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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 19

  1. Carotenoids are a class of terpenoid pigments that contribute to the color and nutritional value of many fruits. Their biosynthetic pathways have been well established in a number of plant species; however, ma...

    Authors: Lina Zhang, Qiuyun Zhang, Wenhui Li, Shikui Zhang and Wanpeng Xi

    Citation: BMC Genomics 2019 20:876

    Content type: Research article

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  2. Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is co...

    Authors: Pernille Gymoese, Kristoffer Kiil, Mia Torpdahl, Mark T. Østerlund, Gitte Sørensen, John E. Olsen, Eva M. Nielsen and Eva Litrup

    Citation: BMC Genomics 2019 20:870

    Content type: Research article

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  3. The adaptation of organisms to changing environments is self-evident, with the adaptive evolution of organisms to environmental changes being a fundamental problem in evolutionary biology. Bees can pollinate i...

    Authors: Li Yancan, Chao Tianle, Fan Yunhan, Lou Delong and Wang Guizhi

    Citation: BMC Genomics 2019 20:869

    Content type: Research article

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  4. With the rise of precision medicine efforts worldwide, our study objective was to describe and map the emerging precision medicine landscape. A Google search was conducted between June 19, 2017 to July 20, 201...

    Authors: Jasmine Lee, Dina Hamideh and Camille Nebeker

    Citation: BMC Genomics 2019 20:868

    Content type: Research article

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  5. APOBEC1 (A1) enzymes are cytidine deaminases involved in RNA editing. In addition to this activity, a few A1 enzymes have been shown to be active on single stranded DNA. As two human ssDNA cytidine deaminases ...

    Authors: Vincent Caval, Wenjuan Jiao, Noémie Berry, Pierre Khalfi, Emmanuelle Pitré, Valérie Thiers, Jean-Pierre Vartanian, Simon Wain-Hobson and Rodolphe Suspène

    Citation: BMC Genomics 2019 20:858

    Content type: Research article

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  6. Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mo...

    Authors: Meryl Vila Nova, Kévin Durimel, Kévin La, Arnaud Felten, Philippe Bessières, Michel-Yves Mistou, Mahendra Mariadassou and Nicolas Radomski

    Citation: BMC Genomics 2019 20:814

    Content type: Research article

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  7. Stability is one of the most fundamental intrinsic characteristics of proteins and can be determined with various methods. Characterization of protein properties does not keep pace with increase in new sequenc...

    Authors: Yang Yang, Xuesong Ding, Guanchen Zhu, Abhishek Niroula, Qiang Lv and Mauno Vihinen

    Citation: BMC Genomics 2019 20:804

    Content type: Methodology article

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  8. Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genome...

    Authors: Adrian Wallner, Eoghan King, Eddy L. M. Ngonkeu, Lionel Moulin and Gilles Béna

    Citation: BMC Genomics 2019 20:803

    Content type: Research article

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  9. The hepatitis E virus (HEV) is the causative pathogen of hepatitis E, a global public health concern. HEV comprises 8 genotypes with a wide host range and geographic distribution. This study aims to determine ...

    Authors: Sarra Baha, Nouredine Behloul, Zhenzhen Liu, Wenjuan Wei, Ruihua Shi and Jihong Meng

    Citation: BMC Genomics 2019 20:790

    Content type: Research article

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  10. We have previously reported on paucity of mitochondrial DNA (mtDNA) haplogroups J and K among Finnish endurance athletes. Here we aimed to further explore differences in mtDNA variants between elite endurance ...

    Authors: Jukka Kiiskilä, Jukka S. Moilanen, Laura Kytövuori, Anna-Kaisa Niemi and Kari Majamaa

    Citation: BMC Genomics 2019 20:784

    Content type: Research article

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  11. Abdominal fat is the major adipose tissue in chickens. The growth status of abdominal fat during postnatal late development ultimately affects meat yield and quality in chickens. MicroRNAs (miRNAs) are endogen...

    Authors: Yi Chen, Yinli Zhao, Wenjiao Jin, Yuanfang Li, Yanhua Zhang, Xuejie Ma, Guirong Sun, Ruili Han, Yadong Tian, Hong Li, Xiangtao Kang and Guoxi Li

    Citation: BMC Genomics 2019 20:778

    Content type: Research article

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  12. Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stre...

    Authors: Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lianxue Fan and Liwang Liu

    Citation: BMC Genomics 2019 20:772

    Content type: Research article

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  13. The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remai...

    Authors: Zhiqiu Yin, Chao Yuan, Yuhui Du, Pan Yang, Chengqian Qian, Yi Wei, Si Zhang, Di Huang and Bin Liu

    Citation: BMC Genomics 2019 20:768

    Content type: Research article

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  14. Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However...

    Authors: Qi Yan, Fan Wu, Tiantian Ma, Xifang Zong, Qian Ma, Jie Li, Yufeng Zhao, Yanrong Wang and Jiyu Zhang

    Citation: BMC Genomics 2019 20:760

    Content type: Research article

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  15. The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies...

    Authors: Jeanne Wilbrandt, Bernhard Misof, Kristen A. Panfilio and Oliver Niehuis

    Citation: BMC Genomics 2019 20:753

    Content type: Research article

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  16. The insect cuticle is mainly composed of exocuticle and endocuticle layers that consist of a large number of structural proteins. The thickness and synthesis of the exocuticle depend on different castes that p...

    Authors: Humaira Rasheed, Chenxu Ye, Yufeng Meng, Yuehua Ran, Jing Li and Xiaohong Su

    Citation: BMC Genomics 2019 20:742

    Content type: Research article

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  17. Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we seq...

    Authors: Si-Qi Tao, Bin Cao, Emmanuelle Morin, Ying-Mei Liang and Sébastien Duplessis

    Citation: BMC Genomics 2019 20:723

    Content type: Research article

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  18. The tribe Sabethini (Diptera: Culicidae) contains important vectors of the yellow fever virus and presents remarkable morphological and ecological diversity unequalled in other mosquito groups. However, there ...

    Authors: Camila Lorenz, João Marcelo Pereira Alves, Peter Gordon Foster, Maria Anice Mureb Sallum and Lincoln Suesdek

    Citation: BMC Genomics 2019 20:721

    Content type: Research article

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  19. 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

    Content type: Research Article

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  20. 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

    Content type: Research article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Database

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Software

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  37. 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

    Content type: Methodology article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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

  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

    Published on:

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

  45. 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

    Content type: Research article

    Published on:

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