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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 5 of 10

  1. Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nons...

    Authors: Karen B Barnard-Kubow, Daniel B Sloan and Laura F Galloway

    Citation: BMC Evolutionary Biology 2014 14:268

    Content type: Research article

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  2. G protein-coupled receptors (GPCRs) play a central role in eukaryotic signal transduction. However, the GPCR component of this signalling system, at the early origins of metazoans is not fully understood. Here...

    Authors: Arunkumar Krishnan, Rohit Dnyansagar, Markus Sällman Almén, Michael J Williams, Robert Fredriksson, Narayanan Manoj and Helgi B Schiöth

    Citation: BMC Evolutionary Biology 2014 14:270

    Content type: Research article

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  3. The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundan...

    Authors: Kalina TJ Davies, Georgia Tsagkogeorga and Stephen J Rossiter

    Citation: BMC Evolutionary Biology 2014 14:261

    Content type: Research article

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  4. Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the ...

    Authors: Lei Wei, Jian He, Xian Jia, Qi Qi, Zhisheng Liang, Hao Zheng, Yao Ping, Shuyu Liu and Jingchen Sun

    Citation: BMC Evolutionary Biology 2014 14:262

    Content type: Research article

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  5. Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of r...

    Authors: Zongji Wang, Jilin Zhang, Wei Yang, Na An, Pei Zhang, Guojie Zhang and Qi Zhou

    Citation: BMC Evolutionary Biology 2014 14:250

    Content type: Research article

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  6. Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We h...

    Authors: Matthew J Greenwold, Weier Bao, Erich D Jarvis, Haofu Hu, Cai Li, M Thomas P Gilbert, Guojie Zhang and Roger H Sawyer

    Citation: BMC Evolutionary Biology 2014 14:249

    Content type: Research article

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  7. The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs i...

    Authors: Niles Lehman, Tess Bernhard, Brian C Larson, Andrew JN Robinson and Christopher CB Southgate

    Citation: BMC Evolutionary Biology 2014 14:248

    Content type: Research article

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  8. Young genes and genes under positive selection commonly contribute to adaptive phenotypic evolution. Early developmental stages are very important for establishing phenotypes, which might be helpful for studyi...

    Authors: He-Qun Liu, Yan Li, David M Irwin, Ya-Ping Zhang and Dong-Dong Wu

    Citation: BMC Evolutionary Biology 2014 14:241

    Content type: Research article

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  9. Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of th...

    Authors: Sivakumar Kannan, Igor B Rogozin and Eugene V Koonin

    Citation: BMC Evolutionary Biology 2014 14:237

    Content type: Research article

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  10. Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability a...

    Authors: Amanda M Larracuente

    Citation: BMC Evolutionary Biology 2014 14:233

    Content type: Research article

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  11. Elucidating the mechanisms underlying coevolution of ligands and receptors is an important challenge in molecular evolutionary biology. Peptide hormones and their receptors are excellent models for such effort...

    Authors: Barry L Williams, Yasuhisa Akazome, Yoshitaka Oka and Heather L Eisthen

    Citation: BMC Evolutionary Biology 2014 14:215

    Content type: Research article

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  12. Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathway...

    Authors: Juanjuan Chai, Guruprasad Kora, Tae-Hyuk Ahn, Doug Hyatt and Chongle Pan

    Citation: BMC Evolutionary Biology 2014 14:207

    Content type: Research article

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  13. The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous st...

    Authors: Evan K Maxwell, Christine E Schnitzler, Paul Havlak, Nicholas H Putnam, Anh-Dao Nguyen, R Travis Moreland and Andreas D Baxevanis

    Citation: BMC Evolutionary Biology 2014 14:212

    Content type: Research article

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  14. Myxozoa are a diverse group of metazoan parasites with a very simple organization, which has for decades eluded their evolutionary origin. Their most prominent and characteristic feature is the polar capsule: ...

    Authors: Erez Shpirer, E Sally Chang, Arik Diamant, Nimrod Rubinstein, Paulyn Cartwright and Dorothée Huchon

    Citation: BMC Evolutionary Biology 2014 14:205

    Content type: Research article

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  15. MicroRNAs (miRNAs) are small non-coding RNA molecules with an important role upon post-transcriptional regulation. These molecules have been shown essential for several cellular processes in vertebrates, inclu...

    Authors: Pedro Gabriel Nachtigall, Marcos Correa Dias and Danillo Pinhal

    Citation: BMC Evolutionary Biology 2014 14:196

    Content type: Research article

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  16. Human bitter taste receptors are encoded by a gene family consisting of 25 functional TAS2R loci. In addition, humans carry 11 TAS2R pseudogenes, some of which display evidence for substantial diversification amo...

