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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 8

  1. 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

    Published on:

  2. 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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  3. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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

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  15. 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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  16. 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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  17. 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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  18. 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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  20. 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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  22. 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

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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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

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  29. Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstruc...

    Authors: Jesse R. Walsh, Margaret R. Woodhouse, Carson M. Andorf and Taner Z. Sen

    Citation: BMC Plant Biology 2020 20:4

    Content type: Research article

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  30. Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections thro...

    Authors: Hélène Muranty, Caroline Denancé, Laurence Feugey, Jean-Luc Crépin, Yves Barbier, Stefano Tartarini, Matthew Ordidge, Michela Troggio, Marc Lateur, Hilde Nybom, Frantisek Paprstein, François Laurens and Charles-Eric Durel

    Citation: BMC Plant Biology 2020 20:2

    Content type: Research article

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  31. The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model p...

    Authors: Feng Chen, Qin Zhou, Lan Wu, Fei Li, Baojun Liu, Shuting Zhang, Jiaqi Zhang, Manzhu Bao and Guofeng Liu

    Citation: BMC Plant Biology 2019 19:600

    Content type: Research article

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  32. Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for ide...

    Authors: Nan Lu, Miaomiao Zhang, Yao Xiao, Donghua Han, Ying Liu, Yu Zhang, Fei Yi, Tianqing Zhu, Wenjun Ma, Erqin Fan, Guanzheng Qu and Junhui Wang

    Citation: BMC Plant Biology 2019 19:596

    Content type: Research article

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  33. Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, littl...

    Authors: Yiyang Liu, Jiao Zhu, Sheng Sun, Feng Cui, Yan Han, Zhenying Peng, Xuejie Zhang, Shubo Wan and Guowei Li

    Citation: BMC Plant Biology 2019 19:593

    Content type: Research article

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  34. Pueraria candollei var. mirifica, a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and de...

    Authors: Nithiwat Suntichaikamolkul, Kittitya Tantisuwanichkul, Pinidphon Prombutara, Khwanlada Kobtrakul, Julie Zumsteg, Siriporn Wannachart, Hubert Schaller, Mami Yamazaki, Kazuki Saito, Wanchai De-eknamkul, Sornkanok Vimolmangkang and Supaart Sirikantaramas

    Citation: BMC Plant Biology 2019 19:581

    Content type: Research article

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  35. Phenotypic diversity of floral organs plays an important role in plant systematic taxonomy and genetic variation studies. Previous research have focused on the direction of variation but disregarded its degree...

    Authors: Ting Zhou, Junjun Fan, Mingming Zhao, Donglin Zhang, Qianhui Li, Guibin Wang, Wangxiang Zhang and Fuliang Cao

    Citation: BMC Plant Biology 2019 19:574

    Content type: Methodology article

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  36. Gynodioecious species exist in two sexes – male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(...

    Authors: Manuela Krüger, Oushadee A. J. Abeyawardana, Miloslav Juříček, Claudia Krüger and Helena Štorchová

    Citation: BMC Plant Biology 2019 19:568

    Content type: Research article

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  37. Sucrose synthase (SUS) is widely considered a key enzyme participating in sucrose metabolism in higher plants and regarded as a biochemical marker for sink strength in crops. However, despite significant progr...

    Authors: Xiaoyang Xu, Yongheng Yang, Chunxiao Liu, Yuming Sun, Ting Zhang, Menglan Hou, Suzhen Huang and Haiyan Yuan

    Citation: BMC Plant Biology 2019 19:566

    Content type: Research article

    Published on:

  38. Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Pa...

    Authors: Yunheng Ji, Lifang Yang, Mark W. Chase, Changkun Liu, Zhenyan Yang, Jin Yang, Jun-Bo Yang and Ting-Shuang Yi

    Citation: BMC Plant Biology 2019 19:543

    Content type: Research article

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  39. Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba ...

