Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).
Identifieur interne : 000254 ( PubMed/Corpus ); précédent : 000253; suivant : 000255Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).
Auteurs : John L. Williams ; Daniela Iamartino ; Kim D. Pruitt ; Tad Sonstegard ; Timothy P L. Smith ; Wai Yee Low ; Tommaso Biagini ; Lorenzo Bomba ; Stefano Capomaccio ; Bianca Castiglioni ; Angelo Coletta ; Federica Corrado ; Fabrizio Ferré ; Leopoldo Iannuzzi ; Cynthia Lawley ; Nicol Macciotta ; Matthew Mcclure ; Giordano Mancini ; Donato Matassino ; Raffaele Mazza ; Marco Milanesi ; Bianca Moioli ; Nicola Morandi ; Luigi Ramunno ; Vincenzo Peretti ; Fabio Pilla ; Paola Ramelli ; Steven Schroeder ; Francesco Strozzi ; Francoise Thibaud-Nissen ; Luigi Zicarelli ; Paolo Ajmone-Marsan ; Alessio Valentini ; Giovanni Chillemi ; Aleksey ZiminSource :
- GigaScience [ 2047-217X ] ; 2017.
Abstract
Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and is necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 species of domestic water buffalo, the river (2 n = 50) and the swamp (2 n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366 983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21 398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues and identified 21 711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.
DOI: 10.1093/gigascience/gix088
PubMed: 29048578
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).</title><author><name sortKey="Williams, John L" sort="Williams, John L" uniqKey="Williams J" first="John L" last="Williams">John L. Williams</name><affiliation><nlm:affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Iamartino, Daniela" sort="Iamartino, Daniela" uniqKey="Iamartino D" first="Daniela" last="Iamartino">Daniela Iamartino</name><affiliation><nlm:affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pruitt, Kim D" sort="Pruitt, Kim D" uniqKey="Pruitt K" first="Kim D" last="Pruitt">Kim D. Pruitt</name><affiliation><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sonstegard, Tad" sort="Sonstegard, Tad" uniqKey="Sonstegard T" first="Tad" last="Sonstegard">Tad Sonstegard</name><affiliation><nlm:affiliation>Recombinetics, 1246 University Ave W, St Paul, MN 55104, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Smith, Timothy P L" sort="Smith, Timothy P L" uniqKey="Smith T" first="Timothy P L" last="Smith">Timothy P L. Smith</name><affiliation><nlm:affiliation>USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Low, Wai Yee" sort="Low, Wai Yee" uniqKey="Low W" first="Wai Yee" last="Low">Wai Yee Low</name><affiliation><nlm:affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Biagini, Tommaso" sort="Biagini, Tommaso" uniqKey="Biagini T" first="Tommaso" last="Biagini">Tommaso Biagini</name><affiliation><nlm:affiliation>IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, S. Giovanni Rotondo, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Bomba, Lorenzo" sort="Bomba, Lorenzo" uniqKey="Bomba L" first="Lorenzo" last="Bomba">Lorenzo Bomba</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Capomaccio, Stefano" sort="Capomaccio, Stefano" uniqKey="Capomaccio S" first="Stefano" last="Capomaccio">Stefano Capomaccio</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Castiglioni, Bianca" sort="Castiglioni, Bianca" uniqKey="Castiglioni B" first="Bianca" last="Castiglioni">Bianca Castiglioni</name><affiliation><nlm:affiliation>CNR, Istituto di Biologia e Biotecnologia Agraria Via Einstein, 26900 Lodi, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Coletta, Angelo" sort="Coletta, Angelo" uniqKey="Coletta A" first="Angelo" last="Coletta">Angelo Coletta</name><affiliation><nlm:affiliation>ANASB Associazione Nazionale Allevatori Specie Bufalina, Centuran, Caserta, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Corrado, Federica" sort="Corrado, Federica" uniqKey="Corrado F" first="Federica" last="Corrado">Federica Corrado</name><affiliation><nlm:affiliation>IZSM, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2-80055, Portici (NA), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ferre, Fabrizio" sort="Ferre, Fabrizio" uniqKey="Ferre F" first="Fabrizio" last="Ferré">Fabrizio Ferré</name><affiliation><nlm:affiliation>Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 8/2, 40126 Bologna, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Iannuzzi, Leopoldo" sort="Iannuzzi, Leopoldo" uniqKey="Iannuzzi L" first="Leopoldo" last="Iannuzzi">Leopoldo Iannuzzi</name><affiliation><nlm:affiliation>CNR, Istituto Per Il Sistema Produzione Animale In Ambiente Mediterraneo, Via Argine, 1085, 80147 Napoli, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Lawley, Cynthia" sort="Lawley, Cynthia" uniqKey="Lawley C" first="Cynthia" last="Lawley">Cynthia Lawley</name><affiliation><nlm:affiliation>Illumina, Inc. 499 Illinois St. Suite 210, San Francisco, CA 94158, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Macciotta, Nicol" sort="Macciotta, Nicol" uniqKey="Macciotta N" first="Nicol" last="Macciotta">Nicol Macciotta</name><affiliation><nlm:affiliation>Università degli Studi di Sassari, Piazza Università 21, 07100 