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  1. Content type: Research article

    Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variet...

    Authors: Angela Kranz, Andrea Steinmann, Ursula Degner, Aliye Mengus-Kaya, Susana Matamouros, Michael Bott and Tino Polen

    Citation: BMC Genomics 2018 19:753

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  2. Content type: Research article

    Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops ...

    Authors: S. Zoledowska, A. Motyka-Pomagruk, W. Sledz, A. Mengoni and E. Lojkowska

    Citation: BMC Genomics 2018 19:751

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  3. Content type: Research article

    Mitochondrial DNA (mtDNA) copy number has been found associated with multiple diseases, including cancers, diabetes and so on. Both environmental and genetic factors could affect the copy number of mtDNA. Howe...

    Authors: Zhihua Li, Meng Zhu, Jiangbo Du, Hongxia Ma, Guangfu Jin and Juncheng Dai

    Citation: BMC Genomics 2018 19:752

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  4. Content type: Research article

    Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine...

    Authors: Arash Akbarzadeh, Oliver P Günther, Aimee Lee Houde, Shaorong Li, Tobi J Ming, Kenneth M Jeffries, Scott G Hinch and Kristina M Miller

    Citation: BMC Genomics 2018 19:749

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  5. Content type: Research article

    Transmissible gastroenteritis virus (TGEV) infection can activate NF-κB pathway in porcine intestinal epithelial cells and result in severe inflammation. Non-coding RNAs (ncRNAs) are not translated into protei...

    Authors: Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang and Dewen Tong

    Citation: BMC Genomics 2018 19:747

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  6. 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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  7. 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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  8. Content type: Research article

    Gray leaf spot (GLS), which is caused by the necrotrophic fungi Cercospora zeae-maydis and Cercospora zeina, is one of the most impactful diseases in maize worldwide. The aim of the present study is to identify t...

    Authors: Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Haichun Shi, Yongpei Ke and Qun Sun

    Citation: BMC Genomics 2018 19:742

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  9. Content type: Research article

    Long noncoding RNAs (lncRNAs) are known to play important roles in different cell contexts, including cancers. However, little is known about lncRNAs in cholangiocarcinoma (CCA), a cholangiocyte malignancy wit...

    Authors: Bo-Wei Han, Hua Ye, Pan-Pan Wei, Bo He, Cai Han, Zhen-Hua Chen, Yue-Qin Chen and Wen-Tao Wang

    Citation: BMC Genomics 2018 19:735

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  10. Content type: Research article

    Transcription factors are essential regulators of gene expression and play critical roles in development, differentiation, and in many cancers. To carry out their regulatory programs, they must cooperate in ne...

    Authors: Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo and Kevin R. Coombes

    Citation: BMC Genomics 2018 19:738

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  11. Content type: Research article

    This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, ...

    Authors: Claudia A Sevillano, Jan ten Napel, Simone E F Guimarães, Fabyano F Silva and Mario P L Calus

    Citation: BMC Genomics 2018 19:740

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  12. Content type: Research article

    Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even af...

    Authors: Sarah R. McCoski, McCauley T. Vailes, Connor E. Owens, Rebecca R. Cockrum and Alan D. Ealy

    Citation: BMC Genomics 2018 19:737

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  13. Content type: Research article

    Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically impo...

    Authors: Peng Luo, Long Yun, Yingying Li, Yushun Tian, Qiuting Liu, Wen Huang and Chaoqun Hu

    Citation: BMC Genomics 2018 19:741

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  14. Content type: Research article

    Capacitation, a prerequisite for oocyte fertilization, is a complex process involving series of structural and functional changes in sperms such as membrane modifications, modulation of enzyme activities, and ...

    Authors: Yuan Li, Rong-Hong Li, Ming-Xia Ran, Yan Zhang, Kai Liang, Ying-Nan Ren, Wen-Cheng He, Ming Zhang, Guang-Bin Zhou, Izhar Hyder Qazi and Chang-Jun Zeng

    Citation: BMC Genomics 2018 19:736

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  15. 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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  16. Content type: Research article

    Studies combining experimental evolution and next-generation sequencing have found that adaptation in sexually reproducing populations is primarily fueled by standing genetic variation. Consequently, the respo...

