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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 1 of 9

  1. Masson pine (Pinus massoniana Lamb.), the dominant native coniferous species in southern China, is commercially important for supplying timber and oleoresin. However, knowledge of the genetic variability of masso...

    Authors: Qinghua Liu, Yini Xie, Bin Liu, HuanhuanYin, Zhichun Zhou, Zhongping Feng and Yadong Chen

    Citation: BMC Plant Biology 2020 20:375

    Content type: Research article

    Published on:

  2. DELLAs play key roles in plant gibberellin signaling pathways and are generally important in plant development and growth. However, DELLAs in many plant taxa have not yet been systematically analyzed.

    Authors: Pengfei Wang, Qianqian Zhang, Yingchun Chen, Yanxia Zhao, Fengshan Ren, Hongmei Shi and Xinying Wu

    Citation: BMC Plant Biology 2020 20:372

    Content type: Research article

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  3. C2H2-type zinc finger protein (ZFPs) form a relatively large family of transcriptional regulators in plants, and play many roles in plant growth, development, and stress response. However, the comprehensive an...

    Authors: Junliang Yin, Lixin Wang, Jiao Zhao, Yiting Li, Rong Huang, Xinchen Jiang, Xiaokang Zhou, Xiongmeng Zhu, Yang He, Yiqin He, Yiqing Liu and Yongxing Zhu

    Citation: BMC Plant Biology 2020 20:359

    Content type: Research article

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  4. Collectively, plants produce a huge variety of secondary metabolites (SMs) which are involved in the adaptation of plants to biotic and abiotic stresses. The most characteristic feature of SMs is their strikin...

    Authors: Yangan Chen, Peter G. L. Klinkhamer, Johan Memelink and Klaas Vrieling

    Citation: BMC Plant Biology 2020 20:342

    Content type: Research article

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  5. Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated align...

    Authors: Xu Zhang, Yanxia Sun, Jacob B. Landis, Zhenyu Lv, Jun Shen, Huajie Zhang, Nan Lin, Lijuan Li, Jiao Sun, Tao Deng, Hang Sun and Hengchang Wang

    Citation: BMC Plant Biology 2020 20:340

    Content type: Research article

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  6. The DnaJ proteins play critical roles in plant development and stress responses. Recently, seventy-six DnaJ genes were identified through a comprehensive bioinformatics analysis in the pepper genome. However, ...

    Authors: Fang Fei Fan, Fawan Liu, Xian Yang, Hongjian Wan and Yunyan Kang

    Citation: BMC Plant Biology 2020 20:326

    Content type: Research article

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  7. Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic rep...

    Authors: Ryan A. Folk, Neeka Sewnath, Chun-Lei Xiang, Brandon T. Sinn and Robert P. Guralnick

    Citation: BMC Plant Biology 2020 20:324

    Content type: Research article

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  8. Nicotiana benthamiana is widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating ...

    Authors: Xinyang Wu, Yuchao Lai, Lanqing Lv, Mengfei Ji, Kelei Han, Dankan Yan, Yuwen Lu, Jiejun Peng, Shaofei Rao, Fei Yan, Hongying Zheng and Jianping Chen

    Citation: BMC Plant Biology 2020 20:305

    Content type: Research article

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  9. Alfalfa has been cultivated in many regions around the world as an important forage crop due to its nutritive value to livestock and ability to adapt to various environments. However, the genetic basis by whic...

    Authors: Sen Lin, Cesar Augusto Medina, Bill Boge, Jinguo Hu, Steven Fransen, Steven Norberg and Long-Xi Yu

    Citation: BMC Plant Biology 2020 20:303

    Content type: Research article

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  10. Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues...

    Authors: Mengdi Li, Aqin Cao, Ruihua Wang, Zeyu Li, Shaoqing Li and Jianbo Wang

    Citation: BMC Plant Biology 2020 20:300

    Content type: Research article

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  11. N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. YT521-B homology (YTH) domain-containing RNA-binding proteins are important RN...

    Authors: Jing Sun, Xiao Min Bie, Ning Wang, Xian Sheng Zhang and Xin-Qi Gao

    Citation: BMC Plant Biology 2020 20:351

    Content type: Research article

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  12. Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvem...

