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  1. Content type: Research article

    Parts of Europe and the United States have witnessed dramatic losses in commercially managed honey bees over the past decade to what is considered an unsustainable extent. The large-scale loss of bees has cons...

    Authors: Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth and Adam G. Dolezal

    Citation: BMC Genomics 2019 20:412

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  2. Content type: Methodology article

    China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chicken...

    Authors: Ranran Liu, Siyuan Xing, Jie Wang, Maiqing Zheng, Huanxian Cui, Richard P. M. A. Crooijmans, Qinghe Li, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2019 20:410

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  3. Content type: Research article

    Overfeeding reduces laying performance in broiler breeder hens, which is associated with obesity, hepatic steatosis and systemic inflammation. To unravel the underlying mechanisms governing the effect of feedi...

    Authors: Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, Chuanyu Liang and Cunling Jia

    Citation: BMC Genomics 2019 20:408

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  4. Content type: Research article

    Fertility in dairy cows depends on ovarian cyclicity and on uterine involution. Ovarian cyclicity and uterine involution are delayed when there is uterine dysbiosis (overgrowth of pathogenic bacteria). Fertili...

    Authors: Stephen G. Moore, Aaron C. Ericsson, Susanta K. Behura, William R. Lamberson, Timothy J. Evans, Matthew S. McCabe, Scott E. Poock and Matthew C. Lucy

    Citation: BMC Genomics 2019 20:405

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  5. Content type: Research article

    Human milk oligosaccharides (OS) play a key role in brain and gut microbiota development of the neonate, but the underlying biosynthetic steps of OS in the mammary gland are still largely unknown. As bovine mi...

    Authors: Nina A. Poulsen, Randall C. Robinson, Daniela Barile, Lotte B. Larsen and Bart Buitenhuis

    Citation: BMC Genomics 2019 20:404

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  6. Content type: Research article

    In the mammary gland transcriptome of lactating dairy cows genes encoding milk proteins are highly abundant, which can impair the detection of lowly expressed transcripts and can bias the outcome in global tra...

    Authors: Johanna Brodhagen, Rosemarie Weikard, Ulrike Thom, Annika Heimes, Juliane Günther, Frieder Hadlich, Holm Zerbe, Wolfgang Petzl, Marie M. Meyerholz, Martina Hoedemaker, Hans-Joachim Schuberth, Susanne Engelmann and Christa Kühn

    Citation: BMC Genomics 2019 20:400

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  7. Content type: Research article

    The three epidemiologically important Opisthorchiidae liver flukes Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, are believed to harbour similar potencies to provoke hepatobiliary diseases in thei...

    Authors: Nikita I. Ershov, Viatcheslav A. Mordvinov, Egor B. Prokhortchouk, Mariya Y. Pakharukova, Konstantin V. Gunbin, Kirill Ustyantsev, Mikhail A. Genaev, Alexander G. Blinov, Alexander Mazur, Eugenia Boulygina, Svetlana Tsygankova, Ekaterina Khrameeva, Nikolay Chekanov, Guangyi Fan, An Xiao, He Zhang…

    Citation: BMC Genomics 2019 20:399

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  8. Content type: Research article

    Phenotypic plasticity is a common and highly adaptive phenomenon where the same genotype produces different phenotypes in response to environmental cues. Sogatella furcifera, a migratory pest of rice exhibits win...

    Authors: Xinlei Gao, Yating Fu, Olugbenga Emmanuel Ajayi, Dongyang Guo, Liqin Zhang and Qingfa Wu

    Citation: BMC Genomics 2019 20:396

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  9. Content type: Research article

    Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusin...

    Authors: Azam Yazdani, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael R. Kosorok, Gita Dangol and Ahmad Samiei

    Citation: BMC Genomics 2019 20:395

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  11. Content type: Research article

    The behavioural transition from nurses to foragers in honey bees is known to be affected by intrinsic and extrinsic factors, including colony demography, hormone levels, brain chemistry and structure, and gene...

