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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 7

  1. Content type: Research article

    Around the Cretaceous-Paleogene (K-Pg) boundary, an obvious global cooling occurred, which resulted in dramatic changes in terrestrial ecosystems and the evolutionary trends of numerous organisms. However, how...

    Authors: Yi-Ming Cui, Wei Wang, David K. Ferguson, Jian Yang and Yu-Fei Wang

    Citation: BMC Plant Biology 2019 19:402

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  2. Content type: Research article

    Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for ...

    Authors: Muhammad Umair Ahsan, Alice Hayward, Mobashwer Alam, Jayeni Hiti Bandaralage, Bruce Topp, Christine Anne Beveridge and Neena Mitter

    Citation: BMC Plant Biology 2019 19:382

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  3. Content type: Research article

    The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, i...

    Authors: Shu-Fen Li, Jia-Rong Li, Jin Wang, Ran Dong, Ke-Li Jia, Hong-Wei Zhu, Ning Li, Jin-Hong Yuan, Chuan-Liang Deng and Wu-Jun Gao

    Citation: BMC Plant Biology 2019 19:361

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  4. Content type: Research article

    The PHOSPHATE1 (PHO1) gene family plays diverse roles in inorganic phosphate (Pi) transfer and signal transduction, and plant development. However, the functions and diversification of soybean PHO1 family are poo...

    Authors: Yan Wang, Huihui Gao, Lingli He, Weiwei Zhu, Lixin Yan, Qingshan Chen and Chaoying He

    Citation: BMC Plant Biology 2019 19:353

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  5. Content type: Research article

    Flavonoid 3′-hydroxlase (F3’H) is an important enzyme in determining the B-ring hydroxylation pattern of flavonoids. In monocots, previous studies indicated the presence of two groups of F3’Hs with different e...

    Authors: Yong Jia, Bo Li, Yujuan Zhang, Xiaoqi Zhang, Yanhao Xu and Chengdao Li

    Citation: BMC Plant Biology 2019 19:347

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  6. Content type: Research article

    In the study, the trihelix family, also referred to as GT factors, is one of the transcription factor families. Trihelix genes play roles in the light response, seed maturation, leaf development, abiotic and biol...

    Authors: Zhaotang Ma, Moyang Liu, Wenjun Sun, Li Huang, Qi Wu, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Plant Biology 2019 19:344

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  7. Content type: Research article

    APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformat...

    Authors: Tengyue Wang, Xiaoke Ping, Yanru Cao, Hongju Jian, Yumin Gao, Jia Wang, Yingchao Tan, Xinfu Xu, Kun Lu, Jiana Li and Liezhao Liu

    Citation: BMC Plant Biology 2019 19:336

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  8. Content type: Research article

    Zinc finger proteins (ZFPs) containing only a single zinc finger domain play important roles in the regulation of plant growth and development, as well as in biotic and abiotic stress responses. To date, the e...

    Authors: Peng He, Yan Yang, Zihua Wang, Peng Zhao, Yi Yuan, Li Zhang, Yueqin Ma, Chaoyou Pang, Jianing Yu and Guanghui Xiao

    Citation: BMC Plant Biology 2019 19:329

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  9. Content type: Research article

    The WOX (WUSCHEL-RELATED HOMEOBOX) gene family encodes a class of transcription factors that are unique to green plants, where they are involved in regulating the development of plant tissues and organs by determ...

    Authors: Peng He, Yuzhou Zhang, Hao Liu, Yi Yuan, Chan Wang, Jianing Yu and Guanghui Xiao

    Citation: BMC Plant Biology 2019 19:312

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  10. Content type: Research article

    DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting et...

    Authors: Liuling Pei, Lin Zhang, Jianying Li, Chao Shen, Ping Qiu, Lili Tu, Xianlong Zhang and Maojun Wang

    Citation: BMC Plant Biology 2019 19:307

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  11. Content type: Research article

    Polyploidy and hybridization are ubiquitous in Rubus L., a large and taxonomically challenging genus. Chinese Rubus are mainly concentrated into two major sections, the diploid Idaeobatus and the polyploid Malach...

    Authors: Yan Wang, Qing Chen, Tao Chen, Jing Zhang, Wen He, Lin Liu, Ya Luo, Bo Sun, Yong Zhang, Hao-ru Tang and Xiao-rong Wang

    Citation: BMC Plant Biology 2019 19:303

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  12. Content type: Research article

    SPL (SQUAMOSA promoter binding protein-like) is a class of plant-specific transcription factors that play important roles in many growth and developmental processes, including shoot and inflorescence branching...