    Authors: Davide Risso, Sergio Tofanelli, Gabriella Morini, Donata Luiselli and Dennis Drayna

    Citation: BMC Evolutionary Biology 2014 14:198

    Content type: Research article

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  17. Lysozyme g is an antibacterial enzyme that was first found in the eggs of some birds, but recently has been found in additional species, including non-vertebrates. Some previously characterized lysozyme g sequenc...

    Authors: David M Irwin

    Citation: BMC Evolutionary Biology 2014 14:188

    Content type: Research article

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  18. Hypoxia-inducible factor (HIF) is a master regulator that mediates major changes in gene expression under hypoxic conditions. Though HIF family has been identified in many organisms, little is known about this...

    Authors: Lihong Guan, Wei Chi, Wuhan Xiao, Liangbiao Chen and Shunping He

    Citation: BMC Evolutionary Biology 2014 14:192

    Content type: Research article

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  19. Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (“T-P spacers”) have been ob...

    Authors: Tor Erik Jørgensen, Ingrid Bakke, Anita Ursvik, Morten Andreassen, Truls Moum and Steinar D Johansen

    Citation: BMC Evolutionary Biology 2014 14:182

    Content type: Research article

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  20. Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical interco...

    Authors: Hong-Hu Meng, Frédéric MB Jacques, Tao Su, Yong-Jiang Huang, Shi-Tao Zhang, Hong-Jie Ma and Zhe-Kun Zhou

    Citation: BMC Evolutionary Biology 2014 14:181

    Content type: Research article

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  21. Dacts are multi-domain adaptor proteins. They have been implicated in Wnt and Tgfβ signaling and serve as a nodal point in regulating many cellular activities. Dact genes have so far only been identified in bony ...

    Authors: Frank Richard Schubert, Débora Rodrigues Sobreira, Ricardo Guerreiro Janousek, Lúcia Elvira Alvares and Susanne Dietrich

    Citation: BMC Evolutionary Biology 2014 14:157

    Content type: Research article

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  22. The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mR...

    Authors: Xiu-Qing Li and Donglei Du

    Citation: BMC Evolutionary Biology 2014 14:162

    Content type: Research article

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  23. The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected...

    Authors: Dianne I Lou, Ross M McBee, Uyen Q Le, Anne C Stone, Gregory K Wilkerson, Ann M Demogines and Sara L Sawyer

    Citation: BMC Evolutionary Biology 2014 14:155

    Content type: Research article

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  24. Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most ch...

    Authors: Hui Huang, Chao Shi, Yuan Liu, Shu-Yan Mao and Li-Zhi Gao

    Citation: BMC Evolutionary Biology 2014 14:151

    Content type: Research article

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  25. Heat stress transcription factors (Hsfs) regulate gene expression in response to heat and many other environmental stresses in plants. Understanding the adaptive evolution of Hsf genes in the grass family will pr...

    Authors: Zefeng Yang, Yifan Wang, Yun Gao, Yong Zhou, Enying Zhang, Yunyun Hu, Yuan Yuan, Guohua Liang and Chenwu Xu

    Citation: BMC Evolutionary Biology 2014 14:147

    Content type: Research article

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  26. The evolution of the coding exome is a major driving force of functional divergence both between species and between protein isoforms. Exons at different positions in the transcript or in different transcript ...

    Authors: Feng-Chi Chen, Trees-Juen Chuang, Hsuan-Yu Lin and Min-Kung Hsu

    Citation: BMC Evolutionary Biology 2014 14:145

    Content type: Research article

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  27. Selection pressure governs the relative mutability and the conservedness of a protein across the protein family. Biomolecules (DNA, RNA and proteins) continuously evolve under the effect of evolutionary pressu...

    Authors: Vineetha Mandlik, Sonali Shinde and Shailza Singh

    Citation: BMC Evolutionary Biology 2014 14:142

    Content type: Research article

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  28. NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where s...

    Authors: Syed Nabeel-Shah, Kanwal Ashraf, Ronald E Pearlman and Jeffrey Fillingham

    Citation: BMC Evolutionary Biology 2014 14:139

    Content type: Research article

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  29. Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique ...

    Authors: Kathryn B Walters-Conte, Diana LE Johnson, Warren E Johnson, Stephen J O’Brien and Jill Pecon-Slattery

    Citation: BMC Evolutionary Biology 2014 14:137

    Content type: Research article

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  30. The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellula...

    Authors: Wanlu Song, Yajuan Qin, Yan Zhu, Guangjun Yin, Ningning Wu, Yaxuan Li and Yingkao Hu

    Citation: BMC Evolutionary Biology 2014 14:124

    Content type: Research article

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  31. Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A ...

    Authors: Åke Strese, Anders Backlund and Cecilia Alsmark

    Citation: BMC Evolutionary Biology 2014 14:119

    Content type: Research article

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  32. Starch is the main source of carbon storage in the Archaeplastida. The starch biosynthesis pathway (sbp) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the pl...

