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Genomics and evolution

This section considers studies in the evolution of plants as well as comparative genomics in relation to plant biology.

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  1. The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several spe...

    Authors: Yinbo Ma, Sushil Satish Chhapekar, Lu Lu, Sangheon Oh, Sonam Singh, Chang Soo Kim, Seungho Kim, Gyung Ja Choi, Yong Pyo Lim and Su Ryun Choi

    Citation: BMC Plant Biology 2021 21:47

    Content type: Research article

    Published on:

  3. Comparative chloroplast genomics could shed light on the major evolutionary events that established plastomic diversity among closely related species. The Polypodiaceae family is one of the most species-rich a...

    Authors: Shanshan Liu, Zhen Wang, Yingjuan Su and Ting Wang

    Citation: BMC Plant Biology 2021 21:31

    Content type: Research article

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  4. Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest nu...

    Authors: Mengli Wang, Xin Wang, Jiahui Sun, Yiheng Wang, Yang Ge, Wenpan Dong, Qingjun Yuan and Luqi Huang

    Citation: BMC Plant Biology 2021 21:26

    Content type: Research article

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  5. Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea,...

    Authors: Jingling Li, Jianmin Tang, Siyuan Zeng, Fang Han, Jing Yuan and Jie Yu

    Citation: BMC Plant Biology 2021 21:25

    Content type: Research article

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  6. DNA methylation is a conserved and important epigenetic modification involved in the regulation of numerous biological processes, including plant development, secondary metabolism, and response to stresses. Ho...

    Authors: Zhenming Yu, Guihua Zhang, Jaime A. Teixeira da Silva, Mingzhi Li, Conghui Zhao, Chunmei He, Can Si, Mingze Zhang and Jun Duan

    Citation: BMC Plant Biology 2021 21:21

    Content type: Research article

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  7. Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, ...

    Authors: Yan Shi, Xingtan Zhang, Xiaojun Chang, Maokai Yan, Heming Zhao, Yuan Qin and Haifeng Wang

    Citation: BMC Plant Biology 2021 21:19

    Content type: Research article

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  8. Carex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order t...

    Authors: Lingyun Liu, Xifeng Fan, Penghui Tan, Juying Wu, Hui Zhang, Chao Han, Chao Chen, Lulu Xun, Weier Guo, Zhihui Chang and Ke Teng

    Citation: BMC Plant Biology 2021 21:17

    Content type: Research article

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  9. Alfalfa (Medicago sativa L.) is a perennial legume extensively planted throughout the world as a high nutritive value livestock forage. Flowering time is an important agronomic trait that contributes to the produ...

    Authors: Dongmei Ma, Bei Liu, Lingqiao Ge, Yinyin Weng, Xiaohui Cao, Fang Liu, Peisheng Mao and Xiqing Ma

    Citation: BMC Plant Biology 2021 21:8

    Content type: Research article

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  10. Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and ...

    Authors: Yushan Liu, Yizhou Wang, Jiabo Pei, Yadong Li and Haiyue Sun

    Citation: BMC Plant Biology 2021 21:5

    Content type: Research article

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  11. Auxin is critical to plant growth and development, as well as stress responses. Small auxin-up RNA (SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of few SAUR ...

    Authors: Hao Zhang, Zhenjia Yu, Xiaodie Yao, Jingli Chen, Xing Chen, Huiwen Zhou, Yuxia Lou, Feng Ming and Yue Jin

    Citation: BMC Plant Biology 2021 21:4

    Content type: Research article

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  12. Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nut...

    Authors: Yi Xiong, Xiong Lei, Shiqie Bai, Yanli Xiong, Wenhui Liu, Wendan Wu, Qingqing Yu, Zhixiao Dong, Jian Yang and Xiao Ma

    Citation: BMC Plant Biology 2021 21:3

    Content type: Research article

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  13. Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the fun...

    Authors: Fangfang Li, Fangming Mei, Yifang Zhang, Shumin Li, Zhensheng Kang and Hude Mao

    Citation: BMC Plant Biology 2020 20:558

    Content type: Research article

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  14. Closely related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. Although gene expression plays a central role in determining ecologically-based phenotypic ...

    Authors: Bárbara Simões Santos Leal, Marcelo Mendes Brandão, Clarisse Palma-Silva and Fabio Pinheiro

    Citation: BMC Plant Biology 2020 20:554

    Content type: Research article

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  15. Organ shape and size covariation (allometry) factors are essential concepts for the study of evolution and development. Although ample research has been conducted on organ shape and size, little research has c...

    Authors: Xin Li, Yaohua Zhang, Suxin Yang, Chunxia Wu, Qun Shao and Xianzhong Feng

    Citation: BMC Plant Biology 2020 20:547

    Content type: Research article

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  16. Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little informati...

    Authors: Weizhuo Zhu, Yiyi Guo, Yeke Chen, Dezhi Wu and Lixi Jiang

    Citation: BMC Plant Biology 2020 20:543

    Content type: Research article

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  17. The AP2/ERFs belong to a large family of transcription factors in plants. The AP2/ERF gene family has been identified as a key player involved in both biotic and abiotic stress responses in plants, however, no...

    Authors: Dandan Li, Xintong Liu, Lizhe Shu, Hua Zhang, Shiya Zhang, Yin Song and Zhao Zhang

    Citation: BMC Plant Biology 2020 20:533

    Content type: Research article

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  18. Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic d...

    Authors: Huimin Hou, Hang Ye, Zhi Wang, Jiahui Wu, Yue Gao, Wei Han, Dongchen Na, Genlou Sun and Yiling Wang

    Citation: BMC Plant Biology 2020 20:526

    Content type: Research article

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  19. A structural phenomenon seen in certain lineages of angiosperms that has captivated many scholars including Charles Darwin is the evolution of plant carnivory. Evidently, these structural features collectively...

