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  1. Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing tech...

    Authors: Yuan Wu, Lin Yang, Wen-Ge Li, Wen Zhu Zhang, Zheng Jie Liu and Jin-Xing Lu

    Citation: BMC Genomics 2019 20:796

    Content type: Research article

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  2. Some Gynura species have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hy...

    Authors: Tianyu Han, Mimi Li, Jiawei Li, Han Lv, Bingru Ren, Jian Chen and Weilin Li

    Citation: BMC Genomics 2019 20:791

    Content type: Research article

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  3. The hepatitis E virus (HEV) is the causative pathogen of hepatitis E, a global public health concern. HEV comprises 8 genotypes with a wide host range and geographic distribution. This study aims to determine ...

    Authors: Sarra Baha, Nouredine Behloul, Zhenzhen Liu, Wenjuan Wei, Ruihua Shi and Jihong Meng

    Citation: BMC Genomics 2019 20:790

    Content type: Research article

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  4. Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation seq...

    Authors: Ke Teng, Wenjun Teng, Haifeng Wen, Yuesen Yue, Weier Guo, Juying Wu and Xifeng Fan

    Citation: BMC Genomics 2019 20:789

    Content type: Research article

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  5. Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that fecal samples representing the gut microbiota of rainb...

    Authors: Pratima Chapagain, Brock Arivett, Beth M. Cleveland, Donald M. Walker and Mohamed Salem

    Citation: BMC Genomics 2019 20:788

    Content type: Research article

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  6. Barley is the world’s fourth most cultivated cereal and is an important crop model for genetic studies. One layer of genomic information that remains poorly explored in barley is presence/absence variation (PA...

    Authors: Marius Weisweiler, Amaury de Montaigu, David Ries, Mara Pfeifer and Benjamin Stich

    Citation: BMC Genomics 2019 20:787

    Content type: Research Article

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  7. The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive...

    Authors: Xiangpeng Leng, Hongru Wei, Xiaozhao Xu, Sandip A. Ghuge, Dongjie Jia, Gengsen Liu, Yongzhang Wang and Yongbing Yuan

    Citation: BMC Genomics 2019 20:786

    Content type: Research article

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  8. The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic bioma...

    Authors: Bryan W. Penning, Tânia M. Shiga, John F. Klimek, Philip J. SanMiguel, Jacob Shreve, Jyothi Thimmapuram, Robert W. Sykes, Mark F. Davis, Maureen C. McCann and Nicholas C. Carpita

    Citation: BMC Genomics 2019 20:785

    Content type: Research article

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  9. We have previously reported on paucity of mitochondrial DNA (mtDNA) haplogroups J and K among Finnish endurance athletes. Here we aimed to further explore differences in mtDNA variants between elite endurance ...

    Authors: Jukka Kiiskilä, Jukka S. Moilanen, Laura Kytövuori, Anna-Kaisa Niemi and Kari Majamaa

    Citation: BMC Genomics 2019 20:784

    Content type: Research article

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  10. Artificial mutagenesis not only provides a new approach to increase the diversity of desirable traits for breeding new varieties but are also beneficial for characterizing the genetic basis of functional genes...

    Authors: Cong Tan, Xiao-Qi Zhang, Yin Wang, Dianxin Wu, Matthew I. Bellgard, Yanhao Xu, Xiaoli Shu, Gaofeng Zhou and Chengdao Li

    Citation: BMC Genomics 2019 20:783

    Content type: Research article

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  11. Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information res...

    Authors: Yang Yang, Xiaobao Liu, Jimiao Cai, Yipeng Chen, Boxun Li, Zhikai Guo and Guixiu Huang

    Citation: BMC Genomics 2019 20:782

    Content type: Research article

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  12. Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hy...

    Authors: Jianjun Fu, Wenbin Zhu, Lanmei Wang, Mingkun Luo, Feibiao Song and Zaijie Dong

    Citation: BMC Genomics 2019 20:781

    Content type: Research article

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  13. Our previous study finds that male sterility in Salvia miltiorrhiza could result in stunted growth and reduced biomass, but their molecular mechanisms have not yet been revealed. In this article, we investigate t...

