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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. Allium sativum (garlic) is an economically important food source and medicinal plant rich in sulfides and other protective substances such as alliin, the precursor of allicin biosynthesis. Cysteine, serine and su...

    Authors: Xuqin Yang, Yiren Su, Jiaying Wu, Wen Wan, Huijian Chen, Xiaoying Cao, Junjuan Wang, Zhong Zhang, Youzhi Wang, Deliang Ma, G. J. Loake and Jihong Jiang

    Citation: BMC Plant Biology 2021 21:174

    Content type: Research article

    Published on:

  3. Identifying the loci and dissecting the genetic architecture underlying wheat yield- and quality-related traits are essential for wheat breeding. A genome-wide association study was conducted using a high-dens...

    Authors: Le Gao, Chengsheng Meng, Tengfei Yi, Ke Xu, Huiwen Cao, Shuhua Zhang, Xueju Yang and Yong Zhao

    Citation: BMC Plant Biology 2021 21:144

    Content type: Research article

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  4. Cannabis, an important industrial crop, has a high sensitivity to photoperiods. The flowering time of cannabis is one of its important agronomic traits, and has a significant effect on its yield and quality. The

    Authors: Gen Pan, Zheng Li, Ming Yin, Siqi Huang, Jie Tao, Anguo Chen, Jianjun Li, Huijuan Tang, Li Chang, Yong Deng, Defang Li and Lining Zhao

    Citation: BMC Plant Biology 2021 21:142

    Content type: Research article

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  5. Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. ...

    Authors: Hao Rong, Wenjing Yang, Haotian Zhu, Bo Jiang, Jinjin Jiang and Youping Wang

    Citation: BMC Plant Biology 2021 21:140

    Content type: Research article

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  6. It has been recognized that a certain amount of habitat disturbance is a facilitating factor for the occurrence of natural hybridization, yet to date we are unaware of any studies exploring hybridization and r...

    Authors: Rongli Liao, Weibang Sun and Yongpeng Ma

    Citation: BMC Plant Biology 2021 21:133

    Content type: Research article

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  8. Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 culti...

    Authors: Ian S. E. Bally, Aureliano Bombarely, Alan H. Chambers, Yuval Cohen, Natalie L. Dillon, David J. Innes, María A. Islas-Osuna, David N. Kuhn, Lukas A. Mueller, Ron Ophir, Aditi Rambani, Amir Sherman and Haidong Yan

    Citation: BMC Plant Biology 2021 21:108

    Content type: Research article

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  9. Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (...

    Authors: Liuyang Fu, Qian Wang, Lina Li, Tao Lang, Junjia Guo, Siyu Wang, Ziqi Sun, Suoyi Han, Bingyan Huang, Wenzhao Dong, Xinyou Zhang and Pei Du

    Citation: BMC Plant Biology 2021 21:107

    Content type: Research article

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  10. Taxol is an efficient anticancer drug accumulated in Taxus species. Pseudotaxus chienii is an important member of Taxaceae, however, the level of six taxoids in P. chienii is largely unknown.

    Authors: Chunna Yu, Chengchao Zhang, Xinyun Xu, Jiefang Huang, Yueyue Chen, Xiujun Luo, Huizhong Wang and Chenjia Shen

    Citation: BMC Plant Biology 2021 21:104

    Content type: Research article

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  11. The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly under...

    Authors: Weijun Zhang, Junjie Zhao, Jinshang He, Ling Kang, Xiaoliang Wang, Fuguo Zhang, Chenyang Hao, Xiongfeng Ma and Dongsheng Chen

    Citation: BMC Plant Biology 2021 21:103

    Content type: Research article

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  12. Male sterility (MS) has important applications in hybrid seed production, and the abortion of anthers has been observed in many plant species. While most studies have focused on the genetic factors affecting m...

    Authors: Lijun Zhang, Mingchuan Ma, Lin Cui and Longlong Liu

    Citation: BMC Plant Biology 2021 21:101

    Content type: Research article

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  13. Acyl-CoA-binding proteins (ACBPs) possess a conserved acyl-CoA-binding (ACB) domain that facilitates binding to acyl-CoA esters and trafficking in eukaryotic cells. Although the various functions of ACBP have ...

    Authors: Jiantang Zhu, Weijun Li, Yuanyuan Zhou, Laming Pei, Jiajia Liu, Xinyao Xia, Ronghui Che and Hui Li

    Citation: BMC Plant Biology 2021 21:94

    Content type: Research article

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  14. Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still...

    Authors: Peng Ma, Xiao Zhang, Bowen Luo, Zhen Chen, Xuan He, Haiying Zhang, Binyang Li, Dan Liu, Ling Wu, Shiqiang Gao, Duojiang Gao, Suzhi Zhang and Shibin Gao

    Citation: BMC Plant Biology 2021 21:93

    Content type: Research article

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  15. Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in ...

    Authors: Zhengwen Liu, Xingfen Wang, Zhengwen Sun, Yan Zhang, Chengsheng Meng, Bin Chen, Guoning Wang, Huifeng Ke, Jinhua Wu, Yuanyuan Yan, Liqiang Wu, Zhikun Li, Jun Yang, Guiyin Zhang and Zhiying Ma

    Citation: BMC Plant Biology 2021 21:89

    Content type: Research article

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  16. The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is...

    Authors: Haomiao Cheng, Zhanru Shao, Chang Lu and Delin Duan

    Citation: BMC Plant Biology 2021 21:87

    Content type: Research article

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  17. Calcium (Ca2+) plays an important role in plant growth and development, and the maintenance of calcium homeostasis is necessary for the survival of all plant species. Ca2+/H+ exchangers (CAXs) are a subgroup of t...

    Authors: Ke Mao, Jie Yang, Min Wang, Huayu Liu, Xin Guo, Shuang Zhao, Qinglong Dong and Fengwang Ma

    Citation: BMC Plant Biology 2021 21:81

    Content type: Research article

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  18. The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGe...

    Authors: Jiongliang Wang, Weixue Mu, Ting Yang, Yue Song, Yin Guang Hou, Yu Wang, Zhimin Gao, Xin Liu, Huan Liu and Hansheng Zhao

    Citation: BMC Plant Biology 2021 21:76

    Content type: Research article

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  19. Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in...

    Authors: Ali Soltani, Katelynn A. Walter, Andrew T. Wiersma, James P. Santiago, Michelle Quiqley, Daniel Chitwood, Timothy G. Porch, Phillip Miklas, Phillip E. McClean, Juan M. Osorno and David B. Lowry

    Citation: BMC Plant Biology 2021 21:58

    Content type: Research article

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  20. 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

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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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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  34. 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

    Published on:

  35. 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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  36. 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

    Published on:

  37. 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

    Published on:

  38. 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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  39. 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

    Published on:

  40. 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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  41. 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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  42. 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

    Published on:

  43. 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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  44. 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

    Published on:

  45. 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:

  46. 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:

  47. 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

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  48. 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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  49. 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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  50. 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:

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