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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 6 of 10

  1. 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 Published on:

  2. 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 Published on:

  3. 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 Published on:

  4. 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 Published on:

  5. 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 Published on:

  6. 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 Published on:

  7. 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 Published on:

  8. 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 Published on:

  9. 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 Published on:

  10. 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 Published on:

  11. 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 Published on:

  12. 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 Published on:

  14. 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 Published on:

  15. 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 Published on:

  16. 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 Published on:

  18. 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 Published on:

  19. 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 Published on:

  20. 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 Published on:

  21. 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 Published on:

  22. 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 Published on:

  23. 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 Published on:

  24. 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 Published on:

  26. 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 Published on:

  27. 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 Published on:

  28. 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 Published on:

  29. 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 Published on:

  30. The existence of introns in eukaryotic genes is believed to provide an evolutionary advantage by increasing protein diversity through exon shuffling and alternative splicing. However, this eukaryotic feature i...

    Authors: Olga Gorlova, Alexey Fedorov, Christopher Logothetis, Christopher Amos and Ivan Gorlov
    Citation: BMC Evolutionary Biology 2014 14:50
    Content type: Research article Published on:

  31. Poecilimon and Isophya are the largest genera of the tribe Barbitistini and among the most systematically complicated and evolutionarily intriguing groups of Palearctic tettigoniids. We examined the genomic organ...

    Authors: Beata Grzywacz, Dragan P Chobanov, Anna Maryańska-Nadachowska, Tatyana V Karamysheva, Klaus-Gerhard Heller and Elżbieta Warchałowska-Śliwa
    Citation: BMC Evolutionary Biology 2014 14:48
    Content type: Research article Published on:

  32. The GTPase eEF1A is the eukaryotic factor responsible for the essential, universal function of aminoacyl-tRNA delivery to the ribosome. Surprisingly, eEF1A is not universally present in eukaryotes, being repla...

    Authors: Gemma C Atkinson, Anton Kuzmenko, Ivan Chicherin, Axel Soosaar, Tanel Tenson, Martin Carr, Piotr Kamenski and Vasili Hauryliuk
    Citation: BMC Evolutionary Biology 2014 14:35
    Content type: Research article Published on:

  33. Spider silks are spectacular examples of phenotypic diversity arising from adaptive molecular evolution. An individual spider can produce an array of specialized silks, with the majority of constituent silk pr...

    Authors: R Crystal Chaw, Yonghui Zhao, Jie Wei, Nadia A Ayoub, Ryan Allen, Kirmanj Atrushi and Cheryl Y Hayashi
    Citation: BMC Evolutionary Biology 2014 14:31
    Content type: Research article Published on:

  34. The neuropeptide Kiss and its receptor KissR are key-actors in the brain control of reproduction in mammals, where they are responsible for the stimulation of the activity of GnRH neurones. Investigation in ot...

    Authors: Jérémy Pasquier, Anne-Gaëlle Lafont, Karine Rousseau, Bruno Quérat, Philippe Chemineau and Sylvie Dufour
    Citation: BMC Evolutionary Biology 2014 14:30
    Content type: Research article Published on:

  36. Methionine adenosyltransferase (MAT) is a ubiquitous essential enzyme that, in eukaryotes, occurs in two relatively divergent paralogues: MAT and MATX. MATX has a punctate distribution across the tree of eukar...

    Authors: Jana Szabová, Naoji Yubuki, Brian S Leander, Richard E Triemer and Vladimír Hampl
    Citation: BMC Evolutionary Biology 2014 14:25
    Content type: Research article Published on:

  37. Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the ...

    Authors: Han Ming Gan, Mark B Schultz and Christopher M Austin
    Citation: BMC Evolutionary Biology 2014 14:19
    Content type: Research article Published on:

  38. The recent availability of sequenced genomes from a broad array of chordates (cephalochordates, urochordates and vertebrates) has allowed us to systematically analyze the evolution of uroplakins: tetraspanins ...

