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Download Special Issue BioMed Research International Molecular Phylogenetics 2016 Guest Editors: Vassily Lyubetsky, William H. Piel, and Peter F. Stadler Molecular Phylogenetics 2016 BioMed Research International Molecular Phylogenetics 2016 Guest Editors: Vassily Lyubetsky, William H. Piel, and Peter F. Stadler Copyright © 2016 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Molecular Phylogenetics 2016 Vassily Lyubetsky, William H. Piel, and Peter F. Stadler Volume 2016, Article ID 9029306, 2 pages Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes Olga L. Voronina, Marina S. Kunda, Natalia N. Ryzhova, Ekaterina I. Aksenova, Andrey N. Semenov, Yulia M. Romanova, and Alexandr L. Gintsburg Volume 2016, Article ID 6560534, 13 pages Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis Sofia Mindlin, Anatolii Petrenko, Anton Kurakov, Alexey Beletsky, Andrey Mardanov, and Mayya Petrova Volume 2016, Article ID 3970831, 9 pages Molecular Cloning and Characterization of Full-Length cDNA of Calmodulin Gene from Pacific Oyster Crassostrea gigas Xing-Xia Li, Wen-Chao Yu, Zhong-Qiang Cai, Cheng He, Na Wei, Xiao-Tong Wang, and Xi-Qing Yue Volume 2016, Article ID 5986519, 7 pages Phylogeographic Structure of a Tethyan Relict Capparis spinosa (Capparaceae) Traces Pleistocene Geologic and Climatic Changes in the Western Himalayas, Tianshan Mountains, and Adjacent Desert Regions Qian Wang, Ming-Li Zhang, and Lin-Ke Yin Volume 2016, Article ID 5792708, 13 pages Reconstructing the Phylogeny of Capsosiphon fulvescens (Ulotrichales, Chlorophyta) from Korea Based on rbcL and 18S rDNA Sequences Sang-Mi Sun, Seung Hwan Yang, Kirill S. Golokhvast, Bao Le, and Gyuhwa Chung Volume 2016, Article ID 1462916, 6 pages Molecular Typing Characteristic and Drug Susceptibility Analysis of Mycobacterium tuberculosis Isolates from Zigong, China Hai-Can Liu, Jian-Ping Deng, Hai-Yan Dong, Ti-Quan Xiao, Xiu-Qin Zhao, Zheng-Dong Zhang, Yi Jiang, Zhi-Guang Liu, Qun Li, and Kang-Lin Wan Volume 2016, Article ID 6790985, 7 pages Hindawi Publishing Corporation BioMed Research International Volume 2016, Article ID 9029306, 2 pages http://dx.doi.org/10.1155/2016/9029306 Editorial Molecular Phylogenetics 2016 Vassily Lyubetsky,1 William H. Piel,2 and Peter F. Stadler3 1 Russian Academy of Sciences, Moscow, Russia 2Yale-NUS College and National University of Singapore, Singapore 3Bioinformatics, Institute for Informatics, Leipzig University, Leipzig, Germany Correspondence should be addressed to Vassily Lyubetsky; [email protected] Received 5 December 2016; Accepted 12 December 2016 Copyright © 2016 Vassily Lyubetsky et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Knowledge of phylogeny is of fundamental importance for an unexpected result: at least for some organelles and taxa, the understanding evolution. It has become an indispensable genome and HCE structures, despite themselves containing tool in modern genomics as a framework for interpreting relatively little information, still adequately resolve the evo- genomes and metagenomes, for understanding the evolution lution of species. The HCEs identification is also important of genes, proteins, and noncoding RNAs, as well as gene in searching for promoters and regulatory elements that regulation by secondary RNA and protein structures, or characterize the functional evolution of the genome. for reconstructing ancestral genomes [1]. The era of next- Another fundamental question is the resolution of generation sequencing (NGS) brought about an influx of ancient taxa with obscure and recalcitrant relationships. A data but also posed new theoretical challenges, for example, classicexampleisthequestionofmonophylyoftheMesozoa, in reducing systematic error, insuring gene orthology, and specifically with respect to the parasitic phyla Orthonectida workingwithincompletedatasets[2].Thecontentsofthespe- and Dicyemida. This question is aggravated by a well-known cial issue exemplify the wide range of uses for phylogenetics: and yet still unsolved problem of long branch attraction. Of traditional medicines, climate change, functional genomics, particular interest is the statistical view on such questions that and microbial resistance to heavy metals and drugs. leads to the problem of a formal description of the classes of Some topics of modern phylogenetics are to be men- trees for a given supermatrix which are generated by popular tioned. Traditionally, studies