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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. Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans a...

    Authors: Simon Bahrndorff, Aritz Ruiz-González, Nadieh de Jonge, Jeppe Lund Nielsen, Henrik Skovgård and Cino Pertoldi

    Citation: BMC Genomics 2020 21:66

    Content type: Research article

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  2. Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum sub...

    Authors: Arun Kumar Jaiswal, Sandeep Tiwari, Syed Babar Jamal, Letícia de Castro Oliveira, Leandro Gomes Alves, Vasco Azevedo, Preetam Ghosh, Carlo Jose Freira Oliveira and Siomar C. Soares

    Citation: BMC Genomics 2020 21:33

    Content type: Research article

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  3. Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are kn...

    Authors: Sivasubramanian Rajarammohan, Kumar Paritosh, Deepak Pental and Jagreet Kaur

    Citation: BMC Genomics 2019 20:1036

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:82

  4. In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant “priority pathogens” that are posing the greatest threats to human health. Six of these dreaded pathogens a...

    Authors: Tungadri Bose, K. V. Venkatesh and Sharmila S. Mande

    Citation: BMC Genomics 2019 20:1022

    Content type: Research article

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  5. Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include ...

    Authors: Eswari PJ Pandaranayaka, Omer Frenkel, Yigal Elad, Dov Prusky and Arye Harel

    Citation: BMC Genomics 2019 20:1020

    Content type: Research article

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  6. Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, on...

    Authors: Robert Bücking, Murray P Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo and Mark Stoneking

    Citation: BMC Genomics 2019 20:1017

    Content type: Research Article

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    The Correction to this article has been published in BMC Genomics 2020 21:55

  7. White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies...

    Authors: A. Zumaquero, S. Kanematsu, H. Nakayashiki, A. Matas, E. Martínez-Ferri, A. Barceló-Muñóz, F. Pliego-Alfaro, C. López-Herrera, F. M. Cazorla and C. Pliego

    Citation: BMC Genomics 2019 20:1016

    Content type: Research article

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  8. Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food pr...

    Authors: Yan Wang, Lijuan Luo, Qun Li, Hong Wang, Yiqian Wang, Hui Sun, Jianguo Xu, Ruiting Lan and Changyun Ye

    Citation: BMC Genomics 2019 20:1014

    Content type: Research article

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  9. Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake dive...

    Authors: Kevin Schneider, Colin E. Adams and Kathryn R. Elmer

    Citation: BMC Genomics 2019 20:1010

    Content type: Research article

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  10. Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific g...

    Authors: Ruijie Liu, Wai Yee Low, Rick Tearle, Sergey Koren, Jay Ghurye, Arang Rhie, Adam M. Phillippy, Benjamin D. Rosen, Derek M. Bickhart, Timothy P. L. Smith, Stefan Hiendleder and John L. Williams

    Citation: BMC Genomics 2019 20:1000

    Content type: Research article

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  11. The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in so...

    Authors: Jean F. Challacombe, Cedar N. Hesse, Lisa M. Bramer, Lee Ann McCue, Mary Lipton, Samuel Purvine, Carrie Nicora, La Verne Gallegos-Graves, Andrea Porras-Alfaro and Cheryl R. Kuske

    Citation: BMC Genomics 2019 20:976

    Content type: Research article

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  12. During infection by intracellular pathogens, a highly complex interplay occurs between the infected cell trying to degrade the invader and the pathogen which actively manipulates the host cell to enable surviv...

    Authors: Jonas Kjellin, Maria Pränting, Frauke Bach, Roshan Vaid, Bart Edelbroek, Zhiru Li, Marc P. Hoeppner, Manfred Grabherr, Ralph R. Isberg, Monica Hagedorn and Fredrik Söderbom

    Citation: BMC Genomics 2019 20:961

    Content type: Research article

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  13. After the extensive implementation of genomic selection (GS), the choice of the statistical model and data used to estimate variance components (VCs) remains unclear. A primary concern is that VCs estimated fr...