    Authors: Yaqiong Wu, Jing Guo, Tongli Wang, Fuliang Cao and Guibin Wang

    Citation: BMC Plant Biology 2019 19:527

    Content type: Research article

    Published on:

  40. The WRKYs are a major family of plant transcription factors that play roles in the responses to biotic and abiotic stresses; however, a comprehensive study of the WRKY family in roses (Rosa sp.) has not previousl...

    Authors: Xintong Liu, Dandan Li, Shiya Zhang, Yaling Xu and Zhao Zhang

    Citation: BMC Plant Biology 2019 19:522

    Content type: Research article

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  41. Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of sampl...

    Authors: Jorge Franco-Duran, José Crossa, Jiafa Chen and Sarah Jane Hearne

    Citation: BMC Plant Biology 2019 19:520

    Content type: Research article

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  42. The structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidati...

    Authors: A. López-Malvar, A. Butrón, L. F. Samayoa, D. J. Figueroa-Garrido, R. A. Malvar and R. Santiago

    Citation: BMC Plant Biology 2019 19:519

    Content type: Research article

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  43. Ascorbate is a powerful antioxidant in plants and an essential micronutrient for humans. The GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting enzyme of the L-galactose pathway—the dominant ascor...

    Authors: Ronan C. Broad, Julien P. Bonneau, Jesse T. Beasley, Sally Roden, Joshua G. Philips, Ute Baumann, Roger P. Hellens and Alexander A. T. Johnson

    Citation: BMC Plant Biology 2019 19:515

    Content type: Research article

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  44. The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especiall...

    Authors: Juan Wang, Yuan Li, Chunjuan Li, Caixia Yan, Xiaobo Zhao, Cuiling Yuan, Quanxi Sun, Chengren Shi and Shihua Shan

    Citation: BMC Plant Biology 2019 19:504

    Content type: Research article

    Published on:

  45. Polygonum cuspidatum of the Polygonaceae family is a traditional medicinal plant with many bioactive compounds that play important roles in human health and stress responses. Research has attempted to identify bi...

    Authors: Xiaowei Wang, Zhijun Wu, Wenqi Bao, Hongyan Hu, Mo Chen, Tuanyao Chai and Hong Wang

    Citation: BMC Plant Biology 2019 19:498

    Content type: Research article

    Published on:

  46. Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the genomic consequences of IGT for both diploid and ...

    Authors: Nan Zhao, Corrinne E. Grover, Zhiwen Chen, Jonathan F. Wendel and Jinping Hua

    Citation: BMC Plant Biology 2019 19:492

    Content type: Research article

    Published on:

  47. Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in the regulation of plant architecture and flowering time. The functions of PEBP genes have been studied in many plant species. However, little is ...

    Authors: Hanqi Jin, Xuemin Tang, Mengge Xing, Hong Zhu, Jiongming Sui, Chunmei Cai and Shuai Li

    Citation: BMC Plant Biology 2019 19:484

    Content type: Research article

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  48. Linoleic acid is an important polyunsaturated fatty acid, required for all eukaryotes. Microsomal delta-12 (Δ12) oleate desaturase (FAD2) is a key enzyme for linoleic acid biosynthesis. Desert shrub Artemisia sph...

    Authors: Xiumei Miao, Lijing Zhang, Xiaowei Hu, Shuzhen Nan, Xiaolong Chen and Hua Fu

    Citation: BMC Plant Biology 2019 19:481

    Content type: Research article

    Published on:

  49. Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid ...

    Authors: Qinzheng Zhao, Yunzhu Wang, Yunfei Bi, Yufei Zhai, Xiaqing Yu, Chunyan Cheng, Panqiao Wang, Ji Li, Qunfeng Lou and Jinfeng Chen

    Citation: BMC Plant Biology 2019 19:471

    Content type: Research article

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  50. Transposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the whe...

    Authors: Katherine Domb, Danielle Keidar-Friedman and Khalil Kashkush

    Citation: BMC Plant Biology 2019 19:461

    Content type: Research article

    Published on:

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