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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

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  1. 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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  2. 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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  3. 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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  4. 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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  5. Content type: Research article

    Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mi...

    Authors: Anna I. Kolesnikova, Yuliya A. Putintseva, Evgeniy P. Simonov, Vladislav V. Biriukov, Natalya V. Oreshkova, Igor N. Pavlov, Vadim V. Sharov, Dmitry A. Kuzmin, James B. Anderson and Konstantin V. Krutovsky

    Citation: BMC Genomics 2019 20:351

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  6. Content type: Research article

    Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been forme...

    Authors: Dorcus Kholofelo Malomane, Henner Simianer, Annett Weigend, Christian Reimer, Armin Otto Schmitt and Steffen Weigend

    Citation: BMC Genomics 2019 20:345

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  7. Content type: Research article

    The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod...

    Authors: Han Ming Gan, Frederic Grandjean, Tom L. Jenkins and Christopher Mervyn Austin

    Citation: BMC Genomics 2019 20:335

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  8. Content type: Research article

    Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitiv...

    Authors: Rute R. da Fonseca, Irene Ureña, Sandra Afonso, Ana Elisabete Pires, Emil Jørsboe, Lounès Chikhi and Catarina Ginja

    Citation: BMC Genomics 2019 20:334

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  9. Content type: Research article

    Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small gen...

    Authors: Marc P. Lorentzen, Hugo Campbell-Sills, Tue S. Jorgensen, Tue K. Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen and Patrick M. Lucas

    Citation: BMC Genomics 2019 20:330

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  10. Content type: Research article

    Growth rate is one of the most important features for aquaculture species and deciphering its regulation mechanism has great significance both in genetics and in economics. Hypothalamus-pituitary growth axis (...

    Authors: Beide Fu, Xiaomu Yu, Jingou Tong, Meixia Pang, Ying Zhou, Qingshan Liu and Wenjing Tao

    Citation: BMC Genomics 2019 20:328

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  11. Content type: Research article

    WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. To date, WOX genes has been identified and analyzed i...

    Authors: Mengdi Li, Ruihua Wang, Zhengyi Liu, Xiaoming Wu and Jianbo Wang

    Citation: BMC Genomics 2019 20:317

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  12. Content type: Research article

    The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultura...

    Authors: Alessandra Villani, Robert H. Proctor, Hye-Seon Kim, Daren W. Brown, Antonio F. Logrieco, Maria Teresa Amatulli, Antonio Moretti and Antonia Susca

    Citation: BMC Genomics 2019 20:314

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  13. Content type: Research article

    Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the ...

    Authors: A. Santos-Zavaleta, E. Pérez-Rueda, M. Sánchez-Pérez, D. A. Velázquez-Ramírez and J. Collado-Vides

    Citation: BMC Genomics 2019 20:299

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  14. Content type: Research article

    Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress p...

    Authors: Yuhui Du, Jinjin Ma, Zhiqiu Yin, Kai Liu, Gan Yao, Wenfeng Xu, Lingchao Fan, Binghai Du, Yanqin Ding and Chengqiang Wang

    Citation: BMC Genomics 2019 20:283

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  15. Content type: Research article

    Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are assoc...

    Authors: Katharina May, Carsten Scheper, Kerstin Brügemann, Tong Yin, Christina Strube, Paula Korkuć, Gudrun A. Brockmann and Sven König

    Citation: BMC Genomics 2019 20:277

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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. Content type: Research article

    Escherichia coli is an important pathogen that causes diarrhea in both humans and animals. To determine the relationships between putative virulence factors and pathotypes or host taxa, many molecular studies on ...

    Authors: Fang Tang, Juanfang Wang, Dezhi Li, Song Gao, Jianluan Ren, Liqing Ma, Fei Liu, Xiangkai Zhuge, Genqiang Yan, Yan Lu and Jianjun Dai

    Citation: BMC Genomics 2019 20:212

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  24. Content type: Research article

    In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as...

    Authors: Yoosook Lee, Hanno Schmidt, Travis C. Collier, William R. Conner, Mark J. Hanemaaijer, Montgomery Slatkin, John M. Marshall, Joanna C. Chiu, Chelsea T. Smartt, Gregory C. Lanzaro, F. Steve Mulligan and Anthony J. Cornel

    Citation: BMC Genomics 2019 20:204

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  25. Content type: Research article

    Although the importance of host plant chemistry in plant–insect interactions is widely recognized, our understanding about the genetic basis underlying the relationship between changes in midgut proteins and a...

    Authors: Zehai Hou and Cong Wei

    Citation: BMC Genomics 2019 20:182

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  26. Content type: Research article

    After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidizatio...

    Authors: Zhenyi Wang, Jinpeng Wang, Yuxin Pan, Tianyu Lei, Weina Ge, Li Wang, Lan Zhang, Yuxian Li, Kanglu Zhao, Tao Liu, Xiaoming Song, Jiaqi Zhang, Jigao Yu, Jingjing Hu and Xiyin Wang

    Citation: BMC Genomics 2019 20:180

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  27. Content type: Research article

    Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. The native Bantu-speaking inhabitants of Bioko, the Bubi, are believed to have colonized the isla...

    Authors: Pere Gelabert, Manuel Ferrando-Bernal, Toni de-Dios, Benedetta Mattorre, Elena Campoy, Amaya Gorostiza, Etienne Patin, Antonio González-Martín and Carles Lalueza-Fox

    Citation: BMC Genomics 2019 20:179

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  28. Content type: Research article

    The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure a...