    Authors: Jeremy Dkhar, Yogendra Kumar Bhaskar, Andrew Lynn and Ashwani Pareek

    Citation: BMC Plant Biology 2020 20:524

    Content type: Research article

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  20. The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the ...

    Authors: Yumei Jiang, Sheng Xu, Rong Wang, Jiayu Zhou, Jian Dou, Qian Yin and Ren Wang

    Citation: BMC Plant Biology 2020 20:522

    Content type: Research article

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  21. The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological charac...

    Authors: Ting Ren, Zi-Xuan Li, Deng-Feng Xie, Ling-Jian Gui, Chang Peng, Jun Wen and Xing-Jin He

    Citation: BMC Plant Biology 2020 20:519

    Content type: Research article

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  22. Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the lar...

    Authors: Yanchao Xu, Richard Odongo Magwanga, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Zheng Juyun, Stephen Gaya Agong, Kunbo Wang, Fang Liu and Zhongli Zhou

    Citation: BMC Plant Biology 2020 20:518

    Content type: Research article

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  23. Diacylglycerol kinases (DGKs) are signaling enzymes that play pivotal roles in response to abiotic and biotic stresses by phosphorylating diacylglycerol (DAG) to form phosphatidic acid (PA). However, no compre...

    Authors: Fang Tang, Zhongchun Xiao, Fujun Sun, Shulin Shen, Si Chen, Rui Chen, Meichen Zhu, Qianwei Zhang, Hai Du, Kun Lu, Jiana Li and Cunmin Qu

    Citation: BMC Plant Biology 2020 20:473

    Content type: Research article

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  24. Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To inve...

    Authors: Changwei Shen and Jingping Yuan

    Citation: BMC Plant Biology 2020 20:471

    Content type: Research article

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  25. Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation o...

    Authors: Boping Wu, Xiaohong Liu, Kai Xu and Bo Zhang

    Citation: BMC Plant Biology 2020 20:459

    Content type: Research article

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  26. Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target ge...

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

    Citation: BMC Plant Biology 2020 20:454

    Content type: Research article

    Published on:

  27. The HD-Zip transcription factors are unique to plants and play an essential role in plant growth, development and stress responses. The HD-Zip transcription factor family consists of a highly conserved homeodo...

    Authors: Jiashuo Zhang, Jinzhang Wu, Mingliang Guo, Mohammad Aslam, Qi Wang, Huayan Ma, Shubin Li, Xingtan Zhang and Shijiang Cao

    Citation: BMC Plant Biology 2020 20:451

    Content type: Research article

    Published on:

  28. Cucumber (Cucumis sativus L.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growt...

    Authors: Chunhua Chen, Xueqian Chen, Jing Han, Wenli Lu and Zhonghai Ren

    Citation: BMC Plant Biology 2020 20:443

    Content type: Research article

    Published on:

  29. In the past several millenniums, we have domesticated several crop species that are crucial for human civilization, which is a symbol of significant human influence on plant evolution. A pressing question to a...

    Authors: Jian-Guo Gao, Hui Liu, Ning Wang, Jing Yang and Xiao-Ling Zhang

    Citation: BMC Plant Biology 2020 20:430

    Content type: Review

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  30. Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Sacch...

    Authors: Panpan Ma, Xingtan Zhang, Lanping Chen, Qian Zhao, Qing Zhang, Xiuting Hua, Zhengchao Wang, Haibao Tang, Qingyi Yu, Muqing Zhang, Ray Ming and Jisen Zhang

    Citation: BMC Plant Biology 2020 20:422

    Content type: Research article

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  31. Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the developme...

    Authors: Ting Zhu, Yue Liu, Liting Ma, Xiaoying Wang, Dazhong Zhang, Yucui Han, Qin Ding and Lingjian Ma

    Citation: BMC Plant Biology 2020 20:420

    Content type: Research article

    Published on:

  33. Histone modification genes (HMs) play potential roles in plant growth and development via influencing gene expression and chromatin structure. However, limited information is available about HMs genes in grapes (

    Authors: Li Wang, Bilal Ahmad, Chen Liang, Xiaoxin Shi, Ruyi Sun, Songlin Zhang and Guoqiang Du

    Citation: BMC Plant Biology 2020 20:412

    Content type: Research article

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  35. Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena sp...

    Authors: Qing Liu, Xiaoyu Li, Mingzhi Li, Wenkui Xu, Trude Schwarzacher and John Seymour Heslop-Harrison

    Citation: BMC Plant Biology 2020 20:406

    Content type: Research article

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  36. C2H2 zinc finger proteins (C2H2 ZFPs) play vital roles in shaping many aspects of plant growth and adaptation to the environment. Plant genomes harbor hundreds of C2H2 ZFPs, which compose one of the most impor...

    Authors: Zhicheng Jiao, Liping Wang, Huan Du, Ying Wang, Weixu Wang, Junjie Liu, Jinhang Huang, Wei Huang and Liangfa Ge

    Citation: BMC Plant Biology 2020 20:401

    Content type: Research article

    Published on:

  37. Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such ...

    Authors: Jin Cheng, Huixia Kao and Shubin Dong

    Citation: BMC Plant Biology 2020 20:391

    Content type: Research article

    Published on:

  38. 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:

  39. 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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  40. 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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  41. 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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  42. 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

    Published on:

  43. 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

    Published on:

  44. 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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  45. 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

    Published on:

  46. 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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  47. 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

    Published on:

  48. 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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  49. 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

    Published on:

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