ALBERT

Description: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Misof, Bernhard -- Liu, Shanlin -- Meusemann, Karen -- Peters, Ralph S -- Donath, Alexander -- Mayer, Christoph -- Frandsen, Paul B -- Ware, Jessica -- Flouri, Tomas -- Beutel, Rolf G -- Niehuis, Oliver -- Petersen, Malte -- Izquierdo-Carrasco, Fernando -- Wappler, Torsten -- Rust, Jes -- Aberer, Andre J -- Aspock, Ulrike -- Aspock, Horst -- Bartel, Daniela -- Blanke, Alexander -- Berger, Simon -- Bohm, Alexander -- Buckley, Thomas R -- Calcott, Brett -- Chen, Junqing -- Friedrich, Frank -- Fukui, Makiko -- Fujita, Mari -- Greve, Carola -- Grobe, Peter -- Gu, Shengchang -- Huang, Ying -- Jermiin, Lars S -- Kawahara, Akito Y -- Krogmann, Lars -- Kubiak, Martin -- Lanfear, Robert -- Letsch, Harald -- Li, Yiyuan -- Li, Zhenyu -- Li, Jiguang -- Lu, Haorong -- Machida, Ryuichiro -- Mashimo, Yuta -- Kapli, Pashalia -- McKenna, Duane D -- Meng, Guanliang -- Nakagaki, Yasutaka -- Navarrete-Heredia, Jose Luis -- Ott, Michael -- Ou, Yanxiang -- Pass, Gunther -- Podsiadlowski, Lars -- Pohl, Hans -- von Reumont, Bjorn M -- Schutte, Kai -- Sekiya, Kaoru -- Shimizu, Shota -- Slipinski, Adam -- Stamatakis, Alexandros -- Song, Wenhui -- Su, Xu -- Szucsich, Nikolaus U -- Tan, Meihua -- Tan, Xuemei -- Tang, Min -- Tang, Jingbo -- Timelthaler, Gerald -- Tomizuka, Shigekazu -- Trautwein, Michelle -- Tong, Xiaoli -- Uchifune, Toshiki -- Walzl, Manfred G -- Wiegmann, Brian M -- Wilbrandt, Jeanne -- Wipfler, Benjamin -- Wong, Thomas K F -- Wu, Qiong -- Wu, Gengxiong -- Xie, Yinlong -- Yang, Shenzhou -- Yang, Qing -- Yeates, David K -- Yoshizawa, Kazunori -- Zhang, Qing -- Zhang, Rui -- Zhang, Wenwei -- Zhang, Yunhui -- Zhao, Jing -- Zhou, Chengran -- Zhou, Lili -- Ziesmann, Tanja -- Zou, Shijie -- Li, Yingrui -- Xu, Xun -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Wang, Jun -- Kjer, Karl M -- Zhou, Xin -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):763-7. doi: 10.1126/science.1257570. Epub 2014 Nov 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia. ; Abteilung Arthropoda, Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. ; Department of Entomology, Rutgers University, New Brunswick, NJ 08854, USA. ; Department of Biological Sciences, Rutgers University, Newark, NJ 08854, USA. ; Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. ; Institut fur Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Jena, FSU Jena, Germany. ; Steinmann-Institut, Bereich Palaontologie, Universitat Bonn, Germany. ; 2. Zoologische Abteilung (Insekten), Naturhistorisches Museum Wien, Vienna, Austria. Department of Integrative Zoology, Universitat Wien, Vienna, Austria. ; Institut fur Spezifische Prophylaxe und Tropenmedizin, Medizinische Parasitologie, Medizinische Universitat Wien (MUW), Vienna, Austria. ; Department of Integrative Zoology, Universitat Wien, Vienna, Austria. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. ; Manaaki Whenua Landcare Research, Auckland, New Zealand. ; Center for Advanced Modeling, Emergency Medicine Department, Johns Hopkins University, Baltimore, MD 21209, USA. ; BGI-Shenzhen, China. ; Biozentrum Grindel und Zoologisches Museum, Universitat Hamburg, Hamburg, Germany. ; Evolutionary Morphology Laboratory, Graduate School of Science and Engineering, Ehime University, Japan. ; Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. ; Land and Water Flagship, CSIRO, Canberra, ACT, Australia. ; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. ; Entomology, Staatliches Museum fur Naturkunde Stuttgart (SMNS), Germany. ; Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia. National Evolutionary Synthesis Center, Durham, NC 27705, USA. Department of Biological Sciences, Macquarie University, Sydney, Australia. ; Department fur Botanik und Biodiversitatsforschung, Universitat Wien, Vienna, Austria. ; Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. Natural History Museum of Crete, University of Crete, Post Office Box 2208, Gr-71409, Iraklio, and Biology Department, University of Crete, Iraklio, Crete, Greece. ; Department of Biological Sciences and Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152, USA. ; Centro Universitario de Ciencias Biologicas y Agropecuarias, Centro de Estudios en Zoologia, Universidad de Guadalajara, Zapopan, Jalisco, Mexico. ; Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities, Garching, Germany. ; Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Bonn, Germany. ; Department of Life Sciences, The Natural History Museum London, London, UK. ; Abteilung Entomologie, Biozentrum Grindel und Zoologisches Museum, Universitat Hamburg, Hamburg, Germany. ; Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia. ; Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. Fakultat fur Informatik, Karlsruher Institut fur Technologie, Karlsruhe, Germany. ; California Academy of Sciences, San Francisco, CA 94118, USA. ; Department of Entomology, College of Natural Resources and Environment, South China Agricultural University, China. ; Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. Yokosuka City Museum, Yokosuka, Kanagawa, Japan. ; Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA. ; Systematic Entomology, Hokkaido University, Sapporo, Japan. ; BGI-Shenzhen, China. Department of Biology, University of Copenhagen, Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, China. Department of Medicine, University of Hong Kong, Hong Kong. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn. ; Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08854, USA. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25378627" target="_blank"〉PubMed〈/a〉

Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.

Description: Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here, we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between nonsister species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380269/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380269/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fontaine, Michael C -- Pease, James B -- Steele, Aaron -- Waterhouse, Robert M -- Neafsey, Daniel E -- Sharakhov, Igor V -- Jiang, Xiaofang -- Hall, Andrew B -- Catteruccia, Flaminia -- Kakani, Evdoxia -- Mitchell, Sara N -- Wu, Yi-Chieh -- Smith, Hilary A -- Love, R Rebecca -- Lawniczak, Mara K -- Slotman, Michel A -- Emrich, Scott J -- Hahn, Matthew W -- Besansky, Nora J -- HHSN272200900039C/PHS HHS/ -- R01 AI063508/AI/NIAID NIH HHS/ -- R01 AI076584/AI/NIAID NIH HHS/ -- R01 AI104956/AI/NIAID NIH HHS/ -- R01AI076584/AI/NIAID NIH HHS/ -- R01AI085079/AI/NIAID NIH HHS/ -- R01AI104956/AI/NIAID NIH HHS/ -- R21 AI101459/AI/NIAID NIH HHS/ -- R21AI094289/AI/NIAID NIH HHS/ -- R21AI099528/AI/NIAID NIH HHS/ -- R21AI101459/AI/NIAID NIH HHS/ -- T32GM007757/GM/NIGMS NIH HHS/ -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2015 Jan 2;347(6217):1258524. doi: 10.1126/science.1258524. Epub 2014 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA. ; Department of Biology, Indiana University, Bloomington, IN 47405, USA. ; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. ; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland. ; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. ; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. ; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. ; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Universita degli Studi di Perugia, Perugia, Italy. ; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. ; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. ; Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. ; Department of Entomology, Texas A&M University, College Station, TX 77843, USA. ; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA. Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. ; Department of Biology, Indiana University, Bloomington, IN 47405, USA. School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA. mwh@indiana.edu nbesansk@nd.edu. ; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA. mwh@indiana.edu nbesansk@nd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25431491" target="_blank"〉PubMed〈/a〉

Description: The genome-wide distribution patterns of the ‘6th base’ 5-hydroxymethylcytosine (5hmC) in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arrays. However, it has been challenging to directly compare different data sets and samples using data generated by this method. Here, we report a new comparative hMeDIP-seq method, which involves barcoding different input DNA samples at the start and then performing hMeDIP-seq for multiple samples in one hMeDIP reaction. This approach extends the barcode technology from simply multiplexing the DNA deep sequencing outcome and provides significant advantages for quantitative control of all experimental steps, from unbiased hMeDIP to deep sequencing data analysis. Using this improved method, we profiled and compared the DNA hydroxymethylomes of mouse ES cells (ESCs) and mouse ESC-derived neural progenitor cells (NPCs). We identified differentially hydroxymethylated regions (DHMRs) between ESCs and NPCs and uncovered an intricate relationship between the alteration of DNA hydroxymethylation and changes in gene expression during neural lineage commitment of ESCs. Presumably, the DHMRs between ESCs and NPCs uncovered by this approach may provide new insight into the function of 5hmC in gene regulation and neural differentiation. Thus, this newly developed comparative hMeDIP-seq method provides a cost-effective and user-friendly strategy for direct genome-wide comparison of DNA hydroxymethylation across multiple samples, lending significant biological, physiological and clinical implications.