    Authors: Ruihong Wang, Han Jiang, Ziyun Zhou, Hongbo Guo and Juane Dong

    Citation: BMC Genomics 2019 20:780

    Content type: Research article

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  14. Pine trees challenged by Bursaphelenchus xylophilus invasion produce phytoalexins to combat this nematode. Nevertheless, the phytoalexins of Asian pine trees are ineffective against B. xylophilus. The anti-phytoa...

    Authors: Feng Wang, Qiaoli Chen, Ruizhi Zhang, Danlei Li, Yaming Ling and Ruiqing Song

    Citation: BMC Genomics 2019 20:779

    Content type: Research article

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  15. Abdominal fat is the major adipose tissue in chickens. The growth status of abdominal fat during postnatal late development ultimately affects meat yield and quality in chickens. MicroRNAs (miRNAs) are endogen...

    Authors: Yi Chen, Yinli Zhao, Wenjiao Jin, Yuanfang Li, Yanhua Zhang, Xuejie Ma, Guirong Sun, Ruili Han, Yadong Tian, Hong Li, Xiangtao Kang and Guoxi Li

    Citation: BMC Genomics 2019 20:778

    Content type: Research article

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  16. Aphid (Macrosiphoniella sanbourni) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect ...

    Authors: Xue-ying Zhang, Xian-zhi Sun, Sheng Zhang, Jing-hui Yang, Fang-fang Liu and Jie Fan

    Citation: BMC Genomics 2019 20:776

    Content type: Research article

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  17. Calcineurin B-like proteins (CBLs) are major Ca2+ sensors that interact with CBL-interacting protein kinases (CIPKs) to regulate growth and development in plants. The CBL-CIPK network is involved in stress respon...

    Authors: Xiao Ma, Wen-Xian Gai, Yi-Ming Qiao, Muhammad Ali, Ai-Min Wei, De-Xu Luo, Quan-Hui Li and Zhen-Hui Gong

    Citation: BMC Genomics 2019 20:775

    Content type: Research article

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  18. Bovine viral diarrhoea virus (BVDV) is the member of the genus Pestivirus within the Flaviviridae family and responsible for severe economic losses in the cattle industry. BVDV can employ ‘infect-and-persist’ str...

    Authors: Cun Liu, Yanhan Liu, Lin Liang, Shangjin Cui and Yanming Zhang

    Citation: BMC Genomics 2019 20:774

    Content type: Research article

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  19. Plant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of hi...

    Authors: Intikhab Alam, Cui-Cui Liu, Hong-Liu Ge, Khadija Batool, Yan-Qing Yang and Yun-Hai Lu

    Citation: BMC Genomics 2019 20:773

    Content type: Research article

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  20. Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stre...

    Authors: Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lianxue Fan and Liwang Liu

    Citation: BMC Genomics 2019 20:772

    Content type: Research article

    Published on:

  21. Host genotype plays a crucial role in microbial composition of laying hens, which may lead to dissimilar odor gas production. The objective of this study was to investigate the relationship among layer breed, ...

    Authors: Chun-Bo Huang, Lei Xiao, Si-Cheng Xing, Jing-Yuan Chen, Yi-Wen Yang, Yang Zhou, Wei Chen, Juan-Boo Liang, Jian-Dui Mi, Yan Wang, Yin-Bao Wu and Xin-Di Liao

    Citation: BMC Genomics 2019 20:770

    Content type: Research article

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  22. Microsatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatelli...

    Authors: Yelin Fu, Lishuang Qi, Wenbing Guo, Liangliang Jin, Kai Song, Tianyi You, Shuobo Zhang, Yunyan Gu, Wenyuan Zhao and Zheng Guo

    Citation: BMC Genomics 2019 20:769

    Content type: Research article

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  23. The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remai...

    Authors: Zhiqiu Yin, Chao Yuan, Yuhui Du, Pan Yang, Chengqian Qian, Yi Wei, Si Zhang, Di Huang and Bin Liu

    Citation: BMC Genomics 2019 20:768

    Content type: Research article

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  24. Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock indust...

    Authors: Stewart T. G. Burgess, Edward J. Marr, Kathryn Bartley, Francesca G. Nunn, Rachel E. Down, Robert J. Weaver, Jessica C. Prickett, Jackie Dunn, Stephane Rombauts, Thomas Van Leeuwen, Yves Van de Peer and Alasdair J. Nisbet

    Citation: BMC Genomics 2019 20:756

    Content type: Research article

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  25. Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E...

