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Start Over Author "Maria V. Sharakhova" Journal genome biology
3 results on '"Maria V. Sharakhova"'

1. Improved reference genome of the arboviral vector Aedes albopictus

Author

Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna-Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Dmitry A. Karagodin, Jeremy Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos A. Papathanos, Ronald P. Van Rij, Omar S. Akbari, Jeffrey Powell, Adam M. Phillippy, and Mariangela Bonizzoni

Subjects
Ae. albopictus, Genome, miRNAs, piRNA clusters, Viral integrations, Immunity, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Published
2020
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2. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Author

Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna-Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Dmitry A. Karagodin, Jeremy Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos A. Papathanos, Ronald P. Van Rij, Omar S. Akbari, Jeffrey Powell, Adam M. Phillippy, and Mariangela Bonizzoni

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Published
2021
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3. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Author

José M. C. Ribeiro, Maria V. Sharakhova, Marta Tojo, Phillip George, Scott J. Emrich, Robert M. Waterhouse, Xiaofang Jiang, Ryan C. Kennedy, Michael A. Riehle, Bo Wang, Chioma Oringanje, Kenneth D. Vernick, Victoria L.M. Davidson, A. Brantley Hall, Kristin Michel, Ashley Peery, Anthony A. James, Gareth Maslen, Shirley Luckhart, Robert E. Settlage, Nazzy Pakpour, Aleksey Komissarov, Yumin Qi, Zhijian Tu, Daniel Lawson, Igor V. Sharakhov, Xiao Guang Chen, Karin Eiglmeier, Maria F. Unger, Michelle M. Riehle, Shrinivasrao P. Mane, Jose M. C. Tubio, Yogesh S. Shouche, Atashi Sharma, Peter Arensburger, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Waterhouse, Robert, Department of Biochemistry [Blacksburg], Virginia Tech [Blacksburg], Program of Genetics, Bioinformatics, and Computational Biology [Blacksburg] (GBCB), Department of Entomology [Blacksburg], Department of Pathogen Biology, Southern Medical University [Guangzhou], Department of Genetic Medicine and Development, University of Geneva Medical School, University of Geneva Medical School-University of Geneva Medical School, Swiss Institute of Bioinformatics [Genève] (SIB), Computer Science and Artificial Intelligence Laboratory [Cambridge] (CSAIL), Massachusetts Institute of Technology (MIT), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University (SPbU), Institute of Cytology, Russian Academy of Sciences [Moscow] (RAS), Department of Microbiology, University of Minnesota, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System-University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, National Center for Cell Science, Pune University, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Department of Medical Microbiology and Immunology, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Department of Biological Sciences [Pomona], California State Polytechnic University [Pomona] (CAL POLY POMONA), Division of Biology, Kansas State University, Génétique et Génomique des Insectes vecteurs, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Department of Computer Science and Engineering, University of Notre Dame [Indiana] (UND), Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] (UC San Francisco), Virginia Bioinformatics Institute, Department of Entomology, University of Arizona, Department of Physiology, School of Medicine – CIMUS, Instituto de Investigaciones Sanitarias, Universidade de Santiago de Compostela [Spain] (USC )-Universidade de Santiago de Compostela [Spain] (USC ), The Wellcome Trust Sanger Institute [Cambridge], Department of Biological Sciences [Notre Dame], Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institutes of Health, Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California [Irvine] (UC Irvine), Fralin Life Science Institute and the Virginia Experimental Station, NIH grants AI77680 and AI105575 to ZT, AI094289 and AI099528 to IVS, AI29746 to AAJ, AI095842 to KM, AI073745 toMAR, AI080799 and AI078183 to SL, and AI042361 and AI073685 to KDV., AP and IVS are supported in part by the Institute for Critical Technology and Applied Science and the NSF award 0850198., RMW is supported by Marie Curie International Outgoing Fellowship PIOF-GA-2011-303312., XC is supported by GDUPS (2009)., This work was also supported in part by NSF grant CNS-0960081, This work was also supported in part the HokieSpeed and BlueRidge supercomputers atVirginia Tech., YS thanks the Department of Biotechnology, Governmentof India for the financial support., University of California-University of California, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of California [San Francisco] (UCSF), and University of California [Irvine] (UCI)

Subjects
Urban Population, Genome, Insect, Retrotransposon, Insect/genetics, 2.2 Factors relating to physical environment, Genome, Anopheles/genetics/metabolism, 0302 clinical medicine, 2.2 Factors relating to the physical environment, Cluster Analysis, ddc:576.5, Aetiology, Phylogeny, Genetics, 0303 health sciences, Anopheles, Chromosome Mapping, Single Nucleotide, Biological Sciences, 3. Good health, Infectious Diseases, Insect Proteins, Infection, Sequence Analysis, Biotechnology, Evolution, Bioinformatics, Interspersed repeat, Biology, Polymorphism, Single Nucleotide, Synteny, Chromosomes, Evolution, Molecular, 03 medical and health sciences, Rare Diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Information and Computing Sciences, parasitic diseases, Animals, Humans, Polymorphism, Anopheles stephensi, 030304 developmental biology, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, Autosome, Research, fungi, Human Genome, Molecular, DNA, Sequence Analysis, DNA, biology.organism_classification, Chromosomes, Insect, Insect Vectors, Malaria, Vector-Borne Diseases, Good Health and Well Being, Evolutionary biology, Malaria/transmission, Transcriptome, Insect Proteins/genetics/metabolism, Insect Vectors/genetics, Insect, Environmental Sciences, 030217 neurology & neurosurgery
Abstract

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions., National Science Foundation (U.S.) (Grant CNS-0960081)

Published
2014
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