    Authors: Moyang Liu, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Plant Biology 2019 19:299

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  13. Content type: Research article

    Premature senescence of flag leaf severely affects wheat yield and quality. Chlorophyll (Chl) degradation is the most obvious symptom during leaf senescence and catalyzed by a series of enzymes. Pheophytin phe...

    Authors: Huiyan Wang, Shuguang Wang, Xiaoping Chang, Chenyang Hao, Daizhen Sun and Ruilian Jing

    Citation: BMC Plant Biology 2019 19:296

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  14. Content type: Research article

    Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) ...

    Authors: Lifang Yang, Zhenyan Yang, Changkun Liu, Zhengshan He, Zhirong Zhang, Jing Yang, Haiyang Liu, Junbo Yang and Yunheng Ji

    Citation: BMC Plant Biology 2019 19:293

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  15. Content type: Research article

    Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine pl...

    Authors: Xu Zhang, Tao Deng, Michael J. Moore, Yunheng Ji, Nan Lin, Huajie Zhang, Aiping Meng, Hengchang Wang, Yanxia Sun and Hang Sun

    Citation: BMC Plant Biology 2019 19:290

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  16. Content type: Research article

    Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each ...

    Authors: Cuihua Gu, Li Ma, Zhiqiang Wu, Kai Chen and Yixiang Wang

    Citation: BMC Plant Biology 2019 19:281

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  17. Content type: Research article

    Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been charact...

    Authors: Shenquan Cao, Mengjie Guo, Chong Wang, Wenjing Xu, Tianyuan Shi, Guimin Tong, Cheng Zhen, Hao Cheng, Chuanping Yang, Nabil Ibrahim Elsheery and Yuxiang Cheng

    Citation: BMC Plant Biology 2019 19:276

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  18. Content type: Research article

    The Growth-regulating factor (GRF) family encodes plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family play vital roles in plant development and stress res...

    Authors: Feng Chen, Yingzeng Yang, Xiaofeng Luo, Wenguan Zhou, Yujia Dai, Chuan Zheng, Weiguo Liu, Wenyu Yang and Kai Shu

    Citation: BMC Plant Biology 2019 19:269

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  19. Content type: Research article

    Brassica napus L. has little or no primary dormancy, but exhibits great variation in secondary dormancy. Secondary dormancy potential in oilseed rape can lead to the emergence of volunteer plants that cause genet...

    Authors: Lei Liu, Fuxia Liu, Jinfang Chu, Xin Yi, Wenqi Fan, Tang Tang, Guimin Chen, Qiuhuan Guo and Xiangxiang Zhao

    Citation: BMC Plant Biology 2019 19:264

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  20. Content type: Research article

    ZF-HD is a family of genes that play an important role in plant growth, development, some studies have found that after overexpression AtZHD1 in Arabidopsis thaliana, florescence advance, the seeds get bigger and...

    Authors: Moyang Liu, Xiaoxiang Wang, Wenjun Sun, Zhaotang Ma, Tianrun Zheng, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Plant Biology 2019 19:248

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  21. Content type: Research article

    MiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expr...

    Authors: Sufang Zhang, Shanshan Yan, Jiali Zhao, Huanhuan Xiong, Peiqi An, Junhui Wang, Hanguo Zhang and Lei Zhang

    Citation: BMC Plant Biology 2019 19:247

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  22. Content type: Research article

    Studies have demonstrated that BBX (B-BOX) genes play crucial roles in regulatory networks controlling plant growth, developmental processes and stress response. Nevertheless, comprehensive study of BBX genes in ...

    Authors: Yunpeng Cao, Dandan Meng, Yahui Han, Tianzhe Chen, Chunyan Jiao, Yu Chen, Qing Jin and Yongping Cai

    Citation: BMC Plant Biology 2019 19:245

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  23. Content type: Research article

    Elymus L. is the largest genus in the tribe Triticeae Dumort., encompassing approximately 150 polyploid perennial species widely distributed in the temperate regions of the world. It is considered to be an import...

    Authors: Zongyu Zhang, Wengang Xie, Yongqiang Zhao, Junchao Zhang, Na Wang, Fabrice Ntakirutimana, Jiajun Yan and Yanrong Wang

    Citation: BMC Plant Biology 2019 19:235

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  24. Content type: Research article

    Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots....