    Authors: Jarosław E. Król, Donald C. Hall Jr, Sergey Balashov, Steven Pastor, Justin Sibert, Jennifer McCaffrey, Steven Lang, Rachel L. Ehrlich, Joshua Earl, Joshua C. Mell, Ming Xiao and Garth D. Ehrlich

    Citation: BMC Genomics 2019 20:767

    Content type: Research article

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  26. Rhizome is the storage underground stem of lotus (Nelumbo nucifera), which is enlarged before winter season and could be used for asexual propagation. In addition, the enlarged rhizome is a nutritional vegetable ...

    Authors: Dingding Cao, Rebecca Njeri Damaris, Yue Zhang, Meihui Liu, Ming Li and Pingfang Yang

    Citation: BMC Genomics 2019 20:766

    Content type: Research article

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  27. Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mi...

    Authors: Gang Wang, Jingxian Lin, Yang Shi, Xiaoguang Chang, Yuanyuan Wang, Lin Guo, Wenhui Wang, Meijie Dou, Youjin Deng, Ray Ming and Jisen Zhang

    Citation: BMC Genomics 2019 20:765

    Content type: Research article

    Published on:

  28. A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs ...

    Authors: María Gabián, Paloma Morán, Ana I. Fernández, Beatriz Villanueva, Amel Chtioui, Matthew P. Kent, Lara Covelo-Soto, Almudena Fernández and María Saura

    Citation: BMC Genomics 2019 20:764

    Content type: Research article

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  29. One fundamental question in biology is how the evolution of eukaryotic signaling networks has taken place. “Loss of function” (lof) mutants from components of the high osmolarity glycerol (HOG) signaling pathw...

    Authors: Stefan Bohnert, Luis Antelo, Christiane Grünewald, Alexander Yemelin, Karsten Andresen and Stefan Jacob

    Citation: BMC Genomics 2019 20:763

    Content type: Research article

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  30. Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm culti...

    Authors: Phongthana Pasookhush, Charles Hindmarch, Paisarn Sithigorngul, Siwaporn Longyant, William G. Bendena and Parin Chaivisuthangkura

    Citation: BMC Genomics 2019 20:762

    Content type: Research article

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  31. Horizontal gene transfer (HGT), which is affected by environmental pollution and climate change, promotes genetic communication, changing bacterial pathogenicity and drug resistance. However, few studies have ...

    Authors: Yiqin Deng, Haidong Xu, Youlu Su, Songlin Liu, Liwen Xu, Zhixun Guo, Jinjun Wu, Changhong Cheng and Juan Feng

    Citation: BMC Genomics 2019 20:761

    Content type: Research article

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  32. Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However...

    Authors: Qi Yan, Fan Wu, Tiantian Ma, Xifang Zong, Qian Ma, Jie Li, Yufeng Zhao, Yanrong Wang and Jiyu Zhang

    Citation: BMC Genomics 2019 20:760

    Content type: Research article

    Published on:

  33. Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentia...

    Authors: Marina Solé, Michela Ablondi, Amrei Binzer-Panchal, Brandon D. Velie, Nina Hollfelder, Nadine Buys, Bart J. Ducro, Liesbeth François, Steven Janssens, Anouk Schurink, Åsa Viklund, Susanne Eriksson, Anders Isaksson, Hanna Kultima, Sofia Mikko and Gabriella Lindgren

    Citation: BMC Genomics 2019 20:759

    Content type: Research article

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  34. The mesocotyl connects the coleoptilar node and the basal part of the seminal root of maize (Zea mays) seedling. The mesocotyl pushes the shoot of the seedling out of the soil during seed germination; thus, its g...

    Authors: Liangjie Niu, Zhaokun Wu, Hui Liu, Xiaolin Wu and Wei Wang

    Citation: BMC Genomics 2019 20:758

    Content type: Research article

    Published on:

  35. The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishin...

    Authors: Inés González-Castellano, Chiara Manfrin, Alberto Pallavicini and Andrés Martínez-Lage

    Citation: BMC Genomics 2019 20:757

    Content type: Research article

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  36. While DNA and RNA methods are routine to disrupt the expression of specific genes, complete understanding of developmental processes requires also protein methods, because: oocytes and early embryos accumulate...