    Authors: Mark A Phillips, Grant A Rutledge, James N Kezos, Zachary S Greenspan, Andrew Talbott, Sara Matty, Hamid Arain, Laurence D Mueller, Michael R Rose and Parvin Shahrestani

    Citation: BMC Genomics 2018 19:743

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  17. Content type: Research article

    Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their gene transcription profile. This technology is widely used in medicine, animal husbandry and other industries. Ho...

    Authors: Yong Liu, Fengrui Wu, Ling Zhang, Xiaoqing Wu, Dengkun Li, Jing Xin, Juan Xie, Feng Kong, Wenying Wang, Qiaoqin Wu, Di Zhang, Rong Wang, Shaorong Gao and Wenyong Li

    Citation: BMC Genomics 2018 19:734

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  18. Content type: Research article

    The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured wor...

    Authors: Oanh T. P. Kim, Phuong T. Nguyen, Eiichi Shoguchi, Kanako Hisata, Thuy T. B. Vo, Jun Inoue, Chuya Shinzato, Binh T. N. Le, Koki Nishitsuji, Miyuki Kanda, Vu H. Nguyen, Hai V. Nong and Noriyuki Satoh

    Citation: BMC Genomics 2018 19:733

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  19. Content type: Research article

    The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early mouse development, SR-B1 is located in the maternal-fetal interf...

    Authors: Nicolás Santander, Carlos Lizama, Leandro Murgas, Sebastián Contreras, Alberto J. M. Martin, Paz Molina, Alonso Quiroz, Katherine Rivera, Francisca Salas-Pérez, Alejandro Godoy, Attilio Rigotti and Dolores Busso

    Citation: BMC Genomics 2018 19:731

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  20. Content type: Research article

    After a short gestation, marsupials give birth to immature neonates with lungs that are not fully developed and in early life the neonate partially relies on gas exchange through the skin. Therefore, significa...

    Authors: Vengamanaidu Modepalli, Amit Kumar, Julie A Sharp, Norman R Saunders, Kevin R Nicholas and Christophe Lefèvre

    Citation: BMC Genomics 2018 19:732

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  21. Content type: Research article

    Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.

    Authors: Bi Jun Li, Dan Li Jiang, Zi Ning Meng, Yong Zhang, Zong Xian Zhu, Hao Ran Lin and Jun Hong Xia

    Citation: BMC Genomics 2018 19:729

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  22. 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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  23. 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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  24. 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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  25. 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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  26. Content type: Research article

    Transposome-based technologies have enabled the streamlined production of sequencer-ready DNA libraries; however, current methods are highly sensitive to the amount and quality of input nucleic acid.

    Authors: Stephen Bruinsma, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, Lee Brady, Anupama Khanna, Lindsay Freeberg, Rosamond G Jackson, Pascale Mathonet, Susan C Verity, Andrew F Slatter, Rooz Golshani, Haiying Grunenwald…

    Citation: BMC Genomics 2018 19:722

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  27. Content type: Research article

    The Ambrosia Fusarium Clade phytopathogenic Fusarium fungi species have a symbiotic relationship with ambrosia beetles in the genus Euwallacea (Coleoptera: Curculionidae). Related beetle species referred to as Eu...

    Authors: Diana Sánchez-Rangel, Eric-Edmundo Hernández-Domínguez, Claudia-Anahí Pérez-Torres, Randy Ortiz-Castro, Emanuel Villafán, Benjamín Rodríguez-Haas, Alexandro Alonso-Sánchez, Abel López-Buenfil, Nayeli Carrillo-Ortiz, Lervin Hernández-Ramos and Enrique Ibarra-Laclette

    Citation: BMC Genomics 2018 19:721

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  28. Content type: Research article

    Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immun...

    Authors: Amy R Ellison, Tamsyn M Uren Webster, Olivier Rey, Carlos Garcia de Leaniz, Sofia Consuegra, Pablo Orozco-terWengel and Jo Cable

    Citation: BMC Genomics 2018 19:723

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  29. Content type: Research article

    High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Ae...

    Authors: Dwight R Causey, Moritz A N Pohl, David A Stead, Samuel A M Martin, Christopher J Secombes and Daniel J Macqueen

    Citation: BMC Genomics 2018 19:719

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  30. 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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  31. Content type: Methodology article

    Analysis of polymorphic microsatellite markers (STR) is a helpful genotyping technique to differentiate Candida parapsilosis sensu stricto isolates. The aim of this study is to develop and perform an initial vali...

