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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 9 of 10

  1. Recent studies of the tick saliva transcriptome have revealed the profound role of salivary proteins in blood feeding. Kunitz/BPTI proteins are abundant in the salivary glands of ticks and perform multiple fun...

    Authors: Shao-Xing Dai, Ai-Di Zhang and Jing-Fei Huang
    Citation: BMC Evolutionary Biology 2012 12:4
    Content type: Research article Published on:

  2. Early marsupial conceptuses differ markedly from those of eutherian mammals, especially during cleavage and early blastocyst stages of development. Additionally, in marsupials the zona pellucida is surrounded ...

    Authors: Stephen Frankenberg, Jane Fenelon, Bonnie Dopheide, Geoff Shaw and Marilyn B Renfree
    Citation: BMC Evolutionary Biology 2011 11:373
    Content type: Research article Published on:

  4. Plant leucine-rich repeat receptor-like kinases (LRR-RLKs) are receptor kinases that contain LRRs in their extracellular domain. In the last 15 years, many research groups have demonstrated major roles played ...

    Authors: Anne Diévart, Nicolas Gilbert, Gaétan Droc, Agnès Attard, Matthieu Gourgues, Emmanuel Guiderdoni and Christophe Périn
    Citation: BMC Evolutionary Biology 2011 11:367
    Content type: Research article Published on:

  5. It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect near...

    Authors: Paul Yenerall, Bradlee Krupa and Leming Zhou
    Citation: BMC Evolutionary Biology 2011 11:364
    Content type: Research article Published on:

  6. Horizontal gene transfer (HGT), a source of genetic variation, is generally considered to facilitate hosts' adaptability to environments. However, convincing evidence supporting the significant contribution of...

    Authors: Zi-Wen Li, Yi-Hong Shen, Zhong-Huai Xiang and Ze Zhang
    Citation: BMC Evolutionary Biology 2011 11:356
    Content type: Research article Published on:

  7. Introgression of mitochondrial DNA (mtDNA) is among the most frequently described cases of reticulate evolution. The tendency of mtDNA to cross interspecific barriers is somewhat counter-intuitive considering ...

    Authors: Zbyszek Boratyński, Paulo Célio Alves, Stefano Berto, Esa Koskela, Tapio Mappes and José Melo-Ferreira
    Citation: BMC Evolutionary Biology 2011 11:355
    Content type: Research article Published on:

  8. In Drosophila, the Enhancer of split complex (E(spl)-C) comprises 11 bHLH and Bearded genes that function during Notch signaling to repress proneural identity in the developing peripheral nervous system. Comparis...

    Authors: Richard H Baker, Jennifer V Kuehl and Gerald S Wilkinson
    Citation: BMC Evolutionary Biology 2011 11:354
    Content type: Research article Published on:

  9. ISAV is a member of the Orthomyxoviridae family that affects salmonids with disastrous results. It was first detected in 1984 in Norway and from then on it has been reported in Canada, United States, Scotland and...

    Authors: Eduardo Castro-Nallar, Marcelo Cortez-San Martín, Carolina Mascayano, Cristian Molina and Keith A Crandall
    Citation: BMC Evolutionary Biology 2011 11:349
    Content type: Research article Published on:

  10. Matrix extracellular phosphoglycoprotein (MEPE) belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs) that play a key role in skeleton development, particularly in mineralizati...

    Authors: João Paulo Machado, Warren E Johnson, Stephen J O'Brien, Vítor Vasconcelos and Agostinho Antunes
    Citation: BMC Evolutionary Biology 2011 11:342
    Content type: Research article Published on:

  11. First identified in fruit flies with temperature-sensitive paralysis phenotypes, the Drosophila melanogaster TipE locus encodes four voltage-gated sodium (NaV) channel auxiliary subunits. This cluster of TipE-lik...

    Authors: Jia Li, Robert M Waterhouse and Evgeny M Zdobnov
    Citation: BMC Evolutionary Biology 2011 11:337
    Content type: Research article Published on:

  12. Little is known of the biological significance and evolutionary maintenance of integrated non-retroviral RNA virus genes in eukaryotic host genomes. Here, we isolated novel filovirus-like genes from bat genome...