    Authors: Steffen Israel, Ellen Casser, Hannes C.A. Drexler, Georg Fuellen and Michele Boiani

    Citation: BMC Genomics 2019 20:755

    Content type: Research article

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  37. Genomic composition has been found to be species specific and is used to differentiate bacterial species. To date, almost no published composition-based approaches are able to distinguish between most closely ...

    Authors: Yizhuang Zhou, Wenting Zhang, Huixian Wu, Kai Huang and Junfei Jin

    Citation: BMC Genomics 2019 20:754

    Content type: Methodology article

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  38. The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies...

    Authors: Jeanne Wilbrandt, Bernhard Misof, Kristen A. Panfilio and Oliver Niehuis

    Citation: BMC Genomics 2019 20:753

    Content type: Research article

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  39. The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacteriu...

    Authors: Hirokazu Yano, Haruo Suzuki, Fumito Maruyama and Tomotada Iwamoto

    Citation: BMC Genomics 2019 20:752

    Content type: Research article

    Published on:

  40. Massive techniques have been evaluated for developing different pest control methods to minimize fertilizer and pesticide inputs. As “push-pull” strategy utilizes generally non-toxic chemicals to manipulate be...

    Authors: Xin Yi, Song Shi, Peidan Wang, Yaoyao Chen, Qiqi Lu, Tianyi Wang, Xiaofan Zhou and Guohua Zhong

    Citation: BMC Genomics 2019 20:751

    Content type: Research article

    Published on:

  41. Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been con...

    Authors: Licao Cui, Guang Yang, Jiali Yan, Yan Pan and Xiaojun Nie

    Citation: BMC Genomics 2019 20:750

    Content type: Research article

    Published on:

  42. The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehe...

    Authors: Mengyuan Wei, Aili Liu, Yujuan Zhang, Yong Zhou, Donghua Li, Komivi Dossa, Rong Zhou, Xiurong Zhang and Jun You

    Citation: BMC Genomics 2019 20:748

    Content type: Research article

    Published on:

  43. Gibberellins (GAs) can have profound effects on growth and development in higher plants. In contrast to their flowering-promotive role in many well-studied plants, GAs can repress flowering in woody perennial ...

    Authors: Songwen Zhang, Christopher Gottschalk and Steve van Nocker

    Citation: BMC Genomics 2019 20:747

    Content type: Research article

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  44. The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of st...

    Authors: Ran Li, Xiaomeng Tian, Peng Yang, Yingzhi Fan, Ming Li, Hongxiang Zheng, Xihong Wang and Yu Jiang

    Citation: BMC Genomics 2019 20:746

    Content type: Research article

    Published on:

  45. The development of next generation sequencing (NGS) methods led to a rapid rise in the generation of large genomic datasets, but the development of user-friendly tools to analyze and visualize these datasets h...

    Authors: Alberto Luiz P. Reyes, Tiago C. Silva, Simon G. Coetzee, Jasmine T. Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther and Michelle R. Jones

    Citation: BMC Genomics 2019 20:745

    Content type: Software

    Published on:

  46. Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Albe...

    Authors: Afsaneh Sedaghatkish, Bruce D. Gossen, Fengqun Yu, Davoud Torkamaneh and Mary Ruth McDonald

    Citation: BMC Genomics 2019 20:744

    Content type: Research article

    Published on:

  47. Gene expression profiling in blood is a potential source of biomarkers to evaluate or predict phenotypic differences between pigs but is expensive and inefficient because of the high abundance of globin mRNA i...

    Authors: Kyu-Sang Lim, Qian Dong, Pamela Moll, Jana Vitkovska, Gregor Wiktorin, Stephanie Bannister, Dalia Daujotyte, Christopher K. Tuggle, Joan K. Lunney, Graham S. Plastow and Jack C. M. Dekkers

    Citation: BMC Genomics 2019 20:741

    Content type: Research article

    Published on:

  48. ERECTA (ER) is a leucine-rich repeat-receptor-like kinase gene (LRR-RLK) encoding a protein isolated from Arabidopsis. Although the regulatory functions of ER genes have been widely explored in plant development ...

    Authors: Hanshuai Li, Xiaodong Han, Xinxiang Liu, Miaoyi Zhou, Wen Ren, Bingbing Zhao, Chuanli Ju, Ya Liu and Jiuran Zhao

    Citation: BMC Genomics 2019 20:737

    Content type: Research article

    Published on:

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