    Authors: Xiujuan Su, Guozhong Zhu, Xiaohui Song, Haijiang Xu, Weixi Li, Xinzhu Ning, Quanjia Chen and Wangzhen Guo

    Citation: BMC Plant Biology 2020 20:289

    Content type: Research article

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  14. Cultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance ...

    Authors: Jana Zwyrtková, Alžběta Němečková, Jana Čížková, Kateřina Holušová, Veronika Kapustová, Radim Svačina, David Kopecký, Bradley John Till, Jaroslav Doležel and Eva Hřibová

    Citation: BMC Plant Biology 2020 20:280

    Content type: Research article

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  15. Theoretically, paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. However, functional divergences...

    Authors: Shuaibin Lian, Yongjie Zhou, Zixiao Liu, Andong Gong and Lin Cheng

    Citation: BMC Plant Biology 2020 20:277

    Content type: Research article

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  16. The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important participants in biological growth and development. To date, the comprehensive genomic and func...

    Authors: Jialin Li, Ting Wang, Jing Han and Zhonghai Ren

    Citation: BMC Plant Biology 2020 20:272

    Content type: Research article

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  17. As a unique sulfated polysaccharide, fucoidan is an important component of cell wall in brown seaweeds. Its biochemical properties are determined by the positions and quantity of sulfate groups. Sulfotransfera...

    Authors: Chang Lu, Zhanru Shao, Pengyan Zhang and Delin Duan

    Citation: BMC Plant Biology 2020 20:271

    Content type: Research article

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  18. Cellular membranes are dynamic structures, continuously adjusting their composition, allowing plants to respond to developmental signals, stresses, and changing environments. To facilitate transmembrane transp...

    Authors: Annamaria De Rosa, Alexander Watson-Lazowski, John R. Evans and Michael Groszmann

    Citation: BMC Plant Biology 2020 20:266

    Content type: Research article

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  19. Ethylene Responsive Factor (ERF) is involved in various processes of plant development and stress responses. In wheat, several ERFs have been identified and their roles in mediating biotic or abiotic stresses ...

    Authors: Lei Zhang, Pan Liu, Jing Wu, Linyi Qiao, Guangyao Zhao, Jizeng Jia, Lifeng Gao and Jianming Wang

    Citation: BMC Plant Biology 2020 20:263

    Content type: Research article

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  20. Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fai...

    Authors: Feng Song, Ting Li, Kevin S. Burgess, Ying Feng and Xue-Jun Ge

    Citation: BMC Plant Biology 2020 20:261

    Content type: Research article

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  21. Plant absorption of ultraviolet (UV) radiation can result in multiple deleterious effects to plant tissues. As a result, plants have evolved an array of strategies to protect themselves from UV radiation, part...

    Authors: Kim Valenta, Kristin Dimac-Stohl, Frances Baines, Todd Smith, Greg Piotrowski, Norman Hill, Jonas Kuppler and Omer Nevo

    Citation: BMC Plant Biology 2020 20:253

    Content type: Research article

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  22. Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneti...

    Authors: Yunsheng Wang, Fei Nie, Muhammad Qasim Shahid and Faheem Shehzad Baloch

    Citation: BMC Plant Biology 2020 20:250

    Content type: Research article

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  23. Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is alread...

    Authors: Monika Ślipiko, Kamil Myszczyński, Katarzyna Buczkowska, Alina Bączkiewicz, Monika Szczecińska and Jakub Sawicki

    Citation: BMC Plant Biology 2020 20:243

    Content type: Research article

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  24. Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is dif...

    Authors: Shangguo Feng, Kaixin Zheng, Kaili Jiao, Yuchen Cai, Chuanlan Chen, Yanyan Mao, Lingyan Wang, Xiaori Zhan, Qicai Ying and Huizhong Wang

    Citation: BMC Plant Biology 2020 20:242

    Content type: Research article

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  25. Pumilio RNA-binding proteins are evolutionarily conserved throughout eukaryotes and are involved in RNA decay, transport, and translation repression in the cytoplasm. Although a majority of Pumilio proteins fu...

