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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.

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  1. The relative influence of diet and phylogeny on snake venom activity is a poorly understood aspect of snake venom evolution. We measured the activity of two enzyme toxin groups – phospholipase A2 (PLA2), and L-am...

    Authors: Theo Tasoulis, Michael S. Y. Lee, Manon Ziajko, Nathan Dunstan, Joanna Sumner and Geoffrey K. Isbister
    Citation: BMC Evolutionary Biology 2020 20:9
    Content type: Research article Published on:

  2. Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly unipa...

    Authors: Davide Guerra, Manuel Lopes-Lima, Elsa Froufe, Han Ming Gan, Paz Ondina, Rafaela Amaro, Michael W. Klunzinger, Claudia Callil, Vincent Prié, Arthur E. Bogan, Donald T. Stewart and Sophie Breton
    Citation: BMC Evolutionary Biology 2019 19:229
    Content type: Research article Published on:

  3. Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, ...

    Authors: Ana Pinheiro, Ana Águeda-Pinto, José Melo-Ferreira, Fabiana Neves, Joana Abrantes and Pedro J. Esteves
    Citation: BMC Evolutionary Biology 2019 19:221
    Content type: Research article Published on:

  4. Lymphotoxin-α (LTα), located in the Major Histocompatibility Complex (MHC) class III region on chromosome 6, encodes a cytotoxic protein that mediates a variety of antiviral responses among other biological funct...

    Authors: Michael C. Campbell, Bryan Ashong, Shaolei Teng, Jayla Harvey and Christopher N. Cross
    Citation: BMC Evolutionary Biology 2019 19:218
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Evolutionary Biology 2019 19:225

  5. In mammals, the natriuretic system contains three natriuretic peptides, NPPA, NPPB and NPPC, that bind to three transmembrane receptors, NPR1, NPR2 and NPR3. The natriuretic peptides are known only in vertebra...

    Authors: Anna Grandchamp, Shifa Tahir and Philippe Monget
    Citation: BMC Evolutionary Biology 2019 19:215
    Content type: Research article Published on:

  6. The buffalo, despite its superior milk-producing ability, suffers from reproductive limitations that constrain its lifetime productivity. Male sub-fertility, manifested as low conception rates (CRs), is a majo...

    Authors: Vipul Batra, Avinash Maheshwarappa, Komal Dagar, Sandeep Kumar, Apoorva Soni, A. Kumaresan, Rakesh Kumar and T. K. Datta
    Citation: BMC Evolutionary Biology 2019 19:214
    Content type: Research article Published on:

  7. Various apolipoproteins widely distributed among vertebrata play key roles in lipid metabolism and have a direct correlation with human diseases as diagnostic markers. However, the evolutionary progress of apo...

    Authors: Jia-Qian Liu, Wen-Xing Li, Jun-Juan Zheng, Qing-Nan Tian, Jing-Fei Huang and Shao-Xing Dai
    Citation: BMC Evolutionary Biology 2019 19:209
    Content type: Research article Published on:

  9. The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our pr...

    Authors: Hyeon-Mu Cho, Sang-Je Park, Se-Hee Choe, Ja-Rang Lee, Sun-Uk Kim, Yeung-Bae Jin, Ji-Su Kim, Sang-Rae Lee, Young-Hyun Kim and Jae-Won Huh
    Citation: BMC Evolutionary Biology 2019 19:196
    Content type: Research article Published on:

  10. The transition from land to sea by the ancestor of cetaceans approximately 50 million years ago was an incredible evolutionary event that led to a series of morphological, physiological, and behavioral adaptat...

    Authors: Di Sun, Xuming Zhou, Zhenpeng Yu, Shixia Xu, Inge Seim and Guang Yang
    Citation: BMC Evolutionary Biology 2019 19:194
    Content type: Research article Published on:

  11. Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew severely affects yield security wheat production in China. Understanding the virulence structure and genetic variations of this pat...

    Authors: Xian Xin Wu, Xiao Feng Xu, De Xin Ma, Rong Zhen Chen, Tian Ya Li and Yuan Yin Cao
    Citation: BMC Evolutionary Biology 2019 19:183
    Content type: Research article Published on:

  12. Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on ...