    Authors: Derek J Taylor, Katharina Dittmar, Matthew J Ballinger and Jeremy A Bruenn
    Citation: BMC Evolutionary Biology 2011 11:336
    Content type: Research article Published on:

  13. The three vertebrate pituitary glycoprotein hormones (GPH) are heterodimers of a common α and a specific β subunit. In human, they are located on different chromosomes but in a similar genomic environment. We ...

    Authors: Sandra Dos Santos, Sylvie Mazan, Byrappa Venkatesh, Joëlle Cohen-Tannoudji and Bruno Quérat
    Citation: BMC Evolutionary Biology 2011 11:332
    Content type: Research article Published on:

  16. Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombi...

    Authors: José L Acosta, Luis E Eguiarte, Rosa I Santamaría, Patricia Bustos, Pablo Vinuesa, Esperanza Martínez-Romero, Guillermo Dávila and Víctor González
    Citation: BMC Evolutionary Biology 2011 11:305
    Content type: Research article Published on:

  17. The forkhead transcription factor gene E1 (FOXE1) plays an important role in regulation of thyroid development, palate formation and hair morphogenesis in mammals. However, avian FOXE1 genes have not been charact...

    Authors: Sergey Yu Yaklichkin, Diana K Darnell, Maricela V Pier, Parker B Antin and Sridhar Hannenhalli
    Citation: BMC Evolutionary Biology 2011 11:302
    Content type: Research article Published on:

  18. The growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolu...

    Authors: Luigi Grassi and Anna Tramontano
    Citation: BMC Evolutionary Biology 2011 11:301
    Content type: Research article Published on:

  19. Homeobox genes are the key regulators during development, and they are in general highly conserved with only a few reported cases of rapid evolution. RHOXF2 is an X-linked homeobox gene in primates. It is highly ...

    Authors: Ao-lei Niu, Yin-qiu Wang, Hui Zhang, Cheng-hong Liao, Jin-kai Wang, Rui Zhang, Jun Che and Bing Su
    Citation: BMC Evolutionary Biology 2011 11:298
    Content type: Research article Published on:

  20. Since the first report of the antiretroviral restriction factor TRIM5α in primates, several orthologs in other mammals have been described. Recent studies suggest that leporid retroviruses like RELIK, the firs...

    Authors: Ana Lemos de Matos, Wessel van der Loo, Helena Areal, Dennis K Lanning and Pedro J Esteves
    Citation: BMC Evolutionary Biology 2011 11:294
    Content type: Research article Published on:

  21. During copulation, the major Afro-tropical malaria vector Anopheles gambiae s.s. transfers male accessory gland (MAG) proteins to females as a solid mass (i.e. the "mating plug"). These proteins are postulated to...

    Authors: Emiliano Mancini, Francesco Baldini, Federica Tammaro, Maria Calzetta, Aurelio Serrao, Phillip George, Isabelle Morlais, Daniel Masiga, Igor V Sharakhov, David W Rogers, Flaminia Catteruccia and Alessandra della Torre
    Citation: BMC Evolutionary Biology 2011 11:292
    Content type: Research article Published on:

  22. Elucidating the pattern of evolutionary changes in drug-metabolizing genes is an important subject not only for evolutionary but for biomedical research. We investigated the pattern of divergence and polymorph...

    Authors: Yasuhiro Uno and Naoki Osada
    Citation: BMC Evolutionary Biology 2011 11:283
    Content type: Research article Published on:

  23. Fungi are asexually and sexually reproducing organisms that can combine the evolutionary advantages of the two reproductive modes. However, for many fungi the sexual cycle has never been observed in the field or

    Authors: Pascal L Zaffarano, Valentin Queloz, Angelo Duò and Christoph R Grünig
    Citation: BMC Evolutionary Biology 2011 11:282
    Content type: Research article Published on:

  24. Duplicated genes frequently experience asymmetric rates of sequence evolution. Relaxed selective constraints and positive selection have both been invoked to explain the observation that one paralog within a g...