    Authors: Su Hyun Park, Hyung-Sae Kim, Prakash Jyoti Kalita and Sang-Bong Choi

    Citation: BMC Plant Biology 2020 20:230

    Content type: Research article

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  27. Expansins (EXPs), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions...

    Authors: Li-Min Lv, Dong-Yun Zuo, Xing-Fen Wang, Hai-Liang Cheng, You-Ping Zhang, Qiao-Lian Wang, Guo-Li Song and Zhi-Ying Ma

    Citation: BMC Plant Biology 2020 20:223

    Content type: Research article

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  28. Members of the cytochrome P450 (CYP450) and UDP-glycosyltransferase (UGT) gene superfamily have been shown to play essential roles in regulating secondary metabolite biosynthesis. However, the systematic ident...

    Authors: Yao Cheng, Hanbing Liu, Xuejiao Tong, Zaimin Liu, Xin Zhang, Dalong Li, Xinmei Jiang and Xihong Yu

    Citation: BMC Plant Biology 2020 20:214

    Content type: Research article

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  29. Flowering is a crucial stage during plant development. Plants may respond to unfavorable conditions by accelerating reproductive processes like flowering. In a recent study, we showed that PRECOCIOUS1 (POCO1) ...

    Authors: Hossein Emami, Abhishek Kumar and Frank Kempken

    Citation: BMC Plant Biology 2020 20:209

    Content type: Research article

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  30. With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degra...

    Authors: Jingfang Chen, Runxian Yu, Jinhong Dai, Ying Liu and Renchao Zhou

    Citation: BMC Plant Biology 2020 20:199

    Content type: Research article

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  31. Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in...

    Authors: Xinghai Yang, Xiuzhong Xia, Yu Zeng, Baoxuan Nong, Zongqiong Zhang, Yanyan Wu, Qinglan Tian, Weiying Zeng, Ju Gao, Weiyong Zhou, Haifu Liang, Danting Li and Guofu Deng

    Citation: BMC Plant Biology 2020 20:193

    Content type: Research article

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  32. Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanism...

    Authors: Lingzi Xue, Mintao Sun, Zhen Wu, Lu Yu, Qinghui Yu, Yaping Tang and Fangling Jiang

    Citation: BMC Plant Biology 2020 20:162

    Content type: Research article

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  33. In most angiosperms, the inheritance of the mitochondria takes place in a typical maternal manner. However, very less information is available about if the existence of structural variations or not in mitochon...

    Authors: Weilong Yang, Jianing Zou, Jiajia Wang, Nengwu Li, Xiaoyun Luo, Xiaofen Jiang and Shaoqing Li

    Citation: BMC Plant Biology 2020 20:159

    Content type: Research article

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  34. Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhil...

    Authors: Qianqian Liu, Zuyu Lu, Wei He, Fang Li, Wenna Chen, Chan Li, Zhi Chao and Enwei Tian

    Citation: BMC Plant Biology 2020 20:152

    Content type: Research article

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  35. NADP-malic enzyme (NAPD-ME), and pyruvate orthophosphate dikinase (PPDK) are important enzymes that participate in C4 photosynthesis. However, the evolutionary history and forces driving evolution of these genes ...

    Authors: Weiping Shi, Linqi Yue, Jiahui Guo, Jianming Wang, Xiangyang Yuan, Shuqi Dong, Jie Guo and Pingyi Guo

    Citation: BMC Plant Biology 2020 20:132

    Content type: Research article

    Published on:

  37. The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in t...

    Authors: Yun-Zhuo Ke, Yun-Wen Wu, Hong-Jun Zhou, Ping Chen, Mang-Mang Wang, Ming-Ming Liu, Peng-Feng Li, Jin Yang, Jia-Na Li and Hai Du

    Citation: BMC Plant Biology 2020 20:115

    Content type: Research article

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  38. The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetati...