    Authors: Fang Liu, Tengfei Shi, Lei Qi, Xin Su, Deqian Wang, Jie Dong and Zachary Y. Huang

    Citation: BMC Genomics 2019 20:393

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  12. Content type: Research article

    Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortio...

    Authors: Hua Chen, Qiang Yang, Kun Chen, Shanshan Zhao, Chong Zhang, Ronglong Pan, Tiecheng Cai, Ye Deng, Xingjun Wang, Yuting Chen, Wenting Chu, Wenping Xie and Weijian Zhuang

    Citation: BMC Genomics 2019 20:392

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  14. Content type: Research article

    Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have bee...

    Authors: Peng-Fei Qi, Yun-Feng Jiang, Zhen-Ru Guo, Qing Chen, Thérèse Ouellet, Lu-Juan Zong, Zhen-Zhen Wei, Yan Wang, Ya-Zhou Zhang, Bin-Jie Xu, Li Kong, Mei Deng, Ji-Rui Wang, Guo-Yue Chen, Qian-Tao Jiang, Xiu-Jin Lan…

    Citation: BMC Genomics 2019 20:390

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  15. Content type: Research article

    Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitti...

    Authors: Camus Nimmo, Liam P. Shaw, Ronan Doyle, Rachel Williams, Kayleen Brien, Carrie Burgess, Judith Breuer, Francois Balloux and Alexander S. Pym

    Citation: BMC Genomics 2019 20:389

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    The Correction to this article has been published in BMC Genomics 2019 20:433

  16. Content type: Research article

    Hydrothermal vents and cold seeps are typical deep-sea chemosynthetically-driven ecosystems that allow high abundance of specialized macro-benthos. To gather knowledge about the genetic basis of adaptation to ...

    Authors: Jiao Cheng, Min Hui and Zhongli Sha

    Citation: BMC Genomics 2019 20:388

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  17. Content type: Database

    Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a specie...

    Authors: Yanjie Zhang, Qian Chen, James Y. Xie, Yip Hung Yeung, Baohua Xiao, Baoling Liao, Jianliang Xu and Jian-Wen Qiu

    Citation: BMC Genomics 2019 20:387

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  18. Content type: Research article

    Adenovirus protein, Gam1, triggers the proteolytic destruction of the E1 SUMO-activating enzyme. Microinjection of an empirically determined amount of Gam1 mRNA into one-cell Xenopus embryos can reduce SUMOylatio...

    Authors: Michelle M. Bertke, Kyle M. Dubiak, Laura Cronin, Erliang Zeng and Paul W. Huber

    Citation: BMC Genomics 2019 20:386

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  19. Content type: Research article

    Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclero...

    Authors: Mahsa Mousavi-Derazmahalleh, Steven Chang, Geoff Thomas, Mark Derbyshire, Phillip E. Bayer, David Edwards, Matthew N. Nelson, William Erskine, Francisco J. Lopez-Ruiz, Jon Clements and James K. Hane

    Citation: BMC Genomics 2019 20:385

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  21. Content type: Research article

    Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from ...

    Authors: Le Xue, Zilong He, Xiaochun Bi, Wei Xu, Ting Wei, Shuangxiu Wu and Songnian Hu

    Citation: BMC Genomics 2019 20:383

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  22. Content type: Research article

    Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in hu...

    Authors: Nandhini Saranathan, Banhi Biswas, Anupam Patra and Perumal Vivekanandan

    Citation: BMC Genomics 2019 20:382

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  23. Content type: Research article

    Salinization seriously threatens land use efficiency and crop yields across the world. Understanding the mechanisms plants use to protect against salt stress will help breeders develop salt-tolerant vegetable ...

    Authors: Yihua Zhan, Qingfei Wu, Yue Chen, Mengling Tang, Chendong Sun, Junwei Sun and Chenliang Yu

    Citation: BMC Genomics 2019 20:381

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  25. Content type: Research article

    Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a ...

    Authors: Mor Rubinstein, Ravit Eshed, Ada Rozen, Tali Zviran, David N. Kuhn, Vered Irihimovitch, Amir Sherman and Ron Ophir

    Citation: BMC Genomics 2019 20:379

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  26. Content type: Research article

    Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate int...

