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Plant genomics

Section edited by David Lightfoot and Keiichi Mochida

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 1 of 27

  1. Content type: Research article

    Carotenoids are widely distributed in plants and algae, and their biosynthesis has attracted widespread interest. Carotenoid-related research has mostly focused on model species, and there is a lack of data on...

    Authors: Yuan He, Yafeng Ma, Yu Du and Songdong Shen

    Citation: BMC Genomics 2018 19:916

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  2. Content type: Research article

    Vaccinium uliginosum (Ericaceae) is an important wild berry having high economic value. The white-fruited V. uliginosum variety found in the wild lacks anthocyanin and bears silvery white fruits. Hence, it is a g...

    Authors: Yang Yang, Baihui Cui, Zhiwen Tan, Bingxue Song, Hounan Cao and Chengwen Zong

    Citation: BMC Genomics 2018 19:930

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  3. Content type: Research article

    Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variant of nonheading Chinese cabbage (Brassica campestris L.), which is one of the major vegetables in China. Cytoplasmic male sterility (CM...

    Authors: Guohu Chen, Xinyu Ye, Shengyun Zhang, Shidong Zhu, Lingyun Yuan, Jinfeng Hou and Chenggang Wang

    Citation: BMC Genomics 2018 19:908

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  4. Content type: Research article

    Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Pol...

    Authors: Odile Rogier, Aurélien Chateigner, Souhila Amanzougarene, Marie-Claude Lesage-Descauses, Sandrine Balzergue, Véronique Brunaud, José Caius, Ludivine Soubigou-Taconnat, Véronique Jorge and Vincent Segura

    Citation: BMC Genomics 2018 19:909

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  5. Content type: Research article

    Quantitative trait loci (QTL) mapping provides a powerful tool to unravel the genetic bases of cotton yield and its components, as well as their heterosis. In the present study, the genetic basis underlying in...

    Authors: Cong Li, Tianlun Zhao, Hurong Yu, Cheng Li, Xiaolei Deng, Yating Dong, Fan Zhang, Yi Zhang, Lei Mei, Jinhong Chen and Shuijin Zhu

    Citation: BMC Genomics 2018 19:910

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  6. Content type: Research article

    Members of the Early Salt Induced 3 (Esi3/RCI2/PMP3) gene family in plants have been shown to be induced in response to both biotic and abiotic stresses and to enhance stress tolerance in both transgenic plants a...

    Authors: Sabrina C. Brunetti, Michelle K. M. Arseneault and Patrick J. Gulick

    Citation: BMC Genomics 2018 19:898

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  7. Content type: Research article

    The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and pro...

    Authors: Kujin Tang, Jie Ren, Richard Cronn, David L. Erickson, Brook G. Milligan, Meaghan Parker-Forney, John L. Spouge and Fengzhu Sun

    Citation: BMC Genomics 2018 19:896

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  8. Content type: Research article

    Expression patterns of many laticifer-specific gens are closely correlative with rubber yield of Hevea brasiliensis (para rubber tree). To unveil the mechanisms underlying the rubber yield, transcript levels of n...

    Authors: Chuntai Wu, Li Lan, Yu Li, Zhiyi Nie and Rizhong Zeng

    Citation: BMC Genomics 2018 19:897

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  9. Content type: Research article

    The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration curren...

    Authors: Jessica V. Fay, Christopher J. Watkins, Ram K. Shrestha, Sergio L. Litwiñiuk, Liliana N. Talavera Stefani, Cristian A. Rojas, Carina F. Argüelles, Julian A. Ferreras, Mario Caccamo and Marcos M. Miretti

    Citation: BMC Genomics 2018 19:891

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  10. Content type: Research article

    Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. ...

    Authors: Qing Lu, Hao Liu, Yanbin Hong, Haifen Li, Haiyan Liu, Xingyu Li, Shijie Wen, Guiyuan Zhou, Shaoxiong Li, Xiaoping Chen and Xuanqiang Liang

    Citation: BMC Genomics 2018 19:887

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  11. Content type: Research article

    Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome...

    Authors: Iftikhar Ali, Zhonghua Teng, Yuting Bai, Qing Yang, Yongshui Hao, Juan Hou, Yongbin Jia, Lixia Tian, Xueying Liu, Zhaoyun Tan, Wenwen Wang, Kiirya Kenneth, Abdalla Yousef Ahmed Sharkh, Dexin Liu, Kai Guo, Jian Zhang…

    Citation: BMC Genomics 2018 19:879

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  12. Content type: Research article

    In upland cotton (Gossypium hirsutum L.), genotypes with the same mature fiber length (FL) might possess different genes and exhibit differential expression of genes related to fiber elongation at different fiber...