    Authors: Liheng He, Ruimin Tang, Xiaowen Shi, Wenbing Wang, Qinghe Cao, Xiayu Liu, Ting Wang, Yan Sun, Hongmei Zhang, Runzhi Li and Xiaoyun Jia

    Citation: BMC Plant Biology 2019 19:232

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  25. Content type: Research article

    Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata ...

    Authors: Ladislava Paštová, Alexander Belyayev and Václav Mahelka

    Citation: BMC Plant Biology 2019 19:230

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  26. Content type: Research article

    Persimmon (Diospyros kaki) is the most economically cultivated species belonging to the genus Diospyros. However, little is known about the interspecific diversity and mechanism of domestication, partly due to th...

    Authors: Changfei Guan, Shuyuan Liu, Mengke Wang, Hao Ji, Xiaofeng Ruan, Renzi Wang and Yong Yang

    Citation: BMC Plant Biology 2019 19:227

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  27. Content type: Research article

    Repetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times – make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the rep...

    Authors: Qing Liu, Xiaoyu Li, Xiangying Zhou, Mingzhi Li, Fengjiao Zhang, Trude Schwarzacher and John Seymour Heslop-Harrison

    Citation: BMC Plant Biology 2019 19:226

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  28. Content type: Research article

    MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes i...

    Authors: Chunmei He, Can Si, Jaime A. Teixeira da Silva, Mingzhi Li and Jun Duan

    Citation: BMC Plant Biology 2019 19:223

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  29. Content type: Research article

    Mature fruit cracking during the normal season in African Pride (AP) atemoya is a major problem in postharvest storage. Our current understanding of the molecular mechanism underlying fruit cracking is limited...

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

    Citation: BMC Plant Biology 2019 19:219

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  30. Content type: Research article

    Banana (Musa spp.) is one of the world’s most important fruits and its production is largely limited by diverse stress conditions. SROs (SIMILAR TO RCD-ONE) have important functions in abiotic stress resistance a...

    Authors: Lu Zhang, Dengbo Zhou, Huigang Hu, Weiming Li, Yulin Hu, Jianghui Xie, Shangzhi Huang and Wei Wang

    Citation: BMC Plant Biology 2019 19:211

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  31. Content type: Research article

    Rice blast disease is one of the most destructive fungal disease of rice worldwide. The avirulence (AVR) genes of Magnaporthe oryzae are recognized by the cognate resistance (R) genes of rice and trigger race-spe...

    Authors: Jinbin Li, Qun Wang, Chengyun Li, Yunqing Bi, Xue Fu and Raoquan Wang

    Citation: BMC Plant Biology 2019 19:204

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  32. Content type: Research article

    The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (th...

    Authors: Li Ma, Li Zhou, Shaowen Quan, Hang Xu, Jieping Yang and Jianxin Niu

    Citation: BMC Plant Biology 2019 19:192

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  33. Content type: Research article

    BRASSINAZOLE-RESISTANT (BZR) family genes encode plant-specific transcription factors (TFs) that participate in brassinosteroid signal transduction. BZR TFs have vital roles in plant growth, including cell elo...

    Authors: Wei Wang, Ya-Qing Sun, Guo-Long Li and Shao-Ying Zhang

    Citation: BMC Plant Biology 2019 19:191

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  34. Content type: Research article

    Senescence affects the quality and yield of plants by regulating different traits of plants. A few members of S40 gene family, the barley HvS40 and the Arabidopsis AtS40–3, have been shown to play a role in leaf ...

    Authors: Xiangzi Zheng, Muhammad Jehanzeb, Habiba, Yuanyuan Zhang, Li Li and Ying Miao

    Citation: BMC Plant Biology 2019 19:174

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  35. Content type: Research article

    Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a ...

    Authors: S. M. Pilkington, J. Tahir, E. Hilario, S. E. Gardiner, D. Chagné, A. Catanach, J. McCallum, L. Jesson, L. G. Fraser, M. A. McNeilage, C. Deng, R. N. Crowhurst, P. M. Datson and Q. Zhang

    Citation: BMC Plant Biology 2019 19:172

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  36. Content type: Research article

    Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes ...

    Authors: Elizabeth W. McCarthy, Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Mark W. Chase, Sandra Knapp, Steven C. Le Comber, Andrew R. Leitch and Amy Litt

    Citation: BMC Plant Biology 2019 19:162

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  37. Content type: Research article

    Although the genome of Chinese white pear (‘Dangshansuli’) has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date.

    Authors: Xin Gong, Liangyi Zhao, Xiaofei Song, Zekun Lin, Bingjie Gu, Jinxuan Yan, Shaoling Zhang, Shutian Tao and Xiaosan Huang

    Citation: BMC Plant Biology 2019 19:161

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  38. Content type: Research article

    Elytrigia lolioides (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into Elytrigia, Elymus, and Lophopyrum genera by taxonomis...

