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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 2 of 10

  1. The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order ev...

    Authors: Pavel V. Shelyakin, Olga O. Bochkareva, Anna A. Karan and Mikhail S. Gelfand

    Citation: BMC Evolutionary Biology 2019 19:83

    Content type: Research article

    Published on:

  2. Transcription factors (TFs) play a key role in regulating plant development and response to environmental stimuli. While most genes revert to single copy after whole genome duplication (WGD) event, transcripti...

    Authors: Nicholas L. Panchy, Christina B. Azodi, Eamon F. Winship, Ronan C. O’Malley and Shin-Han Shiu

    Citation: BMC Evolutionary Biology 2019 19:77

    Content type: Research article

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  3. Frizzled family members belong to G-protein coupled receptors and encode proteins accountable for cell signal transduction, cell proliferation and cell death. Members of Frizzled receptor family are considered...

    Authors: Suman Seemab, Nashaiman Pervaiz, Rabail Zehra, Saneela Anwar, Yiming Bao and Amir Ali Abbasi

    Citation: BMC Evolutionary Biology 2019 19:72

    Content type: Research article

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  4. β-Amylases (BAMs) are a multigene family of glucan hydrolytic enzymes playing a key role not only for plant biology but also for many industrial applications, such as the malting process in the brewing and dis...

    Authors: Matthias Thalmann, Mario Coiro, Tiago Meier, Thomas Wicker, Samuel C. Zeeman and Diana Santelia

    Citation: BMC Evolutionary Biology 2019 19:66

    Content type: Research article

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  5. The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparis...

    Authors: Zhang-Hai Li, Xiao Ma, De-Yi Wang, Yun-Xia Li, Cheng-Wang Wang and Xiao-Hua Jin

    Citation: BMC Evolutionary Biology 2019 19:63

    Content type: Research article

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  6. The C-C motif chemokine ligand 16 (CCL16) is a potent pro-inflammatory chemokine and a chemoattractant for monocytes and lymphocytes. In normal plasma, it is present at high concentrations and elicits its effe...

    Authors: Fabiana Neves, Joana Abrantes, Ana M. Lopes, Luciana A. Fusinatto, Maria J. Magalhães, Wessel van der Loo and Pedro J. Esteves

    Citation: BMC Evolutionary Biology 2019 19:59

    Content type: Research article

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  7. Many physiological processes are influenced by nicotinic acetylcholine receptors (nAChR), ranging from neuromuscular and parasympathetic signaling to modulation of the reward system and long-term memory. Due t...

    Authors: Julia E. Pedersen, Christina A. Bergqvist and Dan Larhammar

    Citation: BMC Evolutionary Biology 2019 19:38

    Content type: Research article

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  8. Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidat...

    Authors: Sidra Aslam, Xin-Ran Lan, Bo-Wen Zhang, Zheng-Lin Chen, Li Wang and Deng-Ke Niu

    Citation: BMC Evolutionary Biology 2019 19:35

    Content type: Research article

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  9. The plasminogen (PLG) activation system is composed by a series of serine proteases, inhibitors and several binding proteins, which together control the temporal and spatial generation of the active serine pro...

    Authors: Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Bendixen and Frank Panitz

    Citation: BMC Evolutionary Biology 2019 19:27

    Content type: Research article

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  10. ALRs (AIM2-like Receptors) are germline encoded PRRs that belong to PYHIN gene family of cytokines, which are having signature N-terminal PYD (Pyrin, PAAD or DAPIN) domain and C-terminal HIN-200 (hematopoietic, i...

    Authors: Sushil Kumar, Jatinder Singh Chera, Ashutosh Vats and Sachinandan De

    Citation: BMC Evolutionary Biology 2019 19:26

    Content type: Research article

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  11. The Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plasti...

    Authors: Jong Im Kim, Hyunmoon Shin, Pavel Škaloud, Jaehee Jung, Hwan Su Yoon, John M. Archibald and Woongghi Shin

    Citation: BMC Evolutionary Biology 2019 19:20

    Content type: Research article

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  12. Oligoadenylate synthetases (OASs) are widely distributed in Metazoa including sponges, fish, reptiles, birds and mammals and show large variation, with one to twelve members in any given species. Upon double-s...

    Authors: Jiaxiang Hu, Xiaoxue Wang, Yanling Xing, Enguang Rong, Mengfei Ning, Jacqueline Smith and Yinhua Huang

    Citation: BMC Evolutionary Biology 2018 18:201

    Content type: Research article

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  13. The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of bi...