    Authors: Jianjiang Ma, Yanhui Geng, Wenfeng Pei, Man Wu, Xingli Li, Guoyuan Liu, Dan Li, Qifeng Ma, XinShan Zang, Shuxun Yu, Jinfa Zhang and Jiwen Yu

    Citation: BMC Genomics 2018 19:882

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  13. Content type: Research article

    Similar to other urban trees, holm oaks (Quercus ilex L.) provide a physiological, ecological and social service in the urban environment, since they remove atmospheric pollution. However, the urban environment h...

    Authors: Lucia Natali, Alberto Vangelisti, Lucia Guidi, Damiano Remorini, Lorenzo Cotrozzi, Giacomo Lorenzini, Cristina Nali, Elisa Pellegrini, Alice Trivellini, Paolo Vernieri, Marco Landi, Andrea Cavallini and Tommaso Giordani

    Citation: BMC Genomics 2018 19:872

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  14. Content type: Research article

    Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential producti...

    Authors: Francesco Panara, Loredana Lopez, Loretta Daddiego, Elio Fantini, Paolo Facella and Gaetano Perrotta

    Citation: BMC Genomics 2018 19:875

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  15. Content type: Research article

    Silene vulgaris (bladder campion) is a gynodioecious species existing as two genders – male-sterile females and hermaphrodites. Cytoplasmic male sterility (CMS) is generally encoded by mitochondrial genes, which ...

    Authors: Helena Štorchová, James D. Stone, Daniel B. Sloan, Oushadee A. J. Abeyawardana, Karel Müller, Jana Walterová and Marie Pažoutová

    Citation: BMC Genomics 2018 19:874

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  16. Content type: Research article

    Nicotiana rustica (Aztec tobacco), like common tobacco (Nicotiana tabacum), is an allotetraploid formed through a recent hybridization event; however, it originated from completely different progenitor species. H...

    Authors: N. Sierro, J. N. D. Battey, L. Bovet, V. Liedschulte, S. Ouadi, J. Thomas, H. Broye, H. Laparra, A. Vuarnoz, G. Lang, S. Goepfert, M. C. Peitsch and N. V. Ivanov

    Citation: BMC Genomics 2018 19:855

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  17. Content type: Research article

    An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective abso...

    Authors: Qi Zhao, Qian Mao, Zheng Zhao, Tongyi Dou, Zhiguo Wang, Xiaoyu Cui, Yuanning Liu and Xiaoya Fan

    Citation: BMC Genomics 2018 19:839

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  18. Content type: Research article

    Nε-Acetylation of lysine residues, a frequently occurring post-translational modification, plays important functions in regulating physiology and metabolism. However, the information of global overview of protei....

    Authors: Jutang Jiang, Zhongshuai Gai, Yu Wang, Kai Fan, Litao Sun, Hui Wang and Zhaotang Ding

    Citation: BMC Genomics 2018 19:840

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  19. Content type: Research article

    Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the Eur...

    Authors: Huabai Xue, Suke Wang, Jia-Long Yao, Cecilia H. Deng, Long Wang, Yanli Su, Huirong Zhang, Huangkai Zhou, Minshan Sun, Xiugen Li and Jian Yang

    Citation: BMC Genomics 2018 19:833

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  20. Content type: Research article

    The marine alga Ulva compressa is the dominant species in coastal areas receiving effluents from copper mines. The alga can accumulate high amounts of copper and possesses a strong antioxidant system. Here, we pe...

    Authors: Felipe E. Rodríguez, Daniel Laporte, Alberto González, Katterinne N. Mendez, Eduardo Castro-Nallar, Claudio Meneses, Juan Pablo Huidobro-Toro and Alejandra Moenne

    Citation: BMC Genomics 2018 19:829

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  21. Content type: Research article

    Despite its relevance, almost no studies account for the genetic control in the early stages of tree development, i.e. from germination on. This study seeks to make a quite complete transcriptome for olive dev...

    Authors: Jaime Jiménez-Ruiz, María de la O Leyva-Pérez, Isabel Vidoy-Mercado, Araceli Barceló and Francisco Luque

    Citation: BMC Genomics 2018 19:824

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  22. Content type: Research article

    The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the mos...

    Authors: Xiaohui Zhang, Yunsong Lai, Wei Zhang, Jalil Ahmad, Yang Qiu, Xiaoxue Zhang, Mengmeng Duan, Tongjin Liu, Jiangping Song, Haiping Wang and Xixiang Li

    Citation: BMC Genomics 2018 19:819

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  23. Content type: Research article

    The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative ...