    Authors: Juan A. Subirana and Xavier Messeguer
    Citation: BMC Evolutionary Biology 2019 19:181
    Content type: Research article Published on:

  13. Vomeronasal type 1 receptor genes (V1Rs) are expected to detect intraspecific pheromones. It is believed that rodents rely heavily on pheromonal communication mediated by V1Rs, but pheromonal signals are thought ...

    Authors: Hengwu Jiao, Wei Hong, Eviatar Nevo, Kexin Li and Huabin Zhao
    Citation: BMC Evolutionary Biology 2019 19:176
    Content type: Research article Published on:

  14. A number of non-visual responses to light in vertebrates, such as circadian rhythm control and pupillary light reflex, are mediated by melanopsins, G-protein coupled membrane receptors, conjugated to a retinal...

    Authors: Einat Hauzman, Venkatasushma Kalava, Daniela Maria Oliveira Bonci and Dora Fix Ventura
    Citation: BMC Evolutionary Biology 2019 19:174
    Content type: Research article Published on:

  15. In the absence of sex and recombination, genomes are expected to accumulate deleterious mutations via an irreversible process known as Muller’s ratchet, especially in the case of polyploidy. In contrast, no ge...

    Authors: Ladislav Hodač, Simone Klatt, Diego Hojsgaard, Timothy F. Sharbel and Elvira Hörandl
    Citation: BMC Evolutionary Biology 2019 19:170
    Content type: Research article Published on:

  16. Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2-dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid...

    Authors: Andrew J. Hudson, David C. McWatters, Bradley A. Bowser, Ashley N. Moore, Graham E. Larue, Scott W. Roy and Anthony G. Russell
    Citation: BMC Evolutionary Biology 2019 19:162
    Content type: Research article Published on:

  18. The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ’s complexity by a tiny amount. This evolutionary process can be studied by comparing closel...

    Authors: Henri van Kruistum, Joost van den Heuvel, Joseph Travis, Ken Kraaijeveld, Bas J. Zwaan, Martien A. M. Groenen, Hendrik-Jan Megens and Bart J. A. Pollux
    Citation: BMC Evolutionary Biology 2019 19:156
    Content type: Research article Published on:

  20. Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Ac...

    Authors: Umberto Rosani, Chang-Ming Bai, Lorenzo Maso, Maxwell Shapiro, Miriam Abbadi, Stefania Domeneghetti, Chong-Ming Wang, Laura Cendron, Thomas MacCarthy and Paola Venier
    Citation: BMC Evolutionary Biology 2019 19:149
    Content type: Research article Published on:

  21. Antioxidative enzymes contribute to a parasite’s ability to counteract the host’s intracellular killing mechanisms. The facultative intracellular oyster parasite, Perkinsus marinus, a sister taxon to dinoflagella...

    Authors: Eric J. Schott, Santiago Di Lella, Tsvetan R. Bachvaroff, L. Mario Amzel and Gerardo R. Vasta
    Citation: BMC Evolutionary Biology 2019 19:146
    Content type: Research article Published on:

  22. Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depend...

    Authors: R. Huttener, L. Thorrez, T. in’t Veld, M. Granvik, L. Snoeck, L. Van Lommel and F. Schuit
    Citation: BMC Evolutionary Biology 2019 19:144
    Content type: Research article Published on:

  23. Our laboratory identified ADGRL4/ELTD1, an orphan GPCR belonging to the adhesion GPCR (aGPCR) family, as a novel regulator of angiogenesis and a potential anti-cancer therapeutic target. Little is known about ...

    Authors: David M. Favara, Alison H. Banham and Adrian L. Harris
    Citation: BMC Evolutionary Biology 2019 19:143
    Content type: Research article Published on:

  24. Previously, we have demonstrated that genes involved in ovarian function are highly conserved throughout evolution. In this study, we aimed to document the conservation of genes involved in spermatogenesis fro...

    Authors: Sophie Fouchécourt, Floriane Picolo, Sébastien Elis, Charlotte Lécureuil, Aurore Thélie, Marina Govoroun, Mégane Brégeon, Pascal Papillier, Jean-Jacques Lareyre and Philippe Monget
    Citation: BMC Evolutionary Biology 2019 19:137
    Content type: Research article Published on:

  25. The evolutionary probability (EP) of an allele in a DNA or protein sequence predicts evolutionarily permissible (ePerm; EP ≥ 0.05) and forbidden (eForb; EP < 0.05) variants. EP of an allele represents an indep...