    Authors: Dorota Matelska, Ivan G. Shabalin, Jagoda Jabłońska, Marcin J. Domagalski, Jan Kutner, Krzysztof Ginalski and Wladek Minor

    Citation: BMC Evolutionary Biology 2018 18:199

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Psychiatry 2019 19:221

  14. Adaptation to local host plants may impact a pollinator’s population genetic structure by reducing gene flow and driving population genetic differentiation, representing an early stage of ecological speciation...

    Authors: Belinda Kahnt, Panagiotis Theodorou, Antonella Soro, Hilke Hollens-Kuhr, Michael Kuhlmann, Anton Pauw and Robert J. Paxton

    Citation: BMC Evolutionary Biology 2018 18:196

    Content type: Research article

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  15. The standard genetic code (SGC) is a unique set of rules which assign amino acids to codons. Similar amino acids tend to have similar codons indicating that the code evolved to minimize the costs of amino acid...

    Authors: Małgorzata Wnętrzak, Paweł Błażej, Dorota Mackiewicz and Paweł Mackiewicz

    Citation: BMC Evolutionary Biology 2018 18:192

    Content type: Research article

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  16. Osteoglycin (OGN, a.k.a. mimecan) belongs to cluster III of the small leucine-rich proteoglycans (SLRP) of the extracellular matrix (ECM). In vertebrates OGN is a characteristic ECM protein of bone. In the pre...

    Authors: R. A. Costa, R. S. T. Martins, E. Capilla, L. Anjos and D. M. Power

    Citation: BMC Evolutionary Biology 2018 18:191

    Content type: Research article

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  17. The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an...

    Authors: Mudassir Iqbal, Mukesh Dubey, Mikael Gudmundsson, Maria Viketoft, Dan Funck Jensen and Magnus Karlsson

    Citation: BMC Evolutionary Biology 2018 18:171

    Content type: Research article

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  18. The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influe...

    Authors: Milica Mandic, Marina L. Ramon, Aleeza C. Gerstein, Andrew Y. Gracey and Jeffrey G. Richards

    Citation: BMC Evolutionary Biology 2018 18:163

    Content type: Research article

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  19. Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts...

    Authors: Shir Portugez, William F. Martin and Einat Hazkani-Covo

    Citation: BMC Evolutionary Biology 2018 18:162

    Content type: Research article

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  20. Provision of long-chain polyunsaturated fatty acids (LC-PUFA) in vertebrates occurs through the diet or via endogenous production from C18 precursors through consecutive elongations and desaturations. It has been...

    Authors: Mónica Lopes-Marques, Naoki Kabeya, Yu Qian, Raquel Ruivo, Miguel M. Santos, Byrappa Venkatesh, Douglas R. Tocher, L. Filipe C. Castro and Óscar Monroig

    Citation: BMC Evolutionary Biology 2018 18:157

    Content type: Research article

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  21. Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not b...

    Authors: Ismael L. Hernández-González, Gabriel Moreno-Hagelsieb and Gabriela Olmedo-Álvarez

    Citation: BMC Evolutionary Biology 2018 18:148

    Content type: Research article

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  22. Confined within the freezing Southern Ocean, the Antarctic notothenioids have evolved to become both cold adapted and cold specialized. A marked signature of cold specialization is an apparent loss of the cell...

    Authors: Kevin T. Bilyk, Luis Vargas-Chacoff and C.-H.Christina Cheng

    Citation: BMC Evolutionary Biology 2018 18:143

    Content type: Research article

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  23. Disparity in the timing of biological events occurs across a variety of systems, yet the understanding of genetic basis underlying diverse phenologies remains limited. Variation in maturation timing occurs in ...

    Authors: Steven J. Micheletti, Jon E. Hess, Joseph S. Zendt and Shawn R. Narum

    Citation: BMC Evolutionary Biology 2018 18:140

    Content type: Research article

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  24. Phylogenetic relationships among Eastern Hemisphere cypresses, Western Hemisphere cypresses, junipers, and their closest relatives are controversial, and generic delimitations have been in flux for the past de...

    Authors: Andan Zhu, Weishu Fan, Robert P. Adams and Jeffrey P. Mower

    Citation: BMC Evolutionary Biology 2018 18:137

    Content type: Research article

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  25. As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controve...