    Authors: Odrade Nougué, Jonathan Corbi, Steven G Ball, Domenica Manicacci and Maud I Tenaillon

    Citation: BMC Evolutionary Biology 2014 14:103

    Content type: Research article

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  33. The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless ...

    Authors: Leon Huynen, Takayuki Suzuki, Toshihiko Ogura, Yusuke Watanabe, Craig D Millar, Michael Hofreiter, Craig Smith, Sara Mirmoeini and David M Lambert

    Citation: BMC Evolutionary Biology 2014 14:75

    Content type: Research article

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  34. Phenylalanine ammonia-lyase (PAL; E.C.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the prod...

    Authors: Zhihua Wu, Songtao Gui, Shuzhen Wang and Yi Ding

    Citation: BMC Evolutionary Biology 2014 14:100

    Content type: Research article

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  35. Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed ...

    Authors: Jingjing Du, Sarah Z Dungan, Amir Sabouhanian and Belinda SW Chang

    Citation: BMC Evolutionary Biology 2014 14:96

    Content type: Research article

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  36. Many studies have found functional RNA secondary structures are selectively conserved among species. But, the effect of RNA structure selection on coding sequence evolution remains unknown. To address this pro...

    Authors: Wanjun Gu, Musheng Li, Yuming Xu, Ting Wang, Jae-Hong Ko and Tong Zhou

    Citation: BMC Evolutionary Biology 2014 14:87

    Content type: Research article

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  37. Reactive carbonyl species (RCS), such as methylglyoxal (MG) and glyoxal (GO), are synthesized as toxic metabolites in living systems. Mechanisms of RCS detoxification include the glutathione (GSH)-dependent sy...

    Authors: Qiaoqiao Zhao, Yang Su, Zhikang Wang, Caiping Chen, Tongsiyu Wu and Ying Huang

    Citation: BMC Evolutionary Biology 2014 14:86

    Content type: Research article

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  38. miRNAs are a major class of regulators of gene expression in metazoans. By targeting cognate mRNAs, miRNAs are involved in regulating most, if not all, biological processes in different cell and tissue types. ...

    Authors: Hossein Zare, Arkady Khodursky and Vittorio Sartorelli

    Citation: BMC Evolutionary Biology 2014 14:74

    Content type: Research article

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  39. Cytochrome P450 CYP2C19 metabolizes a wide range of pharmacologically active substances and a relatively small number of naturally occurring environmental toxins. Poor activity alleles of CYP2C19 are very frequen...

    Authors: Ramatoulie E Janha, Archibald Worwui, Kenneth J Linton, Seif O Shaheen, Fatoumatta Sisay-Joof and Robert T Walton

    Citation: BMC Evolutionary Biology 2014 14:71

    Content type: Research article

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  40. Horizontal gene transfer (HGT) has been suggested as the mechanism by which various plant parasitic nematode species have obtained genes important in parasitism. In particular, cellulase genes have been acquir...

    Authors: Juan E Palomares-Rius, Yuuri Hirooka, Isheng J Tsai, Hayato Masuya, Akina Hino, Natsumi Kanzaki, John T Jones and Taisei Kikuchi

    Citation: BMC Evolutionary Biology 2014 14:69

    Content type: Research article

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  41. Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in ...

    Authors: Christopher Blair, Kellie L Heckman, Amy L Russell and Anne D Yoder

    Citation: BMC Evolutionary Biology 2014 14:57

    Content type: Research article

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  42. The oriental fruit fly, Bactrocera dorsalis s.s., is one of the most important quarantine pests in many countries, including China. Although the oriental fruit fly has been investigated extensively, its origins a...

    Authors: Zhong-Zhen Wu, Hong-Mei Li, Shu-Ying Bin, Jun Ma, Hua-Liang He, Xian-Feng Li, Fei-Liang Gong and Jin-Tian Lin

    Citation: BMC Evolutionary Biology 2014 14:55

    Content type: Research article

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  43. Functionality of the tetrameric hemoglobin molecule seems to be determined by a few amino acids located in key positions. Oxygen binding encompasses structural changes at the interfaces between the α1β2 and α2...

    Authors: Øivind Andersen, Maria Cristina De Rosa, Prakash Yadav, Davide Pirolli, Jorge MO Fernandes, Paul R Berg, Sissel Jentoft and Carl Andrè

    Citation: BMC Evolutionary Biology 2014 14:54

    Content type: Research article

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  44. Pollen donor compositions differ during the early stages of reproduction due to various selection mechanisms. In addition, ovules linearly ordered within a fruit have different probabilities of reaching maturi...

    Authors: Cun-Quan Yuan, Yu-Han Sun, Yun-Fei Li, Ke-Qi Zhao, Rui-Yang Hu and Yun Li

    Citation: BMC Evolutionary Biology 2014 14:53

    Content type: Research article

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