    Authors: Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramirez, Roberto Vera Alvarez, David Landsman and Leonardo Mariño-Ramírez

    Citation: BMC Genomics 2019 20:378

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  27. Content type: Research article

    Sulforaphane is a natural isothiocyanate available from cruciferous vegetables with multiple characteristics including antioxidant, antitumor and anti-inflammatory effect. Single-molecule real-time (SMRT) sequ...

    Authors: Qiuyun Wu, Junwei Wang, Shuxiang Mao, Haoran Xu, Qi Wu, Mantian Liang, Yiming Yuan, Mingyue Liu and Ke Huang

    Citation: BMC Genomics 2019 20:377

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  28. Content type: Research article

    Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we ...

    Authors: Congjun Jia, Hongbo Wang, Chen Li, Xiaoyun Wu, Linsen Zan, Xuezhi Ding, Xian Guo, Pengjia Bao, Jie Pei, Min Chu, Chunnian Liang and Ping Yan

    Citation: BMC Genomics 2019 20:376

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  29. Content type: Research article

    Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, suc...

    Authors: Guojun Li, Menglu Hou, Yaxue Liu, Yue Pei, Minghui Ye, Yao Zhou, Chenxi Huang, Yaqi Zhao and Haoli Ma

    Citation: BMC Genomics 2019 20:375

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  30. Content type: Research article

    Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster ...

    Authors: Swati Sinha, Choy-Eng Nge, Chung Yan Leong, Veronica Ng, Sharon Crasta, Mohammad Alfatah, Falicia Goh, Kia-Ngee Low, Huibin Zhang, Prakash Arumugam, Alexander Lezhava, Swaine L. Chen, Yoganathan Kanagasundaram, Siew Bee Ng, Frank Eisenhaber and Birgit Eisenhaber

    Citation: BMC Genomics 2019 20:374

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  31. Content type: Research article

    Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering ro...

    Authors: Sovanna Tan, Frédéric Debellé, Pascal Gamas, Florian Frugier and Mathias Brault

    Citation: BMC Genomics 2019 20:373

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  32. Content type: Research article

    Dysregulation of adipogenesis causes metabolic diseases, like obesity and fatty liver. Migratory birds such as geese have a high tolerance of massive energy intake and exhibit little pathological development. ...

    Authors: Guosong Wang, Long Jin, Yan Li, Qianzi Tang, Silu Hu, Hengyong Xu, Clare A. Gill, Mingzhou Li and Jiwen Wang

    Citation: BMC Genomics 2019 20:372

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  33. Content type: Research article

    Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a ra...

    Authors: Tong-jin Liu, You-jun Zhang, Niels Agerbirk, Hai-ping Wang, Xiao-chun Wei, Jiang-ping Song, Hong-ju He, Xue-zhi Zhao, Xiao-hui Zhang and Xi-xiang Li

    Citation: BMC Genomics 2019 20:371

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  34. Content type: Research article

    The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation ...

    Authors: Abhijeet Shah, Joseph I. Hoffman and Holger Schielzeth

    Citation: BMC Genomics 2019 20:370

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  35. Content type: Research article

    Heat shock proteins have important functions in regulating plant growth and response to abiotic stress. HSP70 family genes have been described in several plant species, but a comprehensive analysis of the HSP70 f...

    Authors: Henan Su, Miaomiao Xing, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang and Honghao Lv

    Citation: BMC Genomics 2019 20:369

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  36. Content type: Research article

    Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes that are thought to evolve slowly ...

    Authors: Alltalents T. Murahwa, Fredrick Nindo, Harris Onywera, Tracy L. Meiring, Darren P. Martin and Anna-Lise Williamson

    Citation: BMC Genomics 2019 20:368

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  37. Content type: Research article

    Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids ...

    Authors: Joanna Majka, Katarzyna Bzdęga, Agnieszka Janiak, Hanna Ćwiek-Kupczyńska, Paweł Krajewski, Tomasz Książczyk and Zbigniew Zwierzykowski

    Citation: BMC Genomics 2019 20:367

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  38. Content type: Research article

    There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study de...