    Authors: Lijing Bu, Ulfar Bergthorsson and Vaishali Katju
    Citation: BMC Evolutionary Biology 2011 11:279
    Content type: Research article Published on:

  25. In addition to vertical transmission, organisms can also acquire genes from other distantly related species or from their extra-chromosomal elements (plasmids and viruses) via horizontal gene transfer (HGT). I...

    Authors: Huiquan Liu, Yanping Fu, Bo Li, Xiao Yu, Jiatao Xie, Jiasen Cheng, Said A Ghabrial, Guoqing Li, Xianhong Yi and Daohong Jiang
    Citation: BMC Evolutionary Biology 2011 11:276
    Content type: Research article Published on:

  26. Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in respon...

    Authors: Francisco J Fernandez, Fernando Garces, Miguel López-Estepa, Juan Aguilar, Laura Baldomà, Miquel Coll, Josefa Badia and M Cristina Vega
    Citation: BMC Evolutionary Biology 2011 11:273
    Content type: Research article Published on:

  27. Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont Amoebophilu...

    Authors: Stephan Schmitz-Esser, Thomas Penz, Anja Spang and Matthias Horn
    Citation: BMC Evolutionary Biology 2011 11:270
    Content type: Research article Published on:

  28. Revolver is a newly discovered multi-gene family of transposable elements in the Triticeae genome. Revolver encompasses 2929 to 3041 bp, has 20 bp of terminal inverted repeated sequences at both ends, and contain...

    Authors: Motonori Tomita, Asuka Okutani, Avigdor Beiles and Eviatar Nevo
    Citation: BMC Evolutionary Biology 2011 11:269
    Content type: Research article Published on:

  29. Coronins belong to the superfamily of the eukaryotic-specific WD40-repeat proteins and play a role in several actin-dependent processes like cytokinesis, cell motility, phagocytosis, and vesicular trafficking....

    Authors: Christian Eckert, Björn Hammesfahr and Martin Kollmar
    Citation: BMC Evolutionary Biology 2011 11:268
    Content type: Research article Published on:

  32. The Anaphase Promoting Complex or Cyclosome (APC/C) is the largest member of the ubiquitin ligase [E3] family. It plays a crucial role in the control of the cell cycle and cell proliferation by mediating the p...

    Authors: Laura Eme, Aurélie Trilles, David Moreira and Céline Brochier-Armanet
    Citation: BMC Evolutionary Biology 2011 11:265
    Content type: Research article Published on:

  33. Triacylglycerides (TAGs) are a class of neutral lipids that represent the most important storage form of energy for eukaryotic cells. DGAT (acyl-CoA: diacylglycerol acyltransferase; EC 2.3.1.20) is a transmemb...

    Authors: Andreia C Turchetto-Zolet, Felipe S Maraschin, Guilherme L de Morais, Alexandro Cagliari, Cláudia MB Andrade, Marcia Margis-Pinheiro and Rogerio Margis
    Citation: BMC Evolutionary Biology 2011 11:263
    Content type: Research article Published on:

  34. Genome architecture is profoundly influenced by transposable elements (TEs), and natural selection against their harmful effects is a critical factor limiting their spread. Genome defense by the piRNA silencin...

    Authors: Dean M Castillo, Joshua Chang Mell, Kimberly S Box and Justin P Blumenstiel
    Citation: BMC Evolutionary Biology 2011 11:258
    Content type: Research article Published on:

  35. It has been known for over a decade that Plasmodium falciparum proteins are enriched in non-globular domains of unknown function. The potential for these regions of protein sequence to undergo high levels of gene...

    Authors: Kate B Gardner, Ipsita Sinha, Leyla Y Bustamante, Nicholas PJ Day, Nicholas J White and Charles J Woodrow
    Citation: BMC Evolutionary Biology 2011 11:257
    Content type: Research article Published on:

  36. A major goal of molecular evolutionary biology is to understand the fate and consequences of duplicated genes. In this context, aphids are intriguing because the newly sequenced pea aphid genome harbors an ext...