    Authors: E. Jurak, H. Suzuki, G. van Erven, J. A. Gandier, P. Wong, K. Chan, C. Y. Ho, Y. Gong, E. Tillier, M.-N. Rosso, M. A. Kabel, S. Miyauchi and E. R. Master

    Citation: BMC Genomics 2018 19:815

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  24. Content type: Research article

    Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–lo...

    Authors: Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu and M Thomas P Gilbert

    Citation: BMC Genomics 2018 19:811

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  25. Content type: Research article

    Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of t...

    Authors: Qiming Cheng, Shiqie Bai, Gentu Ge, Ping Li, Liying Liu, Chengdong Zhang and Yushan Jia

    Citation: BMC Genomics 2018 19:807

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  26. Content type: Research article

    Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DN...

    Authors: Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas te Lintel Hekkert, Gabino Sanchez Perez, Paul Medvedev, Kateryna D. Makova and Dick de Ridder

    Citation: BMC Genomics 2018 19:798

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  27. Content type: Research article

    WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modi...

    Authors: Rui Hu, Jie Xiao, Ting Gu, Xiaofen Yu, Yang Zhang, Junli Chang, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2018 19:803

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    The Correction to this article has been published in BMC Genomics 2018 19:852

  28. Content type: Research article

    Calanthe masuca and C. sinica are two genetically closely related species in Orchidaceae. C. masuca is widely distributed in Asia, whereas C. sinica is restricted to Yunnan and Guangxi Provinces in southwest Chin...

    Authors: Chao Hu, Hongxing Yang, Kai Jiang, Ling Wang, Boyun Yang, Tungyu Hsieh, Siren Lan and Weichang Huang

    Citation: BMC Genomics 2018 19:800

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  29. Content type: Research article

    Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embry...

    Authors: Yan Chen, Xue Li, Liyao Su, Xu Chen, Shuting Zhang, Xiaoping Xu, Zihao Zhang, Yukun Chen, Xu XuHan, Yuling Lin and Zhongxiong Lai

    Citation: BMC Genomics 2018 19:805

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  30. Content type: Research article

    Ornamental cabbage (Brassica oleracea var. acephala) is an attractive landscape plant that remains colorful at low temperatures during winter. Its key feature is its inner leaf coloration, which can include red, ...

    Authors: Si-Won Jin, Md Abdur Rahim, Khandker Shazia Afrin, Jong-In Park, Jong-Goo Kang and Ill-Sup Nou

    Citation: BMC Genomics 2018 19:797

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  31. Content type: Research article

    Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptatio...

    Authors: Billie A. Gould, Juan Diego Palacio-Mejia, Jerry Jenkins, Sujan Mamidi, Kerrie Barry, Jeremy Schmutz, Thomas E. Juenger and David B. Lowry

    Citation: BMC Genomics 2018 19:792

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  32. Content type: Research article

    Heterosis, a multigenic complex trait extrapolated as sum total of many phenotypic features, is widely utilized phenomenon in agricultural crops for about a century. It is mainly focused on establishing vigoro...

    Authors: Zareen Sarfraz, Muhammad Shahid Iqbal, Zhaoe Pan, Yinhua Jia, Shoupu He, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Zhiying Ma, Dongyong Xu, Jinlong Yang, Jinbiao Zhang, Wenfang Gong, Xiaoli Geng…

    Citation: BMC Genomics 2018 19:776

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  33. Content type: Research article

    The mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitocho...

    Authors: Shuangshuang Li, Zhiwen Chen, Nan Zhao, Yumei Wang, Hushuai Nie and Jinping Hua

    Citation: BMC Genomics 2018 19:775

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  34. Content type: Research article

    Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their allev...

    Authors: Luis M Avila, Wisam Obeidat, Hugh Earl, Xiaomu Niu, William Hargreaves and Lewis Lukens

    Citation: BMC Genomics 2018 19:761

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  35. Content type: Research article

    In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partition...

    Authors: Long Zhao, Lei Han, Chaoxia Xiao, Xiuyun Lin, Chunming Xu and Chunwu Yang

    Citation: BMC Genomics 2018 19:756

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  36. Content type: Research article

    COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCFCOI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown ...

    Authors: Jian-fang Bai, Yu-kun Wang, Peng Wang, Shao-hua Yuan, Jian-gang Gao, Wen-jing Duan, Na Wang, Feng-ting Zhang, Wen-jie Zhang, Meng-ying Qin, Chang-ping Zhao and Li-ping Zhang

    Citation: BMC Genomics 2018 19:754

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  37. Content type: Research article

    Transgenerational plasticity occurs when the environmental experience of an organism modifies the growth and development of its progeny. Leaf damage in Mimulus guttatus exhibits transgenerational plasticity media...