    Authors: Fabian Bratzel, Sascha Heller, Nadine Cyrannek, Juraj Paule, Elton M. C. Leme, Anna Loreth, Annika Nowotny, Markus Kiefer, Walter Till, Michael H. J. Barfuss, Christian Lexer, Marcus A. Koch and Georg Zizka

    Citation: BMC Plant Biology 2020 20:111

    Content type: Research article

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  39. In contrast to most animal species, polyploid plant species are quite tolerant of aneuploidy. Here, the global transcriptome of four aneuploid derivatives of a synthetic hexaploid wheat line was acquired, with...

    Authors: Deying Zeng, Jiantao Guan, Jiangtao Luo, Laibin Zhao, Yazhou Li, Wenshuai Chen, Lianquan Zhang, Shunzong Ning, Zhongwei Yuan, Aili Li, Youliang Zheng, Long Mao, Dengcai Liu and Ming Hao

    Citation: BMC Plant Biology 2020 20:97

    Content type: Research article

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  40. In plants, the key roles played by RopGEF-mediated ROP signaling in diverse processes, including polar tip growth, have been identified. Despite their important roles in reproduction, a comprehensive analysis ...

    Authors: Eui-Jung Kim, Sung-Wook Park, Woo-Jong Hong, Jeniffer Silva, Wanqi Liang, Dabing Zhang, Ki-Hong Jung and Yu-Jin Kim

    Citation: BMC Plant Biology 2020 20:95

    Content type: Research article

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  42. The B-BOX (BBX) proteins are the class of zinc-finger transcription factors and can regulate plant growth, development, and endure stress response. In plants, the BBX gene family has been identified in Arabidopsi...

    Authors: Hongru Wei, Peipei Wang, Jianqing Chen, Changjun Li, Yongzhang Wang, Yongbing Yuan, Jinggui Fang and Xiangpeng Leng

    Citation: BMC Plant Biology 2020 20:72

    Content type: Research article

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  44. Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrence...

    Authors: Jinpeng Wang, Jigao Yu, Yuxian Li, Chendan Wei, He Guo, Ying Liu, Jin Zhang, Xiuqing Li and Xiyin Wang

    Citation: BMC Plant Biology 2020 20:52

    Content type: Research article

    Published on:

  45. Cassava is highly tolerant to stressful conditions, especially drought stress conditions; however, the mechanisms underlying this tolerance are poorly understood. The GRAS gene family is a large family of tran...

    Authors: Zhongying Shan, Xinglu Luo, Meiyan Wu, Limei Wei, Zhupeng Fan and Yanmei Zhu

    Citation: BMC Plant Biology 2020 20:46

    Content type: Research article

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  46. Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) protein...

    Authors: Dong-Hong Chen, Han-Lin Qiu, Yong Huang, Lei Zhang and Jin-Ping Si

    Citation: BMC Plant Biology 2020 20:40

    Content type: Research article

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  47. Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant dev...

    Authors: Xiaomin Feng, Yongjun Wang, Nannan Zhang, Zilin Wu, Qiaoying Zeng, Jiayun Wu, Xiaobin Wu, Lei Wang, Jisen Zhang and Yongwen Qi

    Citation: BMC Plant Biology 2020 20:20

    Content type: Research article

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  48. The BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulating fruit quality, catalytic synthesizing of terpene, phenolics and esters, and improving stress resistance. Howe...

    Authors: Chunxin Liu, Xin Qiao, Qionghou Li, Weiwei Zeng, Shuwei Wei, Xin Wang, Yangyang Chen, Xiao Wu, Jun Wu, Hao Yin and Shaoling Zhang

    Citation: BMC Plant Biology 2020 20:14

    Content type: Research article

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  49. Pectin methylesterase (PME) is a hydrolytic enzyme that catalyzes the demethylesterification of homogalacturonans and controls pectin reconstruction, being essential in regulation of cell wall modification. Du...

    Authors: Cheng Xue, Si-Cong Guan, Jian-Qing Chen, Chen-Jin Wen, Jian-Fa Cai and Xu Chen

    Citation: BMC Plant Biology 2020 20:13

    Content type: Research article

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  50. Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular m...

    Authors: Zihan Liu, Sha Li, Wei Li, Qi Liu, Lingli Zhang and Xiyue Song

    Citation: BMC Plant Biology 2020 20:10

    Content type: Research article

    Published on:

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