    Authors: Georgina Mansell, Tyler J. Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard S. Schalkwyk, Jonathan Mill and Eilis Hannon

    Citation: BMC Genomics 2019 20:366

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  40. Content type: Software

    Data normalization and identification of significant differential expression represent crucial steps in RNA-Seq analysis. Many available tools rely on assumptions that are often not met by real data, including...

    Authors: Wentao Yang, Philip Rosenstiel and Hinrich Schulenburg

    Citation: BMC Genomics 2019 20:364

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  41. Content type: Research article

    The glyoxalase system usually comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII). This system converts cytotoxic methylglyoxal (MG) into non-toxic D-lactate in the presence of reduced glutath...

    Authors: Tiemei Li, Xin Cheng, Yuting Wang, Xiao Yin, Zhiqian Li, Ruiqi Liu, Guotian Liu, Yuejin Wang and Yan Xu

    Citation: BMC Genomics 2019 20:362

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  42. Content type: Research article

    Blood flow restoration is a definitive therapy for salvaging the myocardium following ischemic injury. Nevertheless, the sudden restoration of blood flow to the ischemic myocardium can induce ischemia-reperfus...

    Authors: Zanxin Wang, Junmin Wen, Chuzhi Zhou, Zhiwei Wang and Minxin Wei

    Citation: BMC Genomics 2019 20:361

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  43. Content type: Research article

    Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certa...

    Authors: Zhenpeng Li, Bo Pang, Duochun Wang, Jie Li, Jialiang Xu, Yujie Fang, Xin Lu and Biao Kan

    Citation: BMC Genomics 2019 20:360

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  44. Content type: Research article

    Enormous variability in skin colour and patterning is a characteristic of teleost fish, including Salmonidae fishes, which present themselves as a suitable model for studying mechanisms of pigment patterning. ...

    Authors: Ida Djurdjevič, Tomasz Furmanek, Seita Miyazawa and Simona Sušnik Bajec

    Citation: BMC Genomics 2019 20:359

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  45. Content type: Research article

    Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are...

    Authors: Hugo Oliveira, Marta Sampaio, Luís D. R. Melo, Oscar Dias, Welkin H. Pope, Graham F. Hatfull and Joana Azeredo

    Citation: BMC Genomics 2019 20:357

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  46. Content type: Research article

    Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on sp...

    Authors: De-Long Guan, Rui-Rui Ding, Xiao-Yu Hu, Xing-Ran Yang, Sheng-Quan Xu, Wei Gu and Min Zhang

    Citation: BMC Genomics 2019 20:356

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  47. Content type: Research article

    Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties.

    Authors: Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Yongzhu Liu, Ming Huang, Guili Yang, Hong Liu, Hui Wang, Zhiqiang Chen and Tao Guo

    Citation: BMC Genomics 2019 20:355

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  48. Content type: Research article

    Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evoluti...

    Authors: María Torres-Sánchez, David J. Gower, David Alvarez-Ponce, Christopher J. Creevey, Mark Wilkinson and Diego San Mauro

    Citation: BMC Genomics 2019 20:354

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  49. Content type: Research article

    Bagging is commonly used to enhance red pigmentation and thereby improve fruit quality of apples (Malus domestica). The green-skinned apple cultivar ‘Granny Smith’ develops red pigmentation after bagging removal,...

    Authors: Changqing Ma, Bowen Liang, Bo Chang, Jiuying Yan, Li Liu, Ying Wang, Yazhou Yang and Zhengyang Zhao

    Citation: BMC Genomics 2019 20:353

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  50. Content type: Methodology article

    Gene-set analysis (GSA) has been commonly used to identify significantly altered pathways or functions from omics data. However, GSA often yields a long list of gene-sets, necessitating efficient post-processi...

    Authors: Sora Yoon, Jinhwan Kim, Seon-Kyu Kim, Bukyung Baik, Sang-Mun Chi, Seon-Young Kim and Dougu Nam

    Citation: BMC Genomics 2019 20:352

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