    Authors: Camino Trobajo-Sanmartín, Guillermo Ezpeleta, Célia Pais, Elena Eraso and Guillermo Quindós

    Citation: BMC Genomics 2018 19:718

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  32. 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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  33. Content type: Software

    Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has great potential to illuminate our understanding of biology and medicine, but the ...

    Authors: Natalia Polouliakh, Paul Horton, Kazuhiro Shibanai, Kodai Takata, Vanessa Ludwig, Samik Ghosh and Hiroaki Kitano

    Citation: BMC Genomics 2018 19:715

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  34. Content type: Methodology article

    Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiologi...

    Authors: Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto, Derrick W Crook and David W Eyre

    Citation: BMC Genomics 2018 19:714

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  35. Content type: Research article

    Streptococcus agalactiae (Group B Streptococcus, GBS) is a common bacteria species infecting both human and bovine. Previous studies have shown that the GBS isolated from human and bovine are mostly unrelated and...

    Authors: Rui Wang, Liping Li, Ting Huang, Yan Huang, Weiyi Huang, Xiuying Yang, Aiying Lei and Ming Chen

    Citation: BMC Genomics 2018 19:716

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  36. Content type: Correction

    Following the publication of this article [1], the authors noted two typographical errors: one in Table 1 with regard to the location of the Basilisk Phage, which was incorrectly captured as “Kutaisis, country...

    Authors: J Farlow, D Bolkvadze, L Leshkasheli, I Kusradze, A Kotorashvili, N Kotaria, N Balarjishvili, L Kvachadze, M Nikolich and M Kutateladze

    Citation: BMC Genomics 2018 19:713

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    The original article was published in BMC Genomics 2018 19:685

  37. 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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  38. Content type: Research article

    Ecdysis is an innate behaviour programme by which all arthropods moult their exoskeletons. The complex suite of interacting neuropeptides that orchestrate ecdysis is well studied in insects, but details of the...

    Authors: Andrew Oliphant, Jodi L. Alexander, Martin T. Swain, Simon G. Webster and David C. Wilcockson

    Citation: BMC Genomics 2018 19:711

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  39. Content type: Research article

    Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic fac...

    Authors: Furqan Awan, Yuhao Dong, Jin Liu, Nannan Wang, Muhammad Hassan Mushtaq, Chengping Lu and Yongjie Liu

    Citation: BMC Genomics 2018 19:712

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  40. 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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  41. Content type: Research article

    Listeria monocytogenes is a widespread foodborne pathogen that can cause listeriosis, a potentially fatal infection. L. monocytogenes is subdivided into four phylogenetic lineages, with the highest incidence of l...

    Authors: Cary Pirone-Davies, Yi Chen, Arthur Pightling, Gina Ryan, Yu Wang, Kuan Yao, Maria Hoffmann and Marc W. Allard

    Citation: BMC Genomics 2018 19:708

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  42. Content type: Research article

    Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficie...

    Authors: Leticia P Sanglard, Moysés Nascimento, Philipe Moriel, Jeffrey Sommer, Melissa Ashwell, Matthew H Poore, Márcio de S Duarte and Nick V L Serão

    Citation: BMC Genomics 2018 19:702

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  43. Content type: Research article

    Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi...

    Authors: Ying Wu, Xianfeng Ma, Zhiyong Pan, Shiv D. Kale, Yi Song, Harlan King, Qiong Zhang, Christian Presley, Xiuxin Deng, Cheng-I Wei and Shunyuan Xiao

    Citation: BMC Genomics 2018 19:705

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  44. Content type: Research article

    Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular ...

    Authors: Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss and Jean Paul Delgado

    Citation: BMC Genomics 2018 19:704

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  45. Content type: Research article

    RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to spl...

    Authors: Juan P. Romero, María Ortiz-Estévez, Ander Muniategui, Soraya Carrancio, Fernando J. de Miguel, Fernando Carazo, Luis M. Montuenga, Remco Loos, Rubén Pío, Matthew W. B. Trotter and Angel Rubio

    Citation: BMC Genomics 2018 19:703

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  46. 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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