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  1. Content type: Research

    Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as w...

    Authors: Wenhao Qian, Ting Ma, Mao Ye, Zhiyao Li, Yuanhua Liu and Pei Hao

    Citation: BMC Genomics 2019 20(Suppl 2):189

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    This article is part of a Supplement: Volume 20 Supplement 2

  2. Content type: Software Article

    Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the i...

    Authors: Gurjit S. Randhawa, Kathleen A. Hill and Lila Kari

    Citation: BMC Genomics 2019 20:267

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  3. Content type: Research article

    The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma...

    Authors: Yuqiong Guo, Chen Zhu, Shanshan Zhao, Shuting Zhang, Wenjian Wang, Haifeng Fu, Xiaozhen Li, Chengzhe Zhou, Lan Chen, Yuling Lin and Zhongxiong Lai

    Citation: BMC Genomics 2019 20:265

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  4. Content type: Research article

    Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa, one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GM...

    Authors: Xiuping Shen, Liai Xu, Yanhong Liu, Heng Dong, Dong Zhou, Yuzhi Zhang, Sue Lin, Jiashu Cao and Li Huang

    Citation: BMC Genomics 2019 20:264

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  5. Content type: Research article

    There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of...

    Authors: Diyan Li, Yan Li, Miao Li, Tiandong Che, Shilin Tian, Binlong Chen, Xuming Zhou, Guolong Zhang, Uma Gaur, Majing Luo, Kai Tian, Mengnan He, Shen He, Zhongxian Xu, Long Jin, Qianzi Tang…

    Citation: BMC Genomics 2019 20:263

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  6. Content type: Research article

    The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its gen...

    Authors: Vanessa Carvalho Cayres Pamponét, Margarete Magalhães Souza, Gonçalo Santos Silva, Fabienne Micheli, Cláusio Antônio Ferreira de Melo, Sarah Gomes de Oliveira, Eduardo Almeida Costa and Ronan Xavier Corrêa

    Citation: BMC Genomics 2019 20:262

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    The Correction to this article has been published in BMC Genomics 2019 20:303

  7. Content type: Research article

    Sheep have developed the ability to store fat in their tails, which is a unique way of reserving energy to survive a harsh environment. However, the mechanism underlying this adaptive trait remains largely uns...

    Authors: Zhangyuan Pan, Shengdi Li, Qiuyue Liu, Zhen Wang, Zhengkui Zhou, Ran Di, Xuejiao An, Benpeng Miao, Xiangyu Wang, Wenping Hu, Xiaofei Guo, Shenjin Lv, Fukuan Li, Guohui Ding, Mingxing Chu and Yixue Li

    Citation: BMC Genomics 2019 20:261

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  8. Content type: Research article

    The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to ident...

    Authors: Liang Wang, Yanbo Cheng, Qibin Ma, Yinghui Mu, Zhifeng Huang, Qiuju Xia, Gengyun Zhang and Hai Nian

    Citation: BMC Genomics 2019 20:260

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  9. Content type: Methodology article

    RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The ...

    Authors: Alberto Berral-Gonzalez, Angela L. Riffo-Campos and Guillermo Ayala

    Citation: BMC Genomics 2019 20:259

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  10. Content type: Research article

    Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cow fertility has received much attention in the last decade, while bull fertility has been largely overlooked. The...

    Authors: Juan Pablo Nani, Fernanda M. Rezende and Francisco Peñagaricano

    Citation: BMC Genomics 2019 20:258

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  11. Content type: Research article

    Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, whic...

    Authors: Shuonan Duan, Binhui Liu, Yuanyuan Zhang, Guoliang Li and Xiulin Guo

    Citation: BMC Genomics 2019 20:257

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  12. Content type: Research article

    Histone methylation mainly occurs on the lysine residues and plays a crucial role during flowering and stress responses of plants, through changing the methylation status or ratio of lysine residues. Histone l...