    Authors: Gertrud Grilz-Seger, Thomas Druml, Markus Neuditschko, Max Dobretsberger, Michaela Horna and Gottfried Brem

    Citation: BMC Genomics 2019 20:174

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  29. Content type: Research article

    Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has be...

    Authors: Alongkorn Kurilung, Chantisa Keeratipusana, Prapat Suriyaphol, David J. Hampson and Nuvee Prapasarakul

    Citation: BMC Genomics 2019 20:168

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    The Correction to this article has been published in BMC Genomics 2019 20:246

  30. Content type: Research article

    Saliva of mosquitoes contains anti-platelet, anti-clotting, vasodilatory, anti-complement and anti-inflammatory substances that help the blood feeding process. The salivary polypeptides are at a fast pace of e...

    Authors: Vera Margarete Scarpassa, Humbeto Julio Debat, Ronildo Baiatone Alencar, José Ferreira Saraiva, Eric Calvo, Bruno Arcà and José M. C. Ribeiro

    Citation: BMC Genomics 2019 20:166

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  31. Content type: Research article

    Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite t...

    Authors: Surabhi Srivastava, Akshay Kumar Avvaru, Divya Tej Sowpati and Rakesh K. Mishra

    Citation: BMC Genomics 2019 20:153

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  32. Content type: Research article

    Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of whe...

    Authors: Chengwei Wang, Yu Wang, Qi Pan, Shoukun Chen, Cuizhu Feng, Jiangbo Hai and Haifeng Li

    Citation: BMC Genomics 2019 20:142

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  33. Content type: Research article

    The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical ...

    Authors: Li Ma, Tad S. Sonstegard, John B. Cole, Curtis P. VanTassell, George R. Wiggans, Brian A. Crooker, Cheng Tan, Dzianis Prakapenka, George E. Liu and Yang Da

    Citation: BMC Genomics 2019 20:128

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  34. Content type: Research article

    Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. longan fruit yield, the difficulty and instability of blossom...

    Authors: Dengwei Jue, Xuelian Sang, Liqin Liu, Bo Shu, Yicheng Wang, Chengming Liu, Yi Wang, Jianghui Xie and Shengyou Shi

    Citation: BMC Genomics 2019 20:126

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  35. Content type: Research article

    Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although th...

    Authors: Rick Masonbrink, Tom R. Maier, Usha Muppirala, Arun S. Seetharam, Etienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nathan T. Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves-van den Akker, Matthew Hudson, Andrew J. Severin and Thomas J. Baum

    Citation: BMC Genomics 2019 20:119

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  36. Content type: Research article

    Cytochrome P450 (P450) is a functionally diverse and multifamily class of enzymes which catalyses vast variety of biochemical reactions. P450 genes play regulatory role in growth, development and secondary met...

    Authors: A. P. Vasav and V. T. Barvkar

    Citation: BMC Genomics 2019 20:116

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  37. Content type: Research article

    Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associate...

    Authors: A. A. Kampfraath, L. Klasson, S. Y. Anvar, R. H. A. M. Vossen, D. Roelofs, K. Kraaijeveld and J. Ellers

    Citation: BMC Genomics 2019 20:106

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  38. Content type: Research article

    Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus preda...

    Authors: Nathan D. McDonald, Abish Regmi, Daniel P. Morreale, Joseph D. Borowski and E. Fidelma Boyd

    Citation: BMC Genomics 2019 20:105

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  39. Content type: Research article

    Protein secretion is an essential process in all eukaryotes including organisms belonging to the phylum Apicomplexa, which includes many intracellular parasites. The apicomplexan parasites possess a specialize...

    Authors: K. M. Kaderi Kibria, Jannatul Ferdous, Rahila Sardar, Ashutosh Panda, Dinesh Gupta, Asif Mohmmed and Pawan Malhotra

    Citation: BMC Genomics 2019 20:98

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  40. Content type: Research article

    Toxoplasma gondii is an obligate intracellular parasite that infects humans and other warm-blooded animals. Previous quantitative proteomic analyses of infected host cells revealed that the expression of many hos...

    Authors: Zhaofeng Hou, Dandan Liu, Shijie Su, Lele Wang, Zhenxing Zhao, Yifei Ma, Qiaoqiao Li, Chuanli Jia, Jinjun Xu, Yonghua Zhou and Jianping Tao

    Citation: BMC Genomics 2019 20:97

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  41. Content type: Research article

    The SWEET proteins are a group of sugar transporters that play a role in sugar efflux during a range of biological processes, including stress responses. However, there has been no comprehensive analysis of the S...

    Authors: Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Xi Shan, Kan Bao, Li Yu, Hong Wang, Zhangjun Fei and Jianbin Li

    Citation: BMC Genomics 2019 20:93

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  42. Content type: Research article

    The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. The most protruding tasks are performed by you...

    Authors: Clemens Thölken, Markus Thamm, Christoph Erbacher and Marcus Lechner

    Citation: BMC Genomics 2019 20:88

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  43. Content type: Research article

    Sugarcane served as the model plant for discovery of the C4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynth...

    Authors: Yongjun Wang, Xiuting Hua, Jingsheng Xu, Zhichang Chen, Tianqu Fan, Zhaohui Zeng, Hengbo Wang, Ai-Ling Hour, Qingyi Yu, Ray Ming and Jisen Zhang

    Citation: BMC Genomics 2019 20:83

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  44. 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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  45. 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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  46. 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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