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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. Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two w...

    Authors: Yingxiao Zhang, Brian J. Iaffaldano, Xiaofeng Zhuang, John Cardina and Katrina Cornish

    Citation: BMC Plant Biology 2017 17:34

    Content type: Research article

    Published on:

  2. microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, wh...

    Authors: Xuyan Li, Xin Xie, Ji Li, Yuhai Cui, Yanming Hou, Lulu Zhai, Xiao Wang, Yanli Fu, Ranran Liu and Shaomin Bian

    Citation: BMC Plant Biology 2017 17:32

    Content type: Research article

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  3. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolism and biosynthesis processes. Comprehensive analysis of AAAP genes has been conducted in Arabidops...

    Authors: Huanlong Liu, Min Wu, Dongyue Zhu, Feng Pan, Yujiao Wang, Yue Wang and Yan Xiang

    Citation: BMC Plant Biology 2017 17:29

    Content type: Research article

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  4. Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal stru...

    Authors: Roman A. Volkov, Irina I. Panchuk, Nikolai V. Borisjuk, Marta Hosiawa-Baranska, Jolanta Maluszynska and Vera Hemleben

    Citation: BMC Plant Biology 2017 17:21

    Content type: Research article

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  5. The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (

    Authors: Sathish K. Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu (Kal) Kalavacharla and Muthusamy Manoharan

    Citation: BMC Plant Biology 2017 17:9

    Content type: Research article

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  6. Polyploidy is well studied from a genetic and genomic perspective, but the morphological, anatomical, and physiological consequences of polyploidy remain relatively uncharacterized. Whether these potential cha...

    Authors: Robert L. Baker, Yulia Yarkhunova, Katherine Vidal, Brent E. Ewers and Cynthia Weinig

    Citation: BMC Plant Biology 2017 17:3

    Content type: Research article

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  7. Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these r...

    Authors: Oz Barazani, Alexandra Keren-Keiserman, Erik Westberg, Nir Hanin, Arnon Dag, Giora Ben-Ari, Ori Fragman-Sapir, Yizhar Tugendhaft, Zohar Kerem and Joachim W. Kadereit

    Citation: BMC Plant Biology 2016 16:261

    Content type: Research article

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  8. Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies o...

    Authors: Tracy Raines, Ivory C. Blakley, Yu-Chang Tsai, Jennifer M. Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G. Eric Schaller, Ann E. Loraine and Joseph J. Kieber

    Citation: BMC Plant Biology 2016 16:260

    Content type: Research article

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  9. RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, an...

    Authors: Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang and Jianing Yu

    Citation: BMC Plant Biology 2016 16:257

    Content type: Research article

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  10. Climate change is predicted to be a serious threat to agriculture due to the need for crops to be able to tolerate increased heat stress. Desert plants have already adapted to high levels of heat stress so the...

    Authors: Abdullah Y. Obaid, Jamal S. M. Sabir, Ahmed Atef, Xuan Liu, Sherif Edris, Fotouh M. El-Domyati, Mohammed Z. Mutwakil, Nour O. Gadalla, Nahid H. Hajrah, Magdy A. Al-Kordy, Neil Hall, Ahmed Bahieldin and Robert K. Jansen

    Citation: BMC Plant Biology 2016 16:252

    Content type: Research article

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  11. Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of gro...

    Authors: Edward V. McAssey, Jonathan Corbi and John M. Burke

    Citation: BMC Plant Biology 2016 16:249

    Content type: Research article

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  12. Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glyco...

    Authors: Allan M. Showalter, Brian D. Keppler, Xiao Liu, Jens Lichtenberg and Lonnie R. Welch

    Citation: BMC Plant Biology 2016 16:229

    Content type: Research article

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  13. Blueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information r...

    Authors: Lingli Li, Hehua Zhang, Zhongshuai Liu, Xiaoyue Cui, Tong Zhang, Yanfang Li and Lingyun Zhang

    Citation: BMC Plant Biology 2016 16:223

    Content type: Research article

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  14. Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at ...