Sassari, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Mcclure, Matthew" sort="Mcclure, Matthew" uniqKey="Mcclure M" first="Matthew" last="Mcclure">Matthew Mcclure</name><affiliation><nlm:affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mancini, Giordano" sort="Mancini, Giordano" uniqKey="Mancini G" first="Giordano" last="Mancini">Giordano Mancini</name><affiliation><nlm:affiliation>Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Matassino, Donato" sort="Matassino, Donato" uniqKey="Matassino D" first="Donato" last="Matassino">Donato Matassino</name><affiliation><nlm:affiliation>ConSDABI, Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Contrada Piano Cappelle, Benevento (BN), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Mazza, Raffaele" sort="Mazza, Raffaele" uniqKey="Mazza R" first="Raffaele" last="Mazza">Raffaele Mazza</name><affiliation><nlm:affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Milanesi, Marco" sort="Milanesi, Marco" uniqKey="Milanesi M" first="Marco" last="Milanesi">Marco Milanesi</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Moioli, Bianca" sort="Moioli, Bianca" uniqKey="Moioli B" first="Bianca" last="Moioli">Bianca Moioli</name><affiliation><nlm:affiliation>CRA Centro di Ricerca per la Produzione delle Carni ed il Miglioramento Genetico, Via Salaria 31, 00015, Montorotondo, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Morandi, Nicola" sort="Morandi, Nicola" uniqKey="Morandi N" first="Nicola" last="Morandi">Nicola Morandi</name><affiliation><nlm:affiliation>Merial Italia, via Lorenzini 8, 20139 Milano, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ramunno, Luigi" sort="Ramunno, Luigi" uniqKey="Ramunno L" first="Luigi" last="Ramunno">Luigi Ramunno</name><affiliation><nlm:affiliation>Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Peretti, Vincenzo" sort="Peretti, Vincenzo" uniqKey="Peretti V" first="Vincenzo" last="Peretti">Vincenzo Peretti</name><affiliation><nlm:affiliation>Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Napoli, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pilla, Fabio" sort="Pilla, Fabio" uniqKey="Pilla F" first="Fabio" last="Pilla">Fabio Pilla</name><affiliation><nlm:affiliation>Department of Agriculture, Environment and Food, University of Molise.</nlm:affiliation></affiliation></author><author><name sortKey="Ramelli, Paola" sort="Ramelli, Paola" uniqKey="Ramelli P" first="Paola" last="Ramelli">Paola Ramelli</name><affiliation><nlm:affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Schroeder, Steven" sort="Schroeder, Steven" uniqKey="Schroeder S" first="Steven" last="Schroeder">Steven Schroeder</name><affiliation><nlm:affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Strozzi, Francesco" sort="Strozzi, Francesco" uniqKey="Strozzi F" first="Francesco" last="Strozzi">Francesco Strozzi</name><affiliation><nlm:affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Thibaud Nissen, Francoise" sort="Thibaud Nissen, Francoise" uniqKey="Thibaud Nissen F" first="Francoise" last="Thibaud-Nissen">Francoise Thibaud-Nissen</name><affiliation><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zicarelli, Luigi" sort="Zicarelli, Luigi" uniqKey="Zicarelli L" first="Luigi" last="Zicarelli">Luigi Zicarelli</name><affiliation><nlm:affiliation>Department of Agriculture, Environment and Food, University of Molise.</nlm:affiliation></affiliation></author><author><name sortKey="Ajmone Marsan, Paolo" sort="Ajmone Marsan, Paolo" uniqKey="Ajmone Marsan P" first="Paolo" last="Ajmone-Marsan">Paolo Ajmone-Marsan</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Valentini, Alessio" sort="Valentini, Alessio" uniqKey="Valentini A" first="Alessio" last="Valentini">Alessio Valentini</name><affiliation><nlm:affiliation>Universit à della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Chillemi, Giovanni" sort="Chillemi, Giovanni" uniqKey="Chillemi G" first="Giovanni" last="Chillemi">Giovanni Chillemi</name><affiliation><nlm:affiliation>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185, Rome.</nlm:affiliation></affiliation></author><author><name sortKey="Zimin, Aleksey" sort="Zimin, Aleksey" uniqKey="Zimin A" first="Aleksey" last="Zimin">Aleksey Zimin</name><affiliation><nlm:affiliation>University of Maryland, College Park, MD 20742, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:29048578</idno><idno type="pmid">29048578</idno><idno type="doi">10.1093/gigascience/gix088</idno><idno type="wicri:Area/PubMed/Corpus">000254</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000254</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).