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Bioinformatics of Genome Regulation and Systems Biology BIOINFORMATICS OF GENOME REGULATION AND SYSTEMS BIOLOGY EDITED BY : Yuriy L. Orlov and Ancha Baranova PUBLISHED IN : Frontiers in Genetics and Frontiers in Plant Science Frontiers eBook Copyright Statement About Frontiers The copyright in the text of individual articles in this eBook is the Frontiers is more than just an open-access publisher of scholarly articles: it is a property of their respective authors or their respective institutions or pioneering approach to the world of academia, radically improving the way scholarly funders. The copyright in graphics research is managed. The grand vision of Frontiers is a world where all people have and images within each article may be subject to copyright of other an equal opportunity to seek, share and generate knowledge. Frontiers provides parties. 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All copyright, and all rights therein, What are Frontiers Research Topics? are protected by national and Frontiers Research Topics are very popular trademarks of the Frontiers Journals international copyright laws. The above represents a summary only. Series: they are collections of at least ten articles, all centered on a particular subject. For further information please read With their unique mix of varied contributions from Original Research to Review Frontiers’ Conditions for Website Use and Copyright Statement, and Articles, Frontiers Research Topics unify the most influential researchers, the latest the applicable CC-BY licence. key findings and historical advances in a hot research area! Find out more on how ISSN 1664-8714 to host your own Frontiers Research Topic or contribute to one as an author by ISBN 978-2-88966-014-8 DOI 10.3389/978-2-88966-014-8 contacting the Frontiers Editorial Office: [email protected] Frontiers in Genetics 1 September 2020 | Bioinformatics of Genome Regulation BIOINFORMATICS OF GENOME REGULATION AND SYSTEMS BIOLOGY Topic Editors: Yuriy L. Orlov, First Moscow State Medical University, Russia Ancha Baranova, George Mason University, United States Citation: Orlov, Y. L., Baranova, A., eds. (2020). Bioinformatics of Genome Regulation and Systems Biology. Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88966-014-8 Frontiers in Genetics 2 September 2020 | Bioinformatics of Genome Regulation fgene-10-00443 May 23, 2019 Time: 16:36 # 1 ORIGINAL RESEARCH published: 24 May 2019 doi: 10.3389/fgene.2019.00443 Dicyemida and Orthonectida: Two Stories of Body Plan Simplification Oleg A. Zverkov1, Kirill V. Mikhailov1,2, Sergey V. Isaev1,3, Leonid Y. Rusin1,4, Olga V. Popova2, Maria D. Logacheva1,2,5, Alexey A. Penin1,2, Leonid L. Moroz6, Yuri V. Panchin1,2, Vassily A. Lyubetsky1 and Vladimir V. Aleoshin1,2* 1 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 2 A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 3 Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 4 Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 5 Skolkovo Institute of Science and Technology, Moscow, Russia, 6 Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan Edited by: development and body patterning. Acquiring genomic data for dicyemids, however, Ancha Baranova, George Mason University, remains a challenge due to complex genome rearrangements including chromatin United States diminution and generation of extrachromosomal circular DNAs, which are reported to Reviewed by: occur during the development of somatic cells. We performed genomic sequencing Andreas Hejnol, of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. University of Bergen, Norway Denis Baurain, Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and University of Liège, Belgium many other protein families have undergone a massive reduction in dicyemids compared Max Telford, University College London, to other animals. There is also apparent reduction of the bilaterian gene complements United Kingdom encoding components of the neuromuscular systems. We constructed and analyzed *Correspondence: a large dataset of predicted orthologous proteins from three species of Dicyema and Vladimir V. Aleoshin a set of spiralian animals including the newly sequenced genome of the orthonectid [email protected] Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. Specialty section: In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa This article was submitted to (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting Evolutionary and Population Genetics, a section of the journal that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic Frontiers in Genetics simplification of body plans in dicyemids and orthonectids, as well as their intricate Received: 03 November 2018 life cycles that combine metagenesis and heterogony, evolved independently in these Accepted: 29 April 2019 Published: 24 May 2019 two lineages. Citation: Keywords: Mesozoa, Dicyemida, Orthonectida, genome, mitochondrial DNA, phylogeny Zverkov OA, Mikhailov KV, Isaev SV, Rusin LY, Popova OV, Logacheva MD, Penin AA, Moroz LL, INTRODUCTION Panchin YV, Lyubetsky VA and Aleoshin VV (2019) Dicyemida and Orthonectida: Two Stories In spite of more than one hundred years of studies, the evolutionary relationships of the Mesozoa of Body Plan Simplification. are still elusive. The name of this taxon reflects the traditional view of mesozoans as organisms Front. Genet. 10:443. with intermediate organization between unicellular protozoans and multicellular metazoans (Van doi: 10.3389/fgene.2019.00443 Beneden, 1876; Hyman, 1940). Indeed, the two groups of microscopic parasitic invertebrates, Frontiers in Genetics | www.frontiersin.org 2141 May 2019 | Volume 10 | Article 443 fgene-10-00443 May 23, 2019 Time: 16:36 # 2 Zverkov et al. Dicyemida and Orthonectida: Two Stories the Dicyemida, and Orthonectida, display a remarkably simple and potentially prone to long branch attraction artifacts. morphological organization and a nearly complete absence Complicating the matter is the uncertainty in relationships of tissues and organs (Malakhov, 1990). Adult dicyemids between other spiralian taxa, including the Annelida, Mollusca, inhabit the renal sacs
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