    Authors: Yexiong Qian, Changle Chen, Lingyu Jiang, Jing Zhang and Qiaoyu Ren

    Citation: BMC Genomics 2019 20:256

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  13. Content type: Research article

    An unfavorable genetic correlation between milk production and fertility makes simultaneous improvement of milk production and fertility difficult in cattle breeding. Rapid genetic improvement in milk producti...

    Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

    Citation: BMC Genomics 2019 20:255

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  14. Content type: Research article

    Placental efficiency (PE) describes the relationship between placental and fetal weights (fetal wt/placental wt). Within litters, PE can vary drastically, resulting in similarly sized pigs associated with diff...

    Authors: Shanice K. Krombeen, Vijay Shankar, Rooksana E. Noorai, Christopher A. Saski, Julia L. Sharp, Matthew E. Wilson and Tiffany A. Wilmoth

    Citation: BMC Genomics 2019 20:254

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  15. Content type: Research article

    Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis ...

    Authors: You-jie Zhao, Xin-yi Liu, Ran Guo, Kun-rong Hu, Yong Cao and Fei Dai

    Citation: BMC Genomics 2019 20:253

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  16. Content type: Research article

    Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively ...

    Authors: Yaa E. A. Oppong, Jody Phelan, João Perdigão, Diana Machado, Anabela Miranda, Isabel Portugal, Miguel Viveiros, Taane G. Clark and Martin L. Hibberd

    Citation: BMC Genomics 2019 20:252

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  17. Content type: Software

    The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two fi...

    Authors: Mathieu Bahin, Benoit F. Noël, Valentine Murigneux, Charles Bernard, Leila Bastianelli, Hervé Le Hir, Alice Lebreton and Auguste Genovesio

    Citation: BMC Genomics 2019 20:250

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  18. Content type: Methodology article

    Epigenetic dysregulation is involved in the etiology and progression of various human diseases. Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and ...

    Authors: Jian Zhong, Zhenqing Ye, Chad R. Clark, Samuel W. Lenz, Justin H. Nguyen, Huihuang Yan, Keith D. Robertson, Gianrico Farrugia, Zhiguo Zhang, Tamas Ordog and Jeong-Heon Lee

    Citation: BMC Genomics 2019 20:249

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  19. Content type: Research article

    Functional communications between nervous, endocrine and immune systems are well established in both vertebrates and invertebrates. Circulating hemocytes act as fundamental players in this crosstalk, whose fun...

    Authors: Fuxuan Wang, Shihao Li, Jianhai Xiang and Fuhua Li

    Citation: BMC Genomics 2019 20:247

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  20. Content type: Research article

    Marek’s disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens,...

    Authors: Zhen You, Qinghe Zhang, Changjun Liu, Jiuzhou Song, Ning Yang and Ling Lian

    Citation: BMC Genomics 2019 20:245

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  21. Content type: Research article

    Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, f...

    Authors: Alberto Cenci, Yann Hueber, Yasmin Zorrilla-Fontanesi, Jelle van Wesemael, Ewaut Kissel, Marie Gislard, Julie Sardos, Rony Swennen, Nicolas Roux, Sebastien Christian Carpentier and Mathieu Rouard

    Citation: BMC Genomics 2019 20:244

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  22. Content type: Research article

    Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on t...

    Authors: Annageldi Tayyrov, Claire E. Stanley, Sophie Azevedo and Markus Künzler

    Citation: BMC Genomics 2019 20:243

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  23. Content type: Research article

    Brassica oleracea exhibits extensive phenotypic diversity. As an important trait, petal color varies among different B. oleracea cultivars, enabling the study of the genetic basis of this trait. In a previous stu...

    Authors: Fengqing Han, Huilin Cui, Bin Zhang, Xiaoping Liu, Limei Yang, Mu Zhuang, Honghao Lv, Zhansheng Li, Yong Wang, Zhiyuan Fang, Jianghua Song and Yangyong Zhang

    Citation: BMC Genomics 2019 20:242

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  24. Content type: Research article

    Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pa...