</title><author><name sortKey="Williams, John L" sort="Williams, John L" uniqKey="Williams J" first="John L" last="Williams">John L. Williams</name><affiliation><nlm:affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Iamartino, Daniela" sort="Iamartino, Daniela" uniqKey="Iamartino D" first="Daniela" last="Iamartino">Daniela Iamartino</name><affiliation><nlm:affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pruitt, Kim D" sort="Pruitt, Kim D" uniqKey="Pruitt K" first="Kim D" last="Pruitt">Kim D. Pruitt</name><affiliation><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sonstegard, Tad" sort="Sonstegard, Tad" uniqKey="Sonstegard T" first="Tad" last="Sonstegard">Tad Sonstegard</name><affiliation><nlm:affiliation>Recombinetics, 1246 University Ave W, St Paul, MN 55104, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Smith, Timothy P L" sort="Smith, Timothy P L" uniqKey="Smith T" first="Timothy P L" last="Smith">Timothy P L. Smith</name><affiliation><nlm:affiliation>USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Low, Wai Yee" sort="Low, Wai Yee" uniqKey="Low W" first="Wai Yee" last="Low">Wai Yee Low</name><affiliation><nlm:affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Biagini, Tommaso" sort="Biagini, Tommaso" uniqKey="Biagini T" first="Tommaso" last="Biagini">Tommaso Biagini</name><affiliation><nlm:affiliation>IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, S. Giovanni Rotondo, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Bomba, Lorenzo" sort="Bomba, Lorenzo" uniqKey="Bomba L" first="Lorenzo" last="Bomba">Lorenzo Bomba</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Capomaccio, Stefano" sort="Capomaccio, Stefano" uniqKey="Capomaccio S" first="Stefano" last="Capomaccio">Stefano Capomaccio</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Castiglioni, Bianca" sort="Castiglioni, Bianca" uniqKey="Castiglioni B" first="Bianca" last="Castiglioni">Bianca Castiglioni</name><affiliation><nlm:affiliation>CNR, Istituto di Biologia e Biotecnologia Agraria Via Einstein, 26900 Lodi, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Coletta, Angelo" sort="Coletta, Angelo" uniqKey="Coletta A" first="Angelo" last="Coletta">Angelo Coletta</name><affiliation><nlm:affiliation>ANASB Associazione Nazionale Allevatori Specie Bufalina, Centuran, Caserta, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Corrado, Federica" sort="Corrado, Federica" uniqKey="Corrado F" first="Federica" last="Corrado">Federica Corrado</name><affiliation><nlm:affiliation>IZSM, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2-80055, Portici (NA), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ferre, Fabrizio" sort="Ferre, Fabrizio" uniqKey="Ferre F" first="Fabrizio" last="Ferré">Fabrizio Ferré</name><affiliation><nlm:affiliation>Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 8/2, 40126 Bologna, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Iannuzzi, Leopoldo" sort="Iannuzzi, Leopoldo" uniqKey="Iannuzzi L" first="Leopoldo" last="Iannuzzi">Leopoldo Iannuzzi</name><affiliation><nlm:affiliation>CNR, Istituto Per Il Sistema Produzione Animale In Ambiente Mediterraneo, Via Argine, 1085, 80147 Napoli, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Lawley, Cynthia" sort="Lawley, Cynthia" uniqKey="Lawley C" first="Cynthia" last="Lawley">Cynthia Lawley</name><affiliation><nlm:affiliation>Illumina, Inc. 499 Illinois St. Suite 210, San Francisco, CA 94158, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Macciotta, Nicol" sort="Macciotta, Nicol" uniqKey="Macciotta N" first="Nicol" last="Macciotta">Nicol Macciotta</name><affiliation><nlm:affiliation>Università degli Studi di Sassari, Piazza Università 21, 07100 Sassari, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Mcclure, Matthew" sort="Mcclure, Matthew" uniqKey="Mcclure M" first="Matthew" last="Mcclure">Matthew Mcclure</name><affiliation><nlm:affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mancini, Giordano" sort="Mancini, Giordano" uniqKey="Mancini G" first="Giordano" last="Mancini">Giordano Mancini</name><affiliation><nlm:affiliation>Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Matassino, Donato" sort="Matassino, Donato" uniqKey="Matassino D" first="Donato" last="Matassino">Donato Matassino</name><affiliation><nlm:affiliation>ConSDABI, Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Contrada Piano Cappelle, Benevento (BN), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Mazza, Raffaele" sort="Mazza, Raffaele" uniqKey="Mazza R" first="Raffaele" last="Mazza">Raffaele Mazza</name><affiliation><nlm:affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Milanesi, Marco" sort="Milanesi, Marco" uniqKey="Milanesi M" first="Marco" last="Milanesi">Marco Milanesi</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Moioli, Bianca" sort="Moioli, Bianca" uniqKey="Moioli B" first="Bianca" last="Moioli">Bianca Moioli</name><affiliation><nlm:affiliation>CRA Centro di Ricerca per la Produzione delle Carni ed il Miglioramento Genetico, Via Salaria 31, 00015, Montorotondo, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Morandi, Nicola" sort="Morandi, Nicola" uniqKey="Morandi N" first="Nicola" last="Morandi">Nicola Morandi</name><affiliation><nlm:affiliation>Merial Italia, via Lorenzini 8, 20139 Milano, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ramunno, Luigi" sort="Ramunno, Luigi" uniqKey="Ramunno L" first="Luigi" last="Ramunno">Luigi Ramunno</name><affiliation><nlm:affiliation>Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Peretti, Vincenzo" sort="Peretti, Vincenzo" uniqKey="Peretti V" first="Vincenzo" last="Peretti">Vincenzo Peretti</name><affiliation><nlm:affiliation>Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Napoli, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pilla, Fabio" sort="Pilla, Fabio" uniqKey="Pilla F" first="Fabio" last="Pilla">Fabio Pilla</name><affiliation><nlm:affiliation>Department of Agriculture, Environment and Food, University of Molise.