    Authors: Hongding Gao, Per Madsen, Gert Pedersen Aamand, Jørn Rind Thomasen, Anders Christian Sørensen and Just Jensen

    Citation: BMC Genomics 2019 20:956

    Content type: Research article

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  14. In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available ...

    Authors: Shanshan Dong, Chaoxian Zhao, Shouzhou Zhang, Li Zhang, Hong Wu, Huan Liu, Ruiliang Zhu, Yu Jia, Bernard Goffinet and Yang Liu

    Citation: BMC Genomics 2019 20:953

    Content type: Research article

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  15. Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still ...

    Authors: José Maria Gonzalez-Alba, Fernando Baquero, Rafael Cantón and Juan Carlos Galán

    Citation: BMC Genomics 2019 20:936

    Content type: Research article

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  16. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations...

    Authors: Shengrui Liu, Yanlin An, Wei Tong, Xiuju Qin, Lidia Samarina, Rui Guo, Xiaobo Xia and Chaoling Wei

    Citation: BMC Genomics 2019 20:935

    Content type: Research article

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  17. Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages,...

    Authors: Xiaoyu Wang, Songling Zhu, Jian-Hua Zhao, Hong-Xia Bao, Huidi Liu, Tie-Min Ding, Gui-Rong Liu, Yong-Guo Li, Randal N. Johnston, Feng-Lin Cao, Le Tang and Shu-Lin Liu

    Citation: BMC Genomics 2019 20:930

    Content type: Research article

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  18. Prion diseases are zoonotic diseases with a broad infection spectrum among mammalian hosts and are caused by the misfolded prion protein (PrPSc) derived from the normal prion protein (PrPC), which encodes the pri...

    Authors: Yong-Chan Kim, Sae-Young Won and Byung-Hoon Jeong

    Citation: BMC Genomics 2019 20:922

    Content type: Research article

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  19. The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strai...

    Authors: Alex N. Salazar, Arthur R. Gorter de Vries, Marcel van den Broek, Nick Brouwers, Pilar de la Torre Cortès, Niels G. A. Kuijpers, Jean-Marc G. Daran and Thomas Abeel

    Citation: BMC Genomics 2019 20:916

    Content type: Research article

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  20. Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in popu...

    Authors: Mário Vicente, Edita Priehodová, Issa Diallo, Eliška Podgorná, Estella S. Poloni, Viktor Černý and Carina M. Schlebusch

    Citation: BMC Genomics 2019 20:915

    Content type: Research article

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  21. Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumo...

    Authors: Joon Kee Lee, Moon-Woo Seong, Dongjin Shin, Jong-Il Kim, Mi Seon Han, Youbin Yeon, Sung Im Cho, Sung Sup Park and Eun Hwa Choi

    Citation: BMC Genomics 2019 20:910

    Content type: Research article

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  22. Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton’s content of the essent...

    Authors: Heidrun S. Windisch and Patrick Fink

    Citation: BMC Genomics 2019 20:894

    Content type: Research article

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  23. Dictyostelid social amoebas self-organize into fruiting bodies, consisting of spores and up to four supporting cell types in the phenotypically most complex taxon group 4. High quality genomes and stage- and c...

    Authors: Gillian Forbes, Zhi-hui Chen, Koryu Kin, Hajara M. Lawal, Christina Schilde, Yoko Yamada and Pauline Schaap

    Citation: BMC Genomics 2019 20:890

    Content type: Research article

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  24. The genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order. The previous GTN tool gives a phylogenetic tree and calculate the differen...

    Authors: Xiao Deng, Xuechao Zhao, Yuan Liang, Liang Zhang, Jianping Jiang, Guoping Zhao and Yan Zhou

    Citation: BMC Genomics 2019 20:886

    Content type: Methodology article

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  25. Lipids are important for the cell and organism life since they are major components of membranes, energy reserves and are also signal molecules. The main organs for the energy synthesis and storage are the liv...

    Authors: Kevin Muret, Colette Désert, Laetitia Lagoutte, Morgane Boutin, Florence Gondret, Tatiana Zerjal and Sandrine Lagarrigue

    Citation: BMC Genomics 2019 20:882

    Content type: Review

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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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