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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.

Page 1 of 18

  1. Content type: Research Article

    Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulati...

    Authors: Olga M. Sigalova, Andrei V. Chaplin, Olga O. Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia and Mikhail S. Gelfand

    Citation: BMC Genomics 2019 20:710

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  2. Content type: Research article

    Eggshell breaking strength is critical to reduce egg breaking rate and avoid economic loss. The process of eggshell calcification initiates with the egg entering the uterus and lasts about 18 h. It follows a t...

    Authors: Jiacai Zhang, Yanan Wang, Cong Zhang, Mingxin Xiong, Shahid Ali Rajput, Yun Liu and Desheng Qi

    Citation: BMC Genomics 2019 20:707

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  3. Content type: Research article

    Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted ...

    Authors: José S. L. Patané, Joaquim Martins Jr, Luiz Thiberio Rangel, José Belasque, Luciano A. Digiampietri, Agda Paula Facincani, Rafael Marini Ferreira, Fabrício José Jaciani, Yunzeng Zhang, Alessandro M. Varani, Nalvo F. Almeida, Nian Wang, Jesus A. Ferro, Leandro M. Moreira and João C. Setubal

    Citation: BMC Genomics 2019 20:700

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  4. Content type: Database

    Recently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important tr...

    Authors: Teshome Dagne Mulugeta, Torfinn Nome, Thu-Hien To, Manu Kumar Gundappa, Daniel J. Macqueen, Dag Inge Våge, Simen Rød Sandve and Torgeir R. Hvidsten

    Citation: BMC Genomics 2019 20:694

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  5. Content type: Research article

    Anthrax is a zoonotic disease caused by the gram-positive bacterium Bacillus anthracis. The most anthrax-endemic regions of Russia are Siberia and North Caucasus. Previously, genotyping of Russian B.anthracis iso...

    Authors: Sergey V. Pisarenko, Eugene I. Eremenko, Alla G. Ryazanova, Dmitry A. Kovalev, Nina P. Buravtseva, Lyudmila Yu. Aksenova, Zorigma F. Dugarzhapova, Anna Yu. Evchenko, Elena V. Kravets, Olga V. Semenova, Olga V. Bobrisheva, Irina V. Kuznetsova, Tatyana M. Golovinskaya, Anna S. Volynkina, Sergei V. Balakhonov and Alexander N. Kulichenko

    Citation: BMC Genomics 2019 20:692

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  6. Content type: Research article

    Mitochondria perform many key roles in their eukaryotic hosts, from integrating signaling pathways through to modulating whole organism phenotypes. The > 1 billion years of nuclear and mitochondrial gene co-ev...

    Authors: Jim A. Mossman, Leann M. Biancani and David M. Rand

    Citation: BMC Genomics 2019 20:691

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  7. Content type: Research article

    Olfaction and gustation underlie behaviors that are crucial for insect fitness, such as host and mate selection. The detection of semiochemicals is mediated via proteins from large and rapidly evolving chemose...

    Authors: Martin N. Andersson, Christopher I. Keeling and Robert F. Mitchell

    Citation: BMC Genomics 2019 20:690

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  8. Content type: Research article

    Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the geneti...

    Authors: Evangeline S. Ballerini, Elena M. Kramer and Scott A. Hodges

    Citation: BMC Genomics 2019 20:668

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  9. Content type: Research article

    The class III peroxidase (PRX) gene family is a plant-specific member of the PRX superfamily that is closely related to various physiological processes, such as cell wall loosening, lignification, and abiotic ...

    Authors: Jun Yan, Peisen Su, Wen Li, Guilian Xiao, Yan Zhao, Xin Ma, Hongwei Wang, Eviatar Nevo and Lingrang Kong

    Citation: BMC Genomics 2019 20:666

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  10. Content type: Research article

    Cucurbit yellow stunting disorder virus (CYSDV; genus Crinivirus, Closteroviridae) is transmitted in a semipersistent manner by the whitefly, Bemisia tabaci, and is efficiently transmitted by the widely prevalent...

    Authors: Navneet Kaur, Wenbo Chen, Zhangjun Fei and William M. Wintermantel

    Citation: BMC Genomics 2019 20:654

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  11. Content type: Research article

    As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically anal...

    Authors: Xin Niu, Shoukun Chen, Jiawei Li, Yue Liu, Wanquan Ji and Haifeng Li

    Citation: BMC Genomics 2019 20:635

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  12. Content type: Research article

    Improving the yield and fiber quality of upland cotton is a goal of plant breeders. However, increasing the yield and quality of cotton fibers is becoming more urgent. While the growing human population needs ...

    Authors: Yuan Qin, Huiru Sun, Pengbo Hao, Hantao Wang, Congcong Wang, Liang Ma, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2019 20:633

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  13. Content type: Research article

    Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar...

