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  1. Content type: Research article

    Tuberculosis is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M.tb). M.tb subverts host immune responses to build a favourable niche and survive inside of host macrophages. Macrophag...

    Authors: Elena Denisenko, Reto Guler, Musa Mhlanga, Harukazu Suzuki, Frank Brombacher and Sebastian Schmeier

    Citation: BMC Genomics 2019 20:71

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  2. Content type: Research article

    Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flo...

    Authors: Chakkree Lekklar, Monnat Pongpanich, Duangjai Suriya-arunroj, Aumnart Chinpongpanich, Helen Tsai, Luca Comai, Supachitra Chadchawan and Teerapong Buaboocha

    Citation: BMC Genomics 2019 20:76

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  3. Content type: Research article

    Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it...

    Authors: David L. J. Vendrami, Jaume Forcada and Joseph I. Hoffman

    Citation: BMC Genomics 2019 20:72

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  4. Content type: Methodology article

    Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data fr...

    Authors: Wenbin Ye, Yuqi Long, Guoli Ji, Yaru Su, Pengchao Ye, Hongjuan Fu and Xiaohui Wu

    Citation: BMC Genomics 2019 20:75

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  5. Content type: Research article

    G-protein coupled receptors (GPCRs) are ancient, ubiquitous, constitute the largest family of transducing cell surface proteins, and are integral to cell communication via an array of ligands/neuropeptides. Mo...

    Authors: Nhut M. Tran, Donald L. Mykles, Abigail Elizur and Tomer Ventura

    Citation: BMC Genomics 2019 20:74

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  6. Content type: Research article

    The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and th...

    Authors: Macarena Ruger-Herreros, Obdulia Parra-Rivero, Javier Pardo-Medina, Francisco J. Romero-Campero, M. Carmen Limón and Javier Avalos

    Citation: BMC Genomics 2019 20:67

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  7. Content type: Research article

    The genus Anaplasma is made up of organisms characterized by small genomes that are undergoing reductive evolution. Anaplasma ovis, one of the seven recognized species in this genus, is an understudied pathogen o...

    Authors: Zhijie Liu, Austin M. Peasley, Jifei Yang, Youquan Li, Guiquan Guan, Jianxun Luo, Hong Yin and Kelly A. Brayton

    Citation: BMC Genomics 2019 20:69

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  8. Content type: Research article

    The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genom...

    Authors: Xue Zhao, Haipeng Jiang, Lei Feng, Yingfan Qu, Weili Teng, Lijuan Qiu, Hongkun Zheng, Yingpeng Han and Wenbin Li

    Citation: BMC Genomics 2019 20:68

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  9. Content type: Research article

    The diversity of avian eggshell colour plays important biological roles in ensuring successful reproduction. Eggshell colour is also an important trait in poultry, but the mechanisms underlying it are poorly u...

    Authors: Ding-Ping Bai, Xin-Yu Lin, Yan Wu, Shi-Ye Zhou, Zhong-bin Huang, Yi-Fan Huang, Ang Li and Xiao-Hong Huang

    Citation: BMC Genomics 2019 20:66

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  10. Content type: Research article

    Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antib...

    Authors: Bart J. F. Keijser, Valeria Agamennone, Tim J. van den Broek, Martien Caspers, Adri van de Braak, Richard Bomers, Mieke Havekes, Eric Schoen, Martin van Baak, Daniël Mioch, Lonneke Bomers and Roy C. Montijn

    Citation: BMC Genomics 2019 20:65

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  11. Content type: Research article

    MicroRNAs (miRNAs) are short endogenous, single-stranded, noncoding small RNA molecules of approximately 22 nucleotides in length. They regulate gene expression posttranscriptionally by silencing mRNA expressi...

    Authors: Martin Bilbao-Arribas, Naiara Abendaño, Endika Varela-Martínez, Ramsés Reina, Damián de Andrés and Begoña M. Jugo

    Citation: BMC Genomics 2019 20:62

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  12. Content type: Research article

    Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. ...

    Authors: Yachun Su, Xinhuan Xiao, Hui Ling, Ning Huang, Feng Liu, Weihua Su, Yuye Zhang, Liping Xu, Khushi Muhammad and Youxiong Que

    Citation: BMC Genomics 2019 20:57

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  13. Content type: Research article

    Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. sal...

    Authors: Rui Pan, Dongli He, Le Xu, Meixue Zhou, Chengdao Li, Chu Wu, Yanhao Xu and Wenying Zhang

    Citation: BMC Genomics 2019 20:60

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  14. Content type: Research article

    Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a...

    Authors: Hui Wang, Zhixin Chai, Dan Hu, Qiumei Ji, Jinwei Xin, Chengfu Zhang and Jincheng Zhong

    Citation: BMC Genomics 2019 20:61

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  15. Content type: Research article

    Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria...

