements of gene expression. Similarly to coding genes, miRNA genes follow a birth and death pattern of evolution likely reflecting functional relevance and divergen...

    Authors: Edna Gicela Ortiz Morea, Eder Marques da Silva, Geraldo Felipe Ferreira e Silva, Guilherme Targino Valente, Carlos Hernan Barrera Rojas, Michel Vincentz and Fabio Tebaldi Silveira Nogueira

    Citation: BMC Plant Biology 2016 16:40

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    The Erratum to this article has been published in BMC Plant Biology 2016 16:153

  8. Content type: Research article

    Eragrostis tef is an allotetraploid (2n = 4 × = 40) annual, C4 grass with an estimated nuclear genome size of 730 Mbp. It is widely grown in Ethiopia, where it provides basic nutrition...

    Authors: Yohannes Gedamu Gebre, Edoardo Bertolini, Mario Enrico Pè and Andrea Zuccolo

    Citation: BMC Plant Biology 2016 16:39

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  9. Content type: Research article

    Individual fiber strength is an important quality attribute that greatly influences the strength of the yarn spun from cotton fibers. Fiber strength is usually measured from bundles of fibers due to the diffic...

    Authors: Md S. Islam, David D. Fang, Gregory N. Thyssen, Chris D. Delhom, Yongliang Liu and Hee Jin Kim

    Citation: BMC Plant Biology 2016 16:36

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  10. Content type: Research article

    Photosynthesis plays a vital role as an energy source for plant metabolism, and its efficiency may be drastically reduced owing to abiotic stresses. Moso bamboo (Phyllostachys edulis), is a renewable and versatil...

    Authors: Hansheng Zhao, Yongfeng Lou, Huayu Sun, Lichao Li, Lili Wang, Lili Dong and Zhimin Gao

    Citation: BMC Plant Biology 2016 16:34

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  11. Content type: Research article

    Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of th...

    Authors: Jenny Hagenblad, Hugo R. Oliveira, Nils E. G. Forsberg and Matti W. Leino

    Citation: BMC Plant Biology 2016 16:23

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  12. Content type: Research article

    Although the HKT transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II HKT genes are not clearly understood in bread wheat. The ...

    Authors: H. A. Chandima K. Ariyarathna, Klaus H. Oldach and Michael G. Francki

    Citation: BMC Plant Biology 2016 16:21

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  13. Content type: Database

    For functional genomics studies, it is important to understand the dynamic expression profiles of transcribed genes in different tissues, stages of development and in response to environmental stimuli. The pro...

    Authors: Stephen Pearce, Hans Vazquez-Gross, Sayer Y. Herin, David Hane, Yi Wang, Yong Q. Gu and Jorge Dubcovsky

    Citation: BMC Plant Biology 2015 15:299

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  14. Content type: Research article

    Panax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested t...

    Authors: Feng-Xue Shi, Ming-Rui Li, Ya-Ling Li, Peng Jiang, Cui Zhang, Yue-Zhi Pan, Bao Liu, Hong-Xing Xiao and Lin-Feng Li

    Citation: BMC Plant Biology 2015 15:297

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  15. Content type: Research article

    Exploring genetic differentiation and genomic variation is important for both the utilization of heterosis and the dissection of the genetic bases of complex traits.

    Authors: Xun Wu, Yongxiang Li, Xin Li, Chunhui Li, Yunsu Shi, Yanchun Song, Zuping Zheng, Yu Li and Tianyu Wang

    Citation: BMC Plant Biology 2015 15:256

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  16. Content type: Research article

    In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutat...

    Authors: Marialaura Destefanis, Istvan Nagy, Brian Rigney, Glenn J Bryan, Karen McLean, Ingo Hein, Denis Griffin and Dan Milbourne

    Citation: BMC Plant Biology 2015 15:255

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  17. Content type: Research article

    Self-incompatibility (SI) is a widespread and important mating system that promotes outcrossing in plants. Erigeron breviscapus, a medicinal herb used widely in traditional Chinese medicine, is a self-incompatibl...

    Authors: Wei Zhang, Xiang Wei, Heng-Lin Meng, Chun-Hua Ma, Ni-Hao Jiang, Guang-Hui Zhang and Sheng-Chao Yang

    Citation: BMC Plant Biology 2015 15:248

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  18. Content type: Research article

    Drought is a major environmental stress that can have severe impacts on plant productivity and survival. Understanding molecular mechanisms of drought responses is crucial in order to breed for drought adapted...

    Authors: Pascal Pucholt, Per Sjödin, Martin Weih, Ann Christin Rönnberg-Wästljung and Sofia Berlin

    Citation: BMC Plant Biology 2015 15:244

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    The Erratum to this article has been published in BMC Plant Biology 2015 15:285

  19. Content type: Research article

    Long non-coding RNAs (LncRNAs) have been identified as gene regulatory elements that influence the transcription of their neighbouring protein-coding genes. The discovery of LncRNAs in animals has stimulated g...

    Authors: Setareh Mohammadin, Patrick P. Edger, J. Chris Pires and Michael Eric Schranz

    Citation: BMC Plant Biology 2015 15:217

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  20. Content type: Research article

    Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is ‘Tulsi’ (or ‘Tulasi’ or ‘Thulasi’) and is cons...

    Authors: Atul K. Upadhyay, Anita R. Chacko, A. Gandhimathi, Pritha Ghosh, K. Harini, Agnel P. Joseph, Adwait G. Joshi, Snehal D. Karpe, Swati Kaushik, Nagesh Kuravadi, Chandana S Lingu, J. Mahita, Ramya Malarini, Sony Malhotra, Manoharan Malini, Oommen K. Mathew…

    Citation: BMC Plant Biology 2015 15:212

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  21. Content type: Research article

    GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling...

    Authors: Wei Huang, Zhiqiang Xian, Xia Kang, Ning Tang and Zhengguo Li

    Citation: BMC Plant Biology 2015 15:209

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  22. Content type: Research article

    Maize is a major staple food crop globally and contains various concentrations of vitamins. Folates are essential water-soluble B-vitamins that play an important role as one-carbon (C1) donors and acceptors in...

    Authors: Tong Lian, Wenzhu Guo, Maoran Chen, Jinglai Li, Qiuju Liang, Fang Liu, Hongyan Meng, Bosi Xu, Jinfeng Chen, Chunyi Zhang and Ling Jiang

    Citation: BMC Plant Biology 2015 15:204

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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

  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Software

    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

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  34. Content type: Database

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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  42. Content type: Research article

    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

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  43. Content type: Research article

    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

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  44. Content type: Research article

    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

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  45. Content type: Research article

    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

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