</nlm:affiliation></affiliation></author><author><name sortKey="Ramelli, Paola" sort="Ramelli, Paola" uniqKey="Ramelli P" first="Paola" last="Ramelli">Paola Ramelli</name><affiliation><nlm:affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Schroeder, Steven" sort="Schroeder, Steven" uniqKey="Schroeder S" first="Steven" last="Schroeder">Steven Schroeder</name><affiliation><nlm:affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Strozzi, Francesco" sort="Strozzi, Francesco" uniqKey="Strozzi F" first="Francesco" last="Strozzi">Francesco Strozzi</name><affiliation><nlm:affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Thibaud Nissen, Francoise" sort="Thibaud Nissen, Francoise" uniqKey="Thibaud Nissen F" first="Francoise" last="Thibaud-Nissen">Francoise Thibaud-Nissen</name><affiliation><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zicarelli, Luigi" sort="Zicarelli, Luigi" uniqKey="Zicarelli L" first="Luigi" last="Zicarelli">Luigi Zicarelli</name><affiliation><nlm:affiliation>Department of Agriculture, Environment and Food, University of Molise.</nlm:affiliation></affiliation></author><author><name sortKey="Ajmone Marsan, Paolo" sort="Ajmone Marsan, Paolo" uniqKey="Ajmone Marsan P" first="Paolo" last="Ajmone-Marsan">Paolo Ajmone-Marsan</name><affiliation><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Valentini, Alessio" sort="Valentini, Alessio" uniqKey="Valentini A" first="Alessio" last="Valentini">Alessio Valentini</name><affiliation><nlm:affiliation>Universit à della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Chillemi, Giovanni" sort="Chillemi, Giovanni" uniqKey="Chillemi G" first="Giovanni" last="Chillemi">Giovanni Chillemi</name><affiliation><nlm:affiliation>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185, Rome.</nlm:affiliation></affiliation></author><author><name sortKey="Zimin, Aleksey" sort="Zimin, Aleksey" uniqKey="Zimin A" first="Aleksey" last="Zimin">Aleksey Zimin</name><affiliation><nlm:affiliation>University of Maryland, College Park, MD 20742, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">GigaScience</title><idno type="eISSN">2047-217X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and is necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 species of domestic water buffalo, the river (2 n = 50) and the swamp (2 n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366 983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21 398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues and identified 21 711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">29048578</PMID><DateCreated><Year>2017</Year><Month>10</Month><Day>19</Day></DateCreated><DateRevised><Year>2017</Year><Month>10</Month><Day>25</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">2047-217X</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>10</Issue><PubDate><Year>2017</Year><Month>Oct</Month><Day>01</Day></PubDate></JournalIssue><Title>GigaScience</Title><ISOAbbreviation>Gigascience</ISOAbbreviation></Journal><ArticleTitle>Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).</ArticleTitle><Pagination><MedlinePgn>1-6</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gigascience/gix088</ELocationID><Abstract><AbstractText>Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and is necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 species of domestic water buffalo, the river (2 n = 50) and the swamp (2 n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366 983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21 398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues and identified 21 711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.</AbstractText><CopyrightInformation>© The Author 2017. Published by Oxford University Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>John L</ForeName><Initials>JL</Initials><AffiliationInfo><Affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iamartino</LastName><ForeName>Daniela</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pruitt</LastName><ForeName>Kim D</ForeName><Initials>KD</Initials><AffiliationInfo><Affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sonstegard</LastName><ForeName>Tad</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Recombinetics, 1246 University Ave W, St Paul, MN 55104, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Timothy P L</ForeName><Initials>TPL</Initials><AffiliationInfo><Affiliation>USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Low</LastName><ForeName>Wai Yee</ForeName><Initials>WY</Initials><AffiliationInfo><Affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Biagini</LastName><ForeName>Tommaso</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, S. Giovanni Rotondo, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bomba</LastName><ForeName>Lorenzo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Capomaccio</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Castiglioni</LastName><ForeName>Bianca</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>CNR, Istituto