    Authors: Long Wang, Yuanyuan Jiang, Qinghua Shi, Yi Wang, Lina Sha, Xing Fan, Houyang Kang, Haiqin Zhang, Genlou Sun, Li Zhang and Yonghong Zhou

    Citation: BMC Plant Biology 2019 19:158

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  39. Content type: Research article

    Powdery mildew (PM) is a widespread fungal disease of plants in temperate climates, causing significant economic losses in agricultural settings. Specific homologs of the MLO gene family are PM susceptibility fac...

    Authors: Giuseppe Andolfo, Paolo Iovieno, Luigi Ricciardi, Concetta Lotti, Edgardo Filippone, Stefano Pavan and Maria Raffaella Ercolano

    Citation: BMC Plant Biology 2019 19:150

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  40. Content type: Research article

    Miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons are ubiquitous in plants genomes, and highly important in their evolution and diversity. However, their m...

    Authors: Yan Liu, Muhammad Tahir ul Qamar, Jia-Wu Feng, Yuduan Ding, Shuo Wang, Guizhi Wu, Lingjun Ke, Qiang Xu and Ling-Ling Chen

    Citation: BMC Plant Biology 2019 19:140

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  41. Content type: Research article

    Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a ...

    Authors: Ming Li, Songtao Yang, Wei Xu, Zhigang Pu, Junyan Feng, Zhangying Wang, Cong Zhang, Meifang Peng, Chunguang Du, Feng Lin, Changhe Wei, Shuai Qiao, Hongda Zou, Lei Zhang, Yan Li, Huan Yang…

    Citation: BMC Plant Biology 2019 19:119

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  42. Content type: Research article

    Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid B...

    Authors: Mengdi Li, Ruihua Wang, Ziwei Liang, Xiaoming Wu and Jianbo Wang

    Citation: BMC Plant Biology 2019 19:110

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  43. Content type: Research article

    Adventitious roots (ARs) are roots that are generated from nonrooting tissues. ARs are usually produced both during normal development and in response to stress conditions, such as flooding, nutrient deprivati...

    Authors: Yan Zhang, Zheng’ang Xiao, Chang Zhan, Meifeng Liu, Wenxiu Xia and Nian Wang

    Citation: BMC Plant Biology 2019 19:99

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  44. Content type: Research article

    Brassinosteroids (BRs) play a crucial role in plant vegetative growth and reproductive development. The transcription factors BZR1 and BES1/BZR2 are well characterized as downstream regulators of the BR signal...

    Authors: Li Song, Wei Chen, Biao Wang, Qiu-Ming Yao, Babu Valliyodan, Ming-Yi Bai, Ming-Zhe Zhao, Heng Ye, Zhi-Yong Wang and Henry T. Nguyen

    Citation: BMC Plant Biology 2019 19:86

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  45. Content type: Research article

    There exist differences in morphological traits and phytochemical compositions between field- and mountain-cultivated Panax ginseng (FCG and MCG), which might be attributed to variations of terpenoids metabolism ...

    Authors: Hang Fan, Ke Li, Fan Yao, Liwei Sun and Yujun Liu

    Citation: BMC Plant Biology 2019 19:82

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  46. Content type: Research article

    Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences ...

    Authors: Honghong Deng, Suqiong Xiang, Qigao Guo, Weiwei Jin, Zexi Cai and Guolu Liang

    Citation: BMC Plant Biology 2019 19:77

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  47. Content type: Research article

    Plant photosynthesis can be improved by elevated CO2 concentration (eCO2). In vitro growth under CO2 enriched environment can lead to greater biomass accumulation than the conventional in micropropagation. Howeve...

    Authors: Xin Zhao, Wen-Fang Li, Ying Wang, Zong-Huan Ma, Shi-Jin Yang, Qi Zhou, Juan Mao and Bai-Hong Chen

    Citation: BMC Plant Biology 2019 19:42

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  48. Content type: Research article

    Chloroplasts are one of the most indispensable organelles that make life forms on the earth possible by their capacity to photosynthesize. These organelles possess a circular genome with a number of coding gen...

    Authors: Tapan Kumar Mohanta, Abdul Latif Khan, Abeer Hashem, Elsayed Fathi Abd_ Allah, Dhananjay Yadav and Ahmed Al-Harrasi

    Citation: BMC Plant Biology 2019 19:39

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