    Authors: Dong Zhang, Hong Zou, Shan G. Wu, Ming Li, Ivan Jakovlić, Jin Zhang, Rong Chen, Wen X. Li and Gui T. Wang

    Citation: BMC Evolutionary Biology 2018 18:133

    Content type: Research article

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  26. The adaptive immune system of vertebrates has an extraordinary potential to sense and neutralize foreign antigens entering the body. De novo evolution of genes implies that the genome itself expresses novel antig...

    Authors: Cemalettin Bekpen, Chen Xie and Diethard Tautz

    Citation: BMC Evolutionary Biology 2018 18:121

    Content type: Research article

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  27. The majority of wood decomposing fungi are mushroom-forming Agaricomycetes, which exhibit two main modes of plant cell wall decomposition: white rot, in which all plant cell wall components are degraded, inclu...

    Authors: Franz-Sebastian Krah, Claus Bässler, Christoph Heibl, John Soghigian, Hanno Schaefer and David S. Hibbett

    Citation: BMC Evolutionary Biology 2018 18:119

    Content type: Research article

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  28. Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, ...

    Authors: Marina Pais, Kentaro Yoshida, Artemis Giannakopoulou, Mathieu A. Pel, Liliana M. Cano, Ricardo F. Oliva, Kamil Witek, Hannele Lindqvist-Kreuze, Vivianne G. A. A. Vleeshouwers and Sophien Kamoun

    Citation: BMC Evolutionary Biology 2018 18:93

    Content type: Research article

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  29. Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modificat...

    Authors: Katharina E. Bräuer, Kevin Brockers, Jasmin Moneer, Annette Feuchtinger, Evi Wollscheid-Lengeling, Andreas Lengeling and Alexander Wolf

    Citation: BMC Evolutionary Biology 2018 18:96

    Content type: Research article

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  30. An essential question in evolutionary biology is whether shifts in a set of polygenic behaviors share a genetic basis across species. Such a behavioral shift is seen in the cave-dwelling Mexican tetra, Astyanax m...

    Authors: Masato Yoshizawa, Alexander Settle, Meredith C. Hermosura, Lillian J. Tuttle, Nicolas Cetraro, Courtney N. Passow and Suzanne E. McGaugh

    Citation: BMC Evolutionary Biology 2018 18:89

    Content type: Research article

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  31. Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolutio...

    Authors: Bochra A. Bahri, Guillaume Daverdin, Xiangyang Xu, Jan-Fang Cheng, Kerrie W. Barry, E. Charles Brummer and Katrien M. Devos

    Citation: BMC Evolutionary Biology 2018 18:91

    Content type: Research article

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  32. C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a p...

    Authors: Anke Hein and Volker Knoop

    Citation: BMC Evolutionary Biology 2018 18:85

    Content type: Research article

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  33. It is thought that after whole-genome duplications (WGDs), a large fraction of the duplicated gene copies is lost over time while few duplicates are retained. Which factors promote survival or death of a dupli...

    Authors: Elisabeth Kaltenegger, Svetlana Leng and Alexander Heyl

    Citation: BMC Evolutionary Biology 2018 18:76

    Content type: Research article

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  34. Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evo...

    Authors: Manuela Sann, Oliver Niehuis, Ralph S. Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn and Michael Ohl

    Citation: BMC Evolutionary Biology 2018 18:71

    Content type: Research article

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  35. One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that rec...

    Authors: Niladri Banerjee, Tatiana Polushina, Francesco Bettella, Sudheer Giddaluru, Vidar M. Steen, Ole A. Andreassen and Stephanie Le Hellard

    Citation: BMC Evolutionary Biology 2018 18:63

    Content type: Research article

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  36. Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. ...

    Authors: Hanan Arafat, Ada Alamaru, Carmela Gissi and Dorothée Huchon

    Citation: BMC Evolutionary Biology 2018 18:65

    Content type: Research article

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  37. The role of chromosomal arrangements in adaptation is supported by the repeatable clinal variation in inversion frequencies across continents in colonizing species such as Drosophila subobscura. However, there is...

    Authors: Pedro Simões and Marta Pascual

    Citation: BMC Evolutionary Biology 2018 18:60

    Content type: Research article

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2018 Journal Metrics

  • Citation Impact
    3.045 - 2-year Impact Factor
    3.559 - 5-year Impact Factor
    1.15 - Source Normalized Impact per Paper (SNIP)
    1.687 - SCImago Journal Rank (SJR)

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