    Authors: Rob DeSalle, Javier U Chicote, Tung-Tien Sun and Antonio Garcia-España
    Citation: BMC Evolutionary Biology 2014 14:13
    Content type: Research article Published on:

  39. Nitrogen uptake, reallocation within the plant, and between subcellular compartments involves ammonium, nitrate and peptide transporters. Ammonium transporters are separated into two distinct families (AMT1 an...

    Authors: Neil JJB von Wittgenstein, Cuong H Le, Barbara J Hawkins and Jürgen Ehlting
    Citation: BMC Evolutionary Biology 2014 14:11
    Content type: Research article Published on:

  40. The molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. In this...

    Authors: Lihuan Cao, Fang Chen, Xianmei Yang, Weijin Xu, Jun Xie and Long Yu
    Citation: BMC Evolutionary Biology 2014 14:10
    Content type: Research article Published on:

  41. Ticks are blood-sucking arthropods and a primary function of tick salivary proteins is to counteract the host’s immune response. Tick salivary Kunitz-domain proteins perform multiple functions within the feedi...

    Authors: Alexandra Schwarz, Alejandro Cabezas-Cruz, Jan Kopecký and James J Valdés
    Citation: BMC Evolutionary Biology 2014 14:4
    Content type: Research article Published on:

  42. New World leaf-nosed bats, Phyllostomidae, represent a lineage of Chiroptera marked by unprecedented morphological/ecological diversity and extensive intergeneric chromosomal reorganization. There are still di...

    Authors: Cibele G Sotero-Caio, Marianne Volleth, Lauren S Gollahon, Beiyuan Fu, William Cheng, Bee L Ng, Fengtang Yang and Robert J Baker
    Citation: BMC Evolutionary Biology 2013 13:276
    Content type: Research article Published on:

  43. Fatty acids, a considerable fraction of lipid molecules, participate in fundamental physiological processes. They undergo activation into their corresponding CoA esters for oxidation or esterification into com...

    Authors: Mónica Lopes-Marques, Isabel Cunha, Maria Armanda Reis-Henriques, Miguel M Santos and L Filipe C Castro
    Citation: BMC Evolutionary Biology 2013 13:271
    Content type: Research article Published on:

  44. Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. However, the origin and evolution of most plasmids remains unclear, especially for megaplasmids. Strain...

    Authors: Jinshui Zheng, Donghai Peng, Lifang Ruan and Ming Sun
    Citation: BMC Evolutionary Biology 2013 13:262
    Content type: Research article Published on:

  45. Classical major histocompatibility complex (MHC) class II molecules play an essential role in presenting peptide antigens to CD4+ T lymphocytes in the acquired immune system. The non-classical class II DM molecul...

    Authors: Johannes M Dijkstra, Unni Grimholt, Jong Leong, Ben F Koop and Keiichiro Hashimoto
    Citation: BMC Evolutionary Biology 2013 13:260
    Content type: Research article Published on:

  46. Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data ...

    Authors: Abdul Jabbar, Ian Beveridge, Namitha Mohandas, Neil B Chilton, D Timothy J Littlewood, Aaron R Jex and Robin B Gasser
    Citation: BMC Evolutionary Biology 2013 13:259
    Content type: Research article Published on:

  47. The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and...

    Authors: Janine E Deakin, Margaret L Delbridge, Edda Koina, Nerida Harley, Amber E Alsop, Chenwei Wang, Vidushi S Patel and Jennifer A Marshall Graves
    Citation: BMC Evolutionary Biology 2013 13:258
    Content type: Research article Published on:

  50. Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these trai...

    Authors: Claire C Morgan, Ann M Mc Cartney, Mark TA Donoghue, Noeleen B Loughran, Charles Spillane, Emma C Teeling and Mary J O’Connell
    Citation: BMC Evolutionary Biology 2013 13:251
    Content type: Research article Published on:
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