    Authors: Zhenpeng Li, Xin Lu, Duochun Wang, Wei Li Liang, Jingyun Zhang, Jie Li, Jialiang Xu, Bo Pang and Biao Kan

    Citation: BMC Genomics 2019 20:241

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  25. Content type: Research article

    The most critical step in the pearl formation during aquaculture is issued to the proliferation and differentiation of outer epithelial cells of mantle graft into pearl sac. This pearl sac secretes various mat...

    Authors: Mariom, Saori Take, Yoji Igarashi, Kazutoshi Yoshitake, Shuichi Asakawa, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe and Shigeharu Kinoshita

    Citation: BMC Genomics 2019 20:240

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  26. Content type: Research article

    The phytopathogenic bacterium Xylella fastidiosa was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Ge...

    Authors: Nicolas Denancé, Martial Briand, Romain Gaborieau, Sylvain Gaillard and Marie-Agnès Jacques

    Citation: BMC Genomics 2019 20:239

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  27. Content type: Research article

    Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

    Authors: Haiping Du, Xiao Li, Lihua Ning, Rui Qin, Qing Du, Qing Wang, Haina Song, Fang Huang, Hui Wang and Deyue Yu

    Citation: BMC Genomics 2019 20:237

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  28. Content type: Research article

    The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adap...

    Authors: Isabelle Rosinski-Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart and Philippe Glaser

    Citation: BMC Genomics 2019 20:236

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  29. Content type: Research article

    Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic p...

    Authors: Pooja Yadav, K. B. Saxena, Anupama Hingane, C. V. Sameer Kumar, V. S. Kandalkar, Rajeev K. Varshney and Rachit K. Saxena

    Citation: BMC Genomics 2019 20:235

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  30. Content type: Research article

    Lactation and associated metabolic stresses during the post-partum period have been shown to impair fertility in dairy cows. The oviduct plays key roles in embryo development and the establishment of pregnancy...

    Authors: Yann Locatelli, Niamh Forde, Helmut Blum, Alexander Graf, Benoît Piégu, Pascal Mermillod, Eckhard Wolf, Patrick Lonergan and Marie Saint-Dizier

    Citation: BMC Genomics 2019 20:233

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  31. Content type: Research article

    Accumulation of protein aggregates are a major hallmark of progressive neurodegenerative disorders such as Parkinson’s disease and Alzheimer’s disease. Transgenic Caenorhabditis elegans nematodes expressing the h...

    Authors: Yiru A. Wang, Basten L. Snoek, Mark G. Sterken, Joost A. G. Riksen, Jana J. Stastna, Jan E. Kammenga and Simon C. Harvey

    Citation: BMC Genomics 2019 20:232

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  32. Content type: Methodology article

    We recently described a method for unbiased detection of all known human papillomaviruses (HPV) types with the potential for the determination of their variant and integration from the resulting whole genome s...

    Authors: Tengguo Li, Elizabeth R. Unger and Mangalathu S. Rajeevan

    Citation: BMC Genomics 2019 20:231

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  33. Content type: Research article

    Flowering time and maturity are among the most important adaptive traits in soybean (Glycine max (L.) Merill). Flowering Locus T (FT) family genes function as key flowering integrators, with flowering-promoting m...

    Authors: Bingjun Jiang, Shouwei Zhang, Wenwen Song, Mohammad Abdul Awal Khan, Shi Sun, Chengsheng Zhang, Tingting Wu, Cunxiang Wu and Tianfu Han

    Citation: BMC Genomics 2019 20:230

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  34. Content type: Methodology article

    Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield...

    Authors: Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Frank Speleman and Kaat Durinck

    Citation: BMC Genomics 2019 20:228

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  35. Content type: Research article

    Abiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance ag...