    Authors: Jack M Colicchio, John K Kelly and Lena C Hileman

    Citation: BMC Genomics 2018 19:746

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  38. Content type: Research article

    Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an...

    Authors: Enhui Shen, Xintian Zhu, Shuijin Hua, Hongyu Chen, Chuyu Ye, Longhua Zhou, Qing Liu, Qian-Hao Zhu, Longjiang Fan and Xi Chen

    Citation: BMC Genomics 2018 19:745

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  39. Content type: Research article

    The hop plant (Humulus lupulus L.) is a valuable source of several secondary metabolites, such as flavonoids, bitter acids, and essential oils. These compounds are widely implicated in the beer brewing industry a...

    Authors: Ajay Kumar Mishra, Ganesh Selvaraj Duraisamy, Mudra Khare, Tomáš Kocábek, Jernej Jakse, Jindřich Bříza, Josef Patzak, Teruo Sano and Jaroslav Matoušek

    Citation: BMC Genomics 2018 19:739

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  40. Content type: Research article

    The majority of eukaryote genomes can be actively transcribed into non-coding RNAs (ncRNAs), which are functionally important in development and evolution. In the study of maize, an important crop for both hum...

    Authors: Dandan Li, Huili Qiao, Wujie Qiu, Xin Xu, Tiemei Liu, Qianling Jiang, Renyi Liu, Zhujin Jiao, Kun Zhang, Lijun Bi, Runsheng Chen and Yunchao Kan

    Citation: BMC Genomics 2018 19:730

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  41. Content type: Research article

    Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, ver...

    Authors: Guangyan Feng, Lei Xu, Jianping Wang, Gang Nie, Bradley Shaun Bushman, Wengang Xie, Haidong Yan, Zhongfu Yang, Hao Guan, Linkai Huang and Xinquan Zhang

    Citation: BMC Genomics 2018 19:727

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  42. Content type: Research article

    MADS-box genes encode transcription factors that are known to be involved in several aspects of plant growth and development, especially in floral organ specification. To date, the comprehensive analysis of po...

    Authors: Huhu Gao, Ziming Wang, Silu Li, Menglu Hou, Yao Zhou, Yaqi Zhao, Guojun Li, Hua Zhao and Haoli Ma

    Citation: BMC Genomics 2018 19:726

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  43. Content type: Research article

    Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many g...

    Authors: Lijun Kong, Kun Zhao, Yingying Gao, Liming Miao, Chaoquan Chen, Hang Deng, Zhenning Liu and Xiaolin Yu

    Citation: BMC Genomics 2018 19:728

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  44. Content type: Research article

    Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is ...

    Authors: Guanglong Chen, Yu Zou, Jihong Hu and Yi Ding

    Citation: BMC Genomics 2018 19:720

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  45. Content type: Research article

    Arabidopsis pumila is native to the desert region of northwest China and it is extraordinarily well adapted to the local semi-desert saline soil, thus providing a candidate plant system for environmental adaptati...

    Authors: Lifei Yang, Yuhuan Jin, Wei Huang, Qi Sun, Fang Liu and Xianzhong Huang

    Citation: BMC Genomics 2018 19:717

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  46. Content type: Research article

    Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular u...

    Authors: Dan Cheng, Mingpu Tan, Haijuan Yu, Liang Li, Dandan Zhu, Yahua Chen and Mingyi Jiang

    Citation: BMC Genomics 2018 19:709

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  47. Content type: Research article

    VQ motif-containing (VQ) proteins are plant-specific proteins that interact with WRKY transcription factors and play important roles in plant growth, development and stress response. To date, VQ gene families hav...

    Authors: Junhong Guo, Jiangfei Chen, Jiankun Yang, Youben Yu, Yajun Yang and Weidong Wang

    Citation: BMC Genomics 2018 19:710

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  48. Content type: Research article

    The FK506-binding proteins (FKBPs) play diverse roles in numerous critical processes for plant growth, development, and abiotic stress responses. However, the FKBP gene family in the important fruit crop apple (M...

    Authors: Qinglong Dong, Ke Mao, Dingyue Duan, Shuang Zhao, Yanpeng Wang, Qian Wang, Dong Huang, Chao Li, Changhai Liu, Xiaoqing Gong and Fengwang Ma

    Citation: BMC Genomics 2018 19:707

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