di Biologia e Biotecnologia Agraria Via Einstein, 26900 Lodi, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Coletta</LastName><ForeName>Angelo</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>ANASB Associazione Nazionale Allevatori Specie Bufalina, Centuran, Caserta, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Corrado</LastName><ForeName>Federica</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>IZSM, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2-80055, Portici (NA), Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ferré</LastName><ForeName>Fabrizio</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 8/2, 40126 Bologna, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iannuzzi</LastName><ForeName>Leopoldo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>CNR, Istituto Per Il Sistema Produzione Animale In Ambiente Mediterraneo, Via Argine, 1085, 80147 Napoli, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawley</LastName><ForeName>Cynthia</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Illumina, Inc. 499 Illinois St. Suite 210, San Francisco, CA 94158, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macciotta</LastName><ForeName>Nicolò</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Università degli Studi di Sassari, Piazza Università 21, 07100 Sassari, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McClure</LastName><ForeName>Matthew</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co., Cork, P72 × 050, Ireland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mancini</LastName><ForeName>Giordano</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Matassino</LastName><ForeName>Donato</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>ConSDABI, Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Contrada Piano Cappelle, Benevento (BN), Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mazza</LastName><ForeName>Raffaele</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Milanesi</LastName><ForeName>Marco</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Moioli</LastName><ForeName>Bianca</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>CRA Centro di Ricerca per la Produzione delle Carni ed il Miglioramento Genetico, Via Salaria 31, 00015, Montorotondo, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morandi</LastName><ForeName>Nicola</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Merial Italia, via Lorenzini 8, 20139 Milano, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramunno</LastName><ForeName>Luigi</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peretti</LastName><ForeName>Vincenzo</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Napoli, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pilla</LastName><ForeName>Fabio</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Environment and Food, University of Molise.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramelli</LastName><ForeName>Paola</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schroeder</LastName><ForeName>Steven</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Strozzi</LastName><ForeName>Francesco</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Enterome, 94-96 Avenue Ledru-Rollin, 75011 Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thibaud-Nissen</LastName><ForeName>Francoise</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zicarelli</LastName><ForeName>Luigi</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Environment and Food, University of Molise.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ajmone-Marsan</LastName><ForeName>Paolo</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Valentini</LastName><ForeName>Alessio</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Universit à della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chillemi</LastName><ForeName>Giovanni</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185, Rome.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zimin</LastName><ForeName>Aleksey</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>University of Maryland, College Park, MD 20742, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Gigascience</MedlineTA><NlmUniqueID>101596872</NlmUniqueID><ISSNLinking>2047-217X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Water buffalo</Keyword><Keyword MajorTopicYN="N">annotation</Keyword><Keyword MajorTopicYN="N">genome assembly</Keyword><Keyword MajorTopicYN="N">transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>05</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>08</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>10</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>10</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>10</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29048578</ArticleId><ArticleId IdType="pii">4101552</ArticleId><ArticleId IdType="doi">10.1093/gigascience/gix088</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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