    Authors: Deepika Verma, Neha Lakhanpal and Kashmir Singh

    Citation: BMC Genomics 2019 20:227

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  36. Content type: Research article

    Despite the tremendous therapeutic advances that have stemmed from somatic oncogenetics, survival of some cancers has not improved in 50 years. Osteosarcoma still has a 5-year survival rate of 66%. We propose ...

    Authors: Isain Zapata, Luis E. Moraes, Elise M. Fiala, Sara Zaldivar-Lopez, C. Guillermo Couto, Jennie L. Rowell and Carlos E. Alvarez

    Citation: BMC Genomics 2019 20:226

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  37. Content type: Methodology article

    Large-scale genetic screening using CRISPR-Cas9 technology has emerged as a powerful approach to uncover and validate gene functions. The ability to control the timing of genetic perturbation during CRISPR scr...

    Authors: Ning Sun, Sakina Petiwala, Rui Wang, Charles Lu, Mufeng Hu, Sujana Ghosh, Yan Hao, Christopher P. Miller and Namjin Chung

    Citation: BMC Genomics 2019 20:225

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  38. Content type: Research article

    Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, togeth...

    Authors: Charikleia Karageorgiou, Víctor Gámez-Visairas, Rosa Tarrío and Francisco Rodríguez-Trelles

    Citation: BMC Genomics 2019 20:223

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  39. Content type: Research article

    Aquaporins (AQPs) facilitate transport of water and small solutes across cell membranes and play an important role in different physiological processes in plants. Despite their importance, limited data is avai...

    Authors: S. M. Shivaraj, Rupesh Deshmukh, Humira Sonah and Richard R. Bélanger

    Citation: BMC Genomics 2019 20:222

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  40. Content type: Research article

    The coordination of group behaviors in bacteria is achieved by a cell-cell signaling process called quorum sensing (QS). QS is an intercellular communication system, which synchronously controls expression of ...

    Authors: Miriam Khider, Erik Hjerde, Hilde Hansen and Nils Peder Willassen

    Citation: BMC Genomics 2019 20:220

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  41. Content type: Research article

    Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination be...

    Authors: Isabela Tiemy Pereira, Lucia Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya and Bruno Dallagiovanna

    Citation: BMC Genomics 2019 20:219

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  42. Content type: Research article

    Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infec...

    Authors: Stephen R. Doyle, Christopher J. R. Illingworth, Roz Laing, David J. Bartley, Elizabeth Redman, Axel Martinelli, Nancy Holroyd, Alison A. Morrison, Andrew Rezansoff, Alan Tracey, Eileen Devaney, Matthew Berriman, Neil Sargison, James A. Cotton and John S. Gilleard

    Citation: BMC Genomics 2019 20:218

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  43. Content type: Database Article

    Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can ob...

    Authors: Tong Liu, Jacob Porter, Chenguang Zhao, Hao Zhu, Nan Wang, Zheng Sun, Yin-Yuan Mo and Zheng Wang

    Citation: BMC Genomics 2019 20:217

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  44. Content type: Research article

    Target enrichment is a critical component of targeted deep next-generation sequencing for the cost-effective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or...

    Authors: Jongsuk Chung, Ki-Wook Lee, Chung Lee, Seung-Ho Shin, Sungkyu Kyung, Hyo-Jeong Jeon, Sook-Young Kim, Eunjung Cho, Chang Eun Yoo, Dae-Soon Son, Woong-Yang Park and Donghyun Park

    Citation: BMC Genomics 2019 20:216

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  45. Content type: Research article

    Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability ...

    Authors: Shan-Shan Zhou, Zhen Xing, Hui Liu, Xian-Ge Hu, Qiong Gao, Jie Xu, Si-Qian Jiao, Kai-Hua Jia, Yu Qing Jin, Wei Zhao, Ilga Porth, Yousry A. El-Kassaby and Jian-Feng Mao

    Citation: BMC Genomics 2019 20:213

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