    Authors: Sabyasachi Mukherjee, Zexi Cai, Anupama Mukherjee, Imsusosang Longkumer, Moonmoon Mech, Kezhavituo Vupru, Kobu Khate, Chandan Rajkhowa, Abhijit Mitra, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

    Citation: BMC Genomics 2019 20:617

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  14. Content type: Research article

    The horn fly (Haematobia irritans) is an obligate blood feeder that causes considerable economic losses in livestock industries worldwide. The control of this cattle pest is mainly based on insecticides; unfortun...

    Authors: J. M. Ribeiro, Humberto Julio Debat, M. Boiani, X. Ures, S. Rocha and M. Breijo

    Citation: BMC Genomics 2019 20:616

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  15. Content type: Research article

    Histone deacetylases (HDACs) are the proteins responsible for removing the acetyl group from lysine residues of core histones in chromosomes, a crucial component of gene regulation. Eleven known HDACs exist in...

    Authors: Toni A. Boltz, Sawsan Khuri and Stefan Wuchty

    Citation: BMC Genomics 2019 20:613

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  16. Content type: Research article

    As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolate...

    Authors: Zhi Zhong, Lai-Yu Kwok, Qiangchuan Hou, Yaru Sun, Weicheng Li, Heping Zhang and Zhihong Sun

    Citation: BMC Genomics 2019 20:602

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  17. Content type: Research article

    Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target ...

    Authors: Fazhe Yan, Xuelin Yu, Zhongqu Duan, Jinyuan Lu, Ben Jia, Yuyang Qiao, Chen Sun and Chaochun Wei

    Citation: BMC Genomics 2019 20:595

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  18. Content type: Software

    During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technolo...

    Authors: Jose V. Die, Moamen M. Elmassry, Kimberly H. LeBlanc, Olaitan I. Awe, Allissa Dillman and Ben Busby

    Citation: BMC Genomics 2019 20:591

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  19. Content type: Methodology article

    The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are mi...

    Authors: Keoni Saint-Pé, Maeva Leitwein, Laurence Tissot, Nicolas Poulet, Bruno Guinand, Patrick Berrebi, Geoffrey Marselli, Jean-Marc Lascaux, Pierre-Alexandre Gagnaire and Simon Blanchet

    Citation: BMC Genomics 2019 20:582

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  20. Content type: Research article

    The σ54 factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ54 is present in many Clostridiales species that have ...

    Authors: Xiaoqun Nie, Wenyue Dong and Chen Yang

    Citation: BMC Genomics 2019 20:565

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  21. Content type: Research article

    The Crustacea are an evolutionarily diverse taxon which underpins marine food webs and contributes significantly to the global economy. However, our knowledge of crustacean endocrinology and development is far...

    Authors: Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura

    Citation: BMC Genomics 2019 20:531

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    The Correction to this article has been published in BMC Genomics 2019 20:622

  22. Content type: Research article

    Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, ...

    Authors: Valeria Petrella, Serena Aceto, Vincenza Colonna, Giuseppe Saccone, Remo Sanges, Nikola Polanska, Petr Volf, Luigi Gradoni, Gioia Bongiorno and Marco Salvemini

    Citation: BMC Genomics 2019 20:522

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  23. Content type: Research article

    Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen of domestic and wild ruminants. Apart from cattle, small ruminants (goats and sheep) are also the susceptible hosts for BVDV. BVDV...

    Authors: Wenliang Li, Li Mao, Xin Shu, Runxia Liu, Fei Hao, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Chunyan Zhong and Jieyuan Jiang

    Citation: BMC Genomics 2019 20:516

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  24. Content type: Research article

    Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of C...

    Authors: Min Zhou, Shigang Zheng, Rong Liu, Jing Lu, Lu Lu, Chihong Zhang, Zehou Liu, Congpei Luo, Lei Zhang, Levi Yant and Yu Wu

    Citation: BMC Genomics 2019 20:505

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  25. Content type: Research article

    Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in fi...

    Authors: Ashok Kumar Sharma, Barbora Pafčo, Klára Vlčková, Barbora Červená, Jakub Kreisinger, Samuel Davison, Karen Beeri, Terence Fuh, Steven R. Leigh, Michael B. Burns, Ran Blekhman, Klára J. Petrželková and Andres Gomez

    Citation: BMC Genomics 2019 20:493

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  26. Content type: Research article

    It is hypothesized that the highly conserved inverted repeats (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organization, whereas the mechanism of the occurren...