of species evolution to a large programs such as PhyloBayes and RAxML. Also of interest is extent relied on the comparative analysis of genomic regions the development of statistical tests for monophyly within this coding for rRNAs and proteins apart from the analysis framework which retain accuracy despite increasingly large, of morphological characters. Later, analyses made use of genome-scale, datasets. regulatory elements and the structure of the genome as Using regulatory elements for phylogeny is a complex a whole. More recently, phylogenetic analyses are incor- problem. A key question is how to estimate statistical support porating ultraconserved elements (UCEs) and highly con- for phylogenetic signal derived from regulatory elements served elements (HCEs). Models of evolution of the genome that are highly dynamic and not easily aligned. Even sim- structure and HCE initially faced considerable algorithmic ple computation of distances between genes, leader genes, challenges, which gave rise to (often unnatural) constraints or hairpins in RNA can be nontrivial [5]. An alternative in these models even for conceptually simple tasks such approach is to extract phylogenetic signal from syntenic as the calculation of distance between two structures or patterns of regulatory elements [6], but this comes with its the identification of UCEs. These constraints are now being own computational challenges. addressed with fast and efficient solutions with no constraints Apart from classic molecular systematic applications to ontheunderlyingmodels[3,4].Theseapproacheshaveledto infer taxon phylogenies, the trend is to approach molecular 2 BioMed Research International and biodiversity assessment at different levels in various communities, for example, at the intraspecific level and with environmental samples, including systematic studies of bacterial and viral pathogenic agents. Molecular markers such as mobile elements are being developed and exploited in studies of population polymorphisms, and RNA secondary structures are used to detect signatures of selection. A historical profile of molecular phylogenetics with some extrapolations into the future, as well as a brief outline of hot spots in this field, can be found in this special issue [7]. We truly hope that these contributions will be of use to scientists in various areas in possibly helping them to find answers and pose new questions in their own research. Acknowledgments We gratefully thank all scientific reviewers who dedicated their time to evaluate submissions in this special issue. Vassily Lyubetsky William H. Piel Peter F. Stadler References [1] E. V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution, FT Press, 2011. [2] J. W. Wagele¨ and T. Bartolomaeus, Eds., Deep Metazoan Phylogeny: The Backbone of the Tree of Life: New Insights from Analyses of Molecules, Morphology, and Theory of Data Analysis, Walter de Gruyter, 2014. [3] L.I.Rubanov,A.V.Seliverstov,O.A.Zverkov,andV.A.Lyubet- sky, “A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata,” BMC Bioinformatics,vol.17,article385,2016. [4]V.Lyubetsky,R.Gershgorin,A.Seliverstov,andK.Gorbunov, “Algorithms for reconstruction of chromosomal structures,” BMC Bioinformatics,vol.17,article40,2016. [5]S.A.Korolev,O.A.Zverkov,A.V.Seliverstov,andV.A. Lyubetsky, “Ribosome reinitiation at leader peptides increases translation of bacterial proteins,” Biology Direct,vol.11,article no. 20, 2016. [6] O.A.Zverkov,A.V.Seliverstov,andV.A.Lyubetsky,“Adatabase of plastid protein families from red algae and apicomplexa and expression regulation of the moeB Gene,” BioMed Research International, vol. 2015, Article ID 510598, 5 pages, 2015. [7]V.Lyubetsky,W.H.Piel,andD.Quandt,“Currentadvancesin molecular phylogenetics,” BioMed Research International,vol. 2014,ArticleID596746,2pages,2014. Hindawi Publishing Corporation BioMed Research International Volume 2016, Article ID 6560534, 13 pages http://dx.doi.org/10.1155/2016/6560534 Research Article Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes Olga L. Voronina,1 Marina S. Kunda,1 Natalia N. Ryzhova,1 Ekaterina I. Aksenova,1 Andrey N. Semenov,1 Yulia M. Romanova,1,2 and Alexandr L. Gintsburg1,2 1 N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Gamaleya Street 18, Moscow 123098, Russia 2I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia Correspondence should be addressed to Olga L. Voronina;
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