    Authors: Radoslaw Lukoszek, Peter Feist and Zoya Ignatova

    Citation: BMC Plant Biology 2016 16:221

    Content type: Research article

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  15. Phosphorus (P), an essential macronutrient, is often limiting in soils and affects plant growth and development. In Arabidopsis thaliana, Low Phosphate Root1 (LPR1) and its close paralog LPR2 encode multicopper o...

    Authors: Yue Cao, Hao Ai, Ajay Jain, Xueneng Wu, Liang Zhang, Wenxia Pei, Aiqun Chen, Guohua Xu and Shubin Sun

    Citation: BMC Plant Biology 2016 16:210

    Content type: Research article

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  16. Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigat...

    Authors: Lihui Wang, Xiujuan Bei, Jiansheng Gao, Yaxuan Li, Yueming Yan and Yingkao Hu

    Citation: BMC Plant Biology 2016 16:207

    Content type: Research article

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  17. Avocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree...

    Authors: B. J. Reeksting, N. A. Olivier and N. van den Berg

    Citation: BMC Plant Biology 2016 16:205

    Content type: Research article

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  18. SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological pro...

    Authors: Hongtao Cheng, Mengyu Hao, Wenxiang Wang, Desheng Mei, Chaobo Tong, Hui Wang, Jia Liu, Li Fu and Qiong Hu

    Citation: BMC Plant Biology 2016 16:196

    Content type: Research article

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  19. The new shoots of the albino tea cultivar ‘Anji Baicha’ are yellow or white at low temperatures and turn green as the environmental temperatures increase during the early spring. ‘Anji Baicha’ metabolite profi...

    Authors: Chun-Fang Li, Yan-Xia Xu, Jian-Qiang Ma, Ji-Qiang Jin, Dan-Juan Huang, Ming-Zhe Yao, Chun-Lei Ma and Liang Chen

    Citation: BMC Plant Biology 2016 16:195

    Content type: Research article

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  20. Some plants develop a breeding system that produces both chasmogamous (CH) and cleistogamous (CL) flowers. However, the underlying molecular mechanism remains elusive.

    Authors: Qiaoxia Li, Qingdi Huo, Juan Wang, Jing Zhao, Kun Sun and Chaoying He

    Citation: BMC Plant Biology 2016 16:151

    Content type: Research article

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  21. In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intens...

    Authors: Stephen Pearce, Nestor Kippes, Andrew Chen, Juan Manuel Debernardi and Jorge Dubcovsky

    Citation: BMC Plant Biology 2016 16:141

    Content type: Research article

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  22. Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lac...

    Authors: Sean V. Burke, William P. Wysocki, Fernando O. Zuloaga, Joseph M. Craine, J. Chris Pires, Patrick P. Edger, Dustin Mayfield-Jones, Lynn G. Clark, Scot A. Kelchner and Melvin R. Duvall

    Citation: BMC Plant Biology 2016 16:140

    Content type: Research article

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  23. Dwarfism is one of the most valuable traits in banana breeding because semi-dwarf cultivars show good resistance to damage by wind and rain. Moreover, these cultivars present advantages of convenient cultivati...

    Authors: Jingjing Chen, Jianghui Xie, Yajie Duan, Huigang Hu, Yulin Hu and Weiming Li

    Citation: BMC Plant Biology 2016 16:123

    Content type: Research article

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  24. MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress re...

    Authors: Thangasamy Saminathan, Abiodun Bodunrin, Nripendra V. Singh, Ramajayam Devarajan, Padma Nimmakayala, Moersfelder Jeff, Mallikarjuna Aradhya and Umesh K. Reddy

    Citation: BMC Plant Biology 2016 16:122

    Content type: Research article

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  25. Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the...

    Authors: Teresa Kowar, Falk Zakrzewski, Jiří Macas, Andrea Kobližková, Prisca Viehoever, Bernd Weisshaar and Thomas Schmidt

    Citation: BMC Plant Biology 2016 16:120

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

    Published on:

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

  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Database

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  40. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

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  45. 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

    Content type: Research article

    Published on:

  46. 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

    Content type: Research article

    Published on:

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

  47. 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

    Content type: Research article

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  48. 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

    Content type: Research article

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  49. 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

    Content type: Research article

    Published on:

  50. 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

    Content type: Research article

    Published on:

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