    Authors: Rebecca P Duncan, Lubov Nathanson and Alex CC Wilson
    Citation: BMC Evolutionary Biology 2011 11:253
    Content type: Research article Published on:

  37. The phylogenetic position of the Protura, traditionally considered the most basal hexapod group, is disputed because it has many unique morphological characters compared with other hexapods. Although mitochond...

    Authors: Wan-Jun Chen, Yun Bu, Antonio Carapelli, Romano Dallai, Sheng Li, Wen-Ying Yin and Yun-Xia Luan
    Citation: BMC Evolutionary Biology 2011 11:246
    Content type: Research article Published on:

  39. The recent sequencing of nematode genomes has laid the basis for comparative genomics approaches to study the impact of horizontal gene transfer (HGT) on the adaptation to new environments and the evolution of...

    Authors: Christian Rödelsperger and Ralf J Sommer
    Citation: BMC Evolutionary Biology 2011 11:239
    Content type: Research article Published on:

  40. The synchronous and widespread adoption of the ability to biomineralize was a defining event for metazoan evolution during the late Precambrian/early Cambrian 545 million years ago. However our understanding o...

    Authors: Daniel J Jackson, Luciana Macis, Joachim Reitner and Gert Wörheide
    Citation: BMC Evolutionary Biology 2011 11:238
    Content type: Research article Published on:

  41. Chemosensory receptors, which are all G-protein-coupled receptors (GPCRs), come in four types: odorant receptors (ORs), vomeronasal receptors, trace-amine associated receptors and formyl peptide receptor-like ...

    Authors: Yingsong Zhou, Xiaojun Yan, Shanliang Xu, Peng Zhu, Xianxing He and Jianxin Liu
    Citation: BMC Evolutionary Biology 2011 11:237
    Content type: Research article Published on:

  42. LNX (Ligand of Numb Protein-X) proteins typically contain an amino-terminal RING domain adjacent to either two or four PDZ domains - a domain architecture that is unique to the LNX family. LNX proteins functio...

    Authors: Michael Flynn, Orthis Saha and Paul Young
    Citation: BMC Evolutionary Biology 2011 11:235
    Content type: Research article Published on:

  43. Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important...

    Authors: Stefan Kurtenbach, Christoph Mayer, Thomas Pelz, Hanns Hatt, Florian Leese and Eva M Neuhaus
    Citation: BMC Evolutionary Biology 2011 11:234
    Content type: Research article Published on:

  44. Biotin-dependent carboxylases are a diverse family of carboxylating enzymes widespread in the three domains of life, and thus thought to be very ancient. This family includes enzymes that carboxylate acetyl-Co...

    Authors: Jonathan Lombard and David Moreira
    Citation: BMC Evolutionary Biology 2011 11:232
    Content type: Research article Published on:

  45. The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular sys...

    Authors: Jaret P Bilewitch and Sandie M Degnan
    Citation: BMC Evolutionary Biology 2011 11:228
    Content type: Research article Published on:

  46. Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are diffic...

    Authors: Giltae Song, Chih-Hao Hsu, Cathy Riemer, Yu Zhang, Hie Lim Kim, Federico Hoffmann, Louxin Zhang, Ross C Hardison, Eric D Green and Webb Miller
    Citation: BMC Evolutionary Biology 2011 11:226
    Content type: Research article Published on:

  47. The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which di...

    Authors: Konstantin V Gunbin, Valentin V Suslov, Igor I Turnaev, Dmitry A Afonnikov and Nikolay A Kolchanov
    Citation: BMC Evolutionary Biology 2011 11:224
    Content type: Research article Published on:

  48. tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on...

    Authors: Lijuan Fan, Zhikang Wang, Jinyu Liu, Weili Guo, Jie Yan and Ying Huang
    Citation: BMC Evolutionary Biology 2011 11:219
    Content type: Research article Published on:

  49. In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences...

    Authors: Qing Lu and George E Fox
    Citation: BMC Evolutionary Biology 2011 11:218
    Content type: Research article Published on:
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