    Authors: Ravi Patel and Sudhir Kumar
    Citation: BMC Evolutionary Biology 2019 19:133
    Content type: Methodology article Published on:

  26. The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. e...

    Authors: Jingqiu Liao, Renato Hohl Orsi, Laura M. Carroll, Jasna Kovac, Hongyu Ou, Hailong Zhang and Martin Wiedmann
    Citation: BMC Evolutionary Biology 2019 19:132
    Content type: Research article Published on:

  27. The hypothesis that vertebrates have experienced two ancient, whole genome duplications (WGDs) is of central interest to evolutionary biology and has been implicated in evolution of developmental complexity. T...

    Authors: Nashaiman Pervaiz, Nazia Shakeel, Ayesha Qasim, Rabail Zehra, Saneela Anwar, Neenish Rana, Yongbiao Xue, Zhang Zhang, Yiming Bao and Amir Ali Abbasi
    Citation: BMC Evolutionary Biology 2019 19:128
    Content type: Research article Published on:

  28. L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate au...

    Authors: Sílvia F. Henriques, Pedro Duque, Hugo López-Fernández, Noé Vázquez, Florentino Fdez-Riverola, Miguel Reboiro-Jato, Cristina P. Vieira and Jorge Vieira
    Citation: BMC Evolutionary Biology 2019 19:126
    Content type: Research article Published on:

  29. Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacter...

    Authors: Phani Rama Krishna Behra, B. M. Fredrik Pettersson, Sarbashis Das, Santanu Dasgupta and Leif A. Kirsebom
    Citation: BMC Evolutionary Biology 2019 19:124
    Content type: Research article Published on:

  31. The S100A7 gene, also called psoriasin, was first described as an upregulated protein in psoriatic skin. For the past years, the importance of this protein as a key effector of innate immunity has been clearly es...

    Authors: Ana Águeda-Pinto, L. Filipe C. Castro and Pedro J. Esteves
    Citation: BMC Evolutionary Biology 2019 19:102
    Content type: Research article Published on:

  32. Cellulose, a major polysaccharide of the plant cell wall, consists of β-1,4-linked glucose moieties forming a molecular network recalcitrant to enzymatic breakdown. Although cellulose is potentially a rich sou...

    Authors: André Busch, Etienne G. J. Danchin and Yannick Pauchet
    Citation: BMC Evolutionary Biology 2019 19:100
    Content type: Research article Published on:

  33. The Micronycterinae form a subfamily of leaf-nosed bats (Phyllostomidae) that contains the genera Lampronycteris Sanborn, 1949, and Micronycteris Gray, 1866 (stricto sensu), and is characterized by marked karyoty...

    Authors: T. C. M. Benathar, C. Y. Nagamachi, L. R. R. Rodrigues, P. C. M. O’Brien, M. A. Ferguson-Smith, F. Yang and J. C. Pieczarka
    Citation: BMC Evolutionary Biology 2019 19:98
    Content type: Research article Published on:

  35. Animals have a greater diversity of signalling pathways than their unicellular relatives, consistent with the evolution and expansion of these pathways occurring in parallel with the origin of animal multicell...

    Authors: Arunkumar Krishnan, Bernard M. Degnan and Sandie M. Degnan
    Citation: BMC Evolutionary Biology 2019 19:96
    Content type: Research article Published on:

  36. Standard evolutionary theories of aging postulate that reduced extrinsic mortality leads to evolution of longevity. Clownfishes of the genus Amphiprion live in a symbiotic relationship with sea anemones that p...

    Authors: Arne Sahm, Pedro Almaida-Pagán, Martin Bens, Mirko Mutalipassi, Alejandro Lucas-Sánchez, Jorge de Costa Ruiz, Matthias Görlach and Alessandro Cellerino
    Citation: BMC Evolutionary Biology 2019 19:89
    Content type: Research article Published on:

  37. Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid g...

    Authors: Athanasios Zervas, Gitte Petersen and Ole Seberg
    Citation: BMC Evolutionary Biology 2019 19:87
    Content type: Research article Published on:

  38. 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:

  39. 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 Published on:

  40. 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 Published on:

  42. 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 Published on:

  43. 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 Published on:

  46. 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 Published on:

  49. 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 Published on:

  50. 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 Published on:
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