    Authors: Hong-Rui Zhang, Xian-Chun Zhang and Qiao-Ping Xiang

    Citation: BMC Genomics 2019 20:484

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    The Correction to this article has been published in BMC Genomics 2019 20:523

  27. Content type: Research article

    Plasmids play an vital role in driving the rapid global spread of antimicrobial resistance and adaptation to changing ambient conditions. It has been suggested that the presence of plasmids can pose tremendous...

    Authors: Dan Long, Lan-lan Zhu, Fang-ling Du, Tian-xin Xiang, La-Gen Wan, Dan-dan Wei, Wei Zhang and Yang Liu

    Citation: BMC Genomics 2019 20:480

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  28. Content type: Research article

    The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is av...

    Authors: Chaokun Li, Longxin Chen, Xuefeng Liu, Xiaoqian Shi, Yu Guo, Rui Huang, Fangyuan Nie, Changming Zheng, Chenglin Zhang and Runlin Z. Ma

    Citation: BMC Genomics 2019 20:479

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  29. Content type: Research article

    The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly ...

    Authors: J. Blommaert, S. Riss, B. Hecox-Lea, D. B. Mark Welch and C. P. Stelzer

    Citation: BMC Genomics 2019 20:466

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  30. Content type: Research article

    Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especiall...

    Authors: Marius Bredon, Benjamin Herran, Baptiste Lheraud, Joanne Bertaux, Pierre Grève, Bouziane Moumen and Didier Bouchon

    Citation: BMC Genomics 2019 20:462

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  31. Content type: Methodology article

    Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relat...

    Authors: Zach K. O’Brown, Konstantinos Boulias, Jie Wang, Simon Yuan Wang, Natasha M. O’Brown, Ziyang Hao, Hiroki Shibuya, Paul-Enguerrand Fady, Yang Shi, Chuan He, Sean G. Megason, Tao Liu and Eric L. Greer

    Citation: BMC Genomics 2019 20:445

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  32. Content type: Research article

    Host genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-ass...

    Authors: Tiantian Li, Zhiwei Fang, Hai Peng, Junfei Zhou, Pengcheng Liu, Yanyan Wang, Wenhui Zhu, Lun Li, Quanfang Zhang, Lihong Chen, Lili Li, Zhihao Liu, Weixiong Zhang, Wenxue Zhai, Long Lu and Lifen Gao

    Citation: BMC Genomics 2019 20:444

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  33. Content type: Research article

    Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environm...

    Authors: Xian Zhang, Xueduan Liu, Liangzhi Li, Guanyun Wei, Danli Zhang, Yili Liang and Bo Miao

    Citation: BMC Genomics 2019 20:438

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  34. Content type: Research article

    The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol f...

    Authors: Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli-Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulin, Petri Auvinen and Taina Lundell

    Citation: BMC Genomics 2019 20:430

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  35. Content type: Research article

    The role of Salmonella virulence factor (VF) allelic variation in modulating pathogenesis or host specificity has only been demonstrated in a few cases, mostly through serendipitous findings. Virulence factor (VF...

    Authors: Alexey V. Rakov, Emilio Mastriani, Shu-Lin Liu and Dieter M. Schifferli

    Citation: BMC Genomics 2019 20:429

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  36. Content type: Research article

    The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura...

    Authors: Yu-Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Su Kim, Kuo-Ping Chiu and Yu-Shin Nai

    Citation: BMC Genomics 2019 20:419

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  37. Content type: Research article

    Lactobacillus brevis is a member of the lactic acid bacteria (LAB), and strains of L. brevis have been isolated from silage, as well as from fermented cabbage and other fermented foods. However, this bacterium is...

    Authors: Marine Feyereisen, Jennifer Mahony, Philip Kelleher, Richard John Roberts, Tadhg O’Sullivan, Jan-Maarten A. Geertman and Douwe van Sinderen

    Citation: BMC Genomics 2019 20:416

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  38. Content type: Research article

    Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex...

    Authors: Qiaomu Hu, Cuifang Chang, Quanhe Wang, Haifeng Tian, Zhigang Qiao, Lei Wang, Yan Meng, Cunshuan Xu and Hanbing Xiao

    Citation: BMC Genomics 2019 20:415

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  39. Content type: Research article

    Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mec...

    Authors: Yinzhao Wang, Giorgio Casaburi, Wei Lin, Ying Li, Fengping Wang and Yongxin Pan

    Citation: BMC Genomics 2019 20:407

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  40. 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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  41. Content type: Research article

    Salmonella enterica consists of over 2500 serovars and displays dichotomy in disease manifestations and host range. Except for the enrichment of pseudogenes in genomes for human-restricted serovars, no hallmark h...

    Authors: Ye Feng, Enze Lin, Shengmei Zou, Chyi-Liang Chen and Cheng-Hsun Chiu

    Citation: BMC Genomics 2019 20:398

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  42. 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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  43. 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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