    Authors: Dekang Zhu, Jiao He, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu, Yu You, Xiaoyue Chen…

    Citation: BMC Genomics 2019 20:63

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  16. Content type: Research article

    Many small peptides regulate eukaryotic cell biology. In fungi, some of these peptides are produced after KEX2 protease activity on proteins displaying repetitions of identical or nearly identical motifs. Foll...

    Authors: Morgane Le Marquer, Hélène San Clemente, Christophe Roux, Bruno Savelli and Nicolas Frei dit Frey

    Citation: BMC Genomics 2019 20:64

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  17. Content type: Methodology article

    Chromatin-immunoprecipitation followed by sequencing (ChIP-seq) is the method of choice for mapping genome-wide binding of chromatin-associated factors. However, broadly applicable methods for between-sample c...

    Authors: Luis A. Vale-Silva, Tovah E. Markowitz and Andreas Hochwagen

    Citation: BMC Genomics 2019 20:54

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  18. Content type: Research article

    The gram-negative Xanthomonas genus contains a large group of economically important plant pathogens, which cause severe diseases on many crops worldwide. The diffusible signal factor (DSF) - mediated quorum sens...

    Authors: Lei Li, Jinyun Li, Yunzeng Zhang and Nian Wang

    Citation: BMC Genomics 2019 20:55

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  19. Content type: Software

    Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is oft...

    Authors: Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, Andrés Ritter, Régis Lavigne, Dominique Marie, Pierre Peterlongo, Philippe Potin and Charles Pineau

    Citation: BMC Genomics 2019 20:56

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  20. Content type: Research article

    Cymbidium goeringii is one of the most horticulturally important and popular ornamental plants in the orchid family (Orchidaceae). It blooms in winter during January–March and a period of low temperature is neces...

    Authors: Fengxi Yang, Genfa Zhu, Yonglu Wei, Jie Gao, Gang Liang, Lingyuan Peng, Chuqiao Lu and Jianpeng Jin

    Citation: BMC Genomics 2019 20:53

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  21. Content type: Research article

    Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in pea...

    Authors: Zhihui Wang, Liying Yan, Liyun Wan, Dongxin Huai, Yanping Kang, Lei Shi, Huifang Jiang, Yong Lei and Boshou Liao

    Citation: BMC Genomics 2019 20:51

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  22. Content type: Research article

    Aging is accompanied with loss of tissue homeostasis and accumulation of cellular damages. As one of the important metabolic centers, liver shows age-related dysregulation of lipid metabolism, impaired detoxif...

    Authors: Kerui Huang, Wenhao Chen, Fang Zhu, Patrick Wai-Lun Li, Pankaj Kapahi and Hua Bai

    Citation: BMC Genomics 2019 20:50

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  23. Content type: Research article

    The mechanism of latency and the ability of the cyprinid herpesvirus 3 (CyHV-3) to establish life-long infections in carp remains poorly understood. To explain the role of miRNAs in this process we applied a r...

    Authors: Michal Reichert, Anna Lukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj-Paluch, Magdalena Stachnik and Ewa Borzym

    Citation: BMC Genomics 2019 20:46

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  24. Content type: Research article

    Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilizat...

    Authors: Liana Apolis, Joanna Olivas, Prakash Srinivasan, Ambuj K. Kushwaha and Sanjay A. Desai

    Citation: BMC Genomics 2019 20:47

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  25. Content type: Research article

    Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adap...

    Authors: Rahul V. Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Goujie Zhang, Siu F. Lee, Ary A. Hoffmann and John G. Oakeshott

    Citation: BMC Genomics 2019 20:52

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  26. Content type: Research article

    Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and acceler...

    Authors: Chen Huang, Dongliang Leng, Shixue Sun and Xiaohua Douglas Zhang

    Citation: BMC Genomics 2019 20:48

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  27. Content type: Research article

    Red-fleshed papaya is a good material to study the different carotenoids accumulation mechanism in the peel and flesh. Although the peel and flesh of papaya closely integrated into one body, the flesh colorati...

    Authors: Yan Hong Shen, Fei Ying Yang, Bing Guo Lu, Wan Wan Zhao, Tao Jiang, Li Feng, Xiao Jing Chen and Ray Ming

    Citation: BMC Genomics 2019 20:49

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  28. Content type: Research article

    Taste and aroma, which are important organoleptic qualities of apricot (Prunus armeniaca L.) fruit, undergo rapid and substantial changes during ripening. However, the associated molecular mechanisms remain uncle...

    Authors: Qiuyun Zhang, Chao Feng, Wenhui Li, Zehui Qu, Ming Zeng and Wanpeng Xi

    Citation: BMC Genomics 2019 20:45

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  29. Content type: Research article

    Tomato is an economically important crop with fruits that are a significant source of bioactive compounds such as ascorbic acid and phenolics. Nowadays, the majority of the enzymes of the biosynthetic pathways...

    Authors: Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone and Maria Manuela Rigano

    Citation: BMC Genomics 2019 20:43

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  30. Content type: Correction

    Following the publication of this article [1], the authors informed us of the following typographical errors in the Results section (the changes are marked in bold).

    Authors: Thomas J. F. Pranzatelli, Drew G. Michae and John A. Chiorini

    Citation: BMC Genomics 2019 20:44

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    The original article was published in BMC Genomics 2018 19:563

  31. Content type: Research article

    Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichli...

    Authors: Athimed El Taher, Nicolás Lichilín, Walter Salzburger and Astrid Böhne

    Citation: BMC Genomics 2019 20:39

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  32. Content type: Research article

    Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key...

    Authors: Chenrong Wang, Limin Liu, Huili Zhu, Lu Zhang, Rongjun Wang, Zhenjie Zhang, Jianying Huang, Sumei Zhang, Fuchun Jian, Changshen Ning and Longxian Zhang

    Citation: BMC Genomics 2019 20:37

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  33. Content type: Software

    Target enrichment combined with chromosome conformation capturing methodologies such as capture Hi-C (CHC) can be used to investigate spatial layouts of genomic regions with high resolution and at scalable cos...

    Authors: Peter Hansen, Salaheddine Ali, Hannah Blau, Daniel Danis, Jochen Hecht, Uwe Kornak, Darío G. Lupiáñez, Stefan Mundlos, Robin Steinhaus and Peter N. Robinson

    Citation: BMC Genomics 2019 20:40

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  34. Content type: Review

    The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protei...

    Authors: Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo and John M. Archibald

    Citation: BMC Genomics 2019 20:38

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  35. Content type: Research article

    The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode...

    Authors: Margaret Worthington, Masumi Ebina, Naoki Yamanaka, Christopher Heffelfinger, Constanza Quintero, Yeny Patricia Zapata, Juan Guillermo Perez, Michael Selvaraj, Manabu Ishitani, Jorge Duitama, Juan Fernando de la Hoz, Idupulapati Rao, Stephen Dellaporta, Joe Tohme and Jacobo Arango

    Citation: BMC Genomics 2019 20:41

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  36. Content type: Research article

    Long non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human (Homo sapiens) (96,308 vs. 20,376) and mouse

    Authors: Chang Lu, Yanling Xing, Han Cai, Yirong Shi, Jinhua Liu and Yinhua Huang

    Citation: BMC Genomics 2019 20:36

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  37. Content type: Research article

    The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution an...

    Authors: Špela Alič, Jacques Pédron, Tanja Dreo and Frédérique Van Gijsegem

    Citation: BMC Genomics 2019 20:34

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  38. Content type: Research article

    Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer’s payment. The select...

    Authors: Bárbara Silva-Vignato, Luiz L. Coutinho, Mirele D. Poleti, Aline S. M. Cesar, Cristina T. Moncau, Luciana C. A. Regitano and Júlio C. C. Balieiro

    Citation: BMC Genomics 2019 20:32

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  39. Content type: Research article

    Co-colonization by Pseudomonas aeruginosa and Staphylococcus aureus is frequent in cystic fibrosis patients. Polymicrobial infections involve both detrimental and beneficial interactions between different bacteri...

    Authors: Mikaël Tognon, Thilo Köhler, Alexandre Luscher and Christian van Delden

    Citation: BMC Genomics 2019 20:30

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  40. Content type: Research article

    Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored ...

    Authors: Lingyang Xu, Liu Yang, Lei Wang, Bo Zhu, Yan Chen, Huijiang Gao, Xue Gao, Lupei Zhang, George E. Liu and Junya Li

    Citation: BMC Genomics 2019 20:31

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  41. Content type: Research article

    Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that pla...

    Authors: Hong Zhu, Yu Zhang, Ruifang Tang, Hongxia Qu, Xuewu Duan and Yueming Jiang

    Citation: BMC Genomics 2019 20:33

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  42. Content type: Research article

    Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants la...

    Authors: Rongzhi Zhang, Shuaifeng Geng, Zhengrui Qin, Zongxiang Tang, Cheng Liu, Dongfeng Liu, Guoqi Song, Yulian Li, Shujuan Zhang, Wei Li, Jie Gao, Xiaodong Han and Genying Li

    Citation: BMC Genomics 2019 20:29

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  43. Content type: Research article

    The prevalence of azole resistance in clinical and environmental Aspergillus fumigatus isolates is rising over the past decades, but the molecular basis of the development of antifungal drug resistance is not wel...

    Authors: Margriet W. J. Hokken, Jan Zoll, Jordy P. M. Coolen, Bas J. Zwaan, Paul E. Verweij and Willem J. G. Melchers

    Citation: BMC Genomics 2019 20:28

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  44. Content type: Research article

    Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candid...

    Authors: Wenxian Liang, Lin Ni, Rebeca Carballar-Lejarazú, Xiaoxing Zou, Weihong Sun, Lingjiao Wu, Xueyuan Yuan, Yanling Mao, Wei Huang and Shuangquan Zou

    Citation: BMC Genomics 2019 20:24

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