Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).
Identifieur interne : 000B66 ( Main/Exploration ); précédent : 000B65; suivant : 000B67Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).
Auteurs : John L. Williams [Australie] ; Daniela Iamartino [Italie] ; Kim D. Pruitt [États-Unis] ; Tad Sonstegard [États-Unis] ; Timothy P L. Smith [États-Unis] ; Wai Yee Low [Australie] ; Tommaso Biagini [Italie] ; Lorenzo Bomba [Italie] ; Stefano Capomaccio [Italie] ; Bianca Castiglioni [Italie] ; Angelo Coletta [Italie] ; Federica Corrado [Italie] ; Fabrizio Ferré [Italie] ; Leopoldo Iannuzzi [Italie] ; Cynthia Lawley [États-Unis] ; Nicol Macciotta [Italie] ; Matthew Mcclure [États-Unis] ; Giordano Mancini [Italie] ; Donato Matassino [Italie] ; Raffaele Mazza [Italie] ; Marco Milanesi [Italie] ; Bianca Moioli [Italie] ; Nicola Morandi [Italie] ; Luigi Ramunno [Italie] ; Vincenzo Peretti [Italie] ; Fabio Pilla ; Paola Ramelli [Italie] ; Steven Schroeder [États-Unis] ; Francesco Strozzi [Italie] ; Francoise Thibaud-Nissen [États-Unis] ; Luigi Zicarelli ; Paolo Ajmone-Marsan [Italie] ; Alessio Valentini [Italie] ; Giovanni Chillemi [Italie] ; Aleksey Zimin [États-Unis]Source :
- 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
Affiliations:
- Australie, Italie, États-Unis
- Californie, Latium, Maryland, Minnesota, Nebraska, Toscane
- College Park (Maryland), Pise, Rome
- Université du Maryland
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Camillo de Lellis, 01100 Viterbo</wicri:regionArea><wicri:noRegion>01100 Viterbo</wicri:noRegion></affiliation></author><author><name sortKey="Chillemi, Giovanni" sort="Chillemi, Giovanni" uniqKey="Chillemi G" first="Giovanni" last="Chillemi">Giovanni Chillemi</name><affiliation wicri:level="3"><nlm:affiliation>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185, Rome.</nlm:affiliation><country>Italie</country><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName><wicri:orgArea>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185</wicri:orgArea></affiliation></author><author><name sortKey="Zimin, Aleksey" sort="Zimin, Aleksey" uniqKey="Zimin A" first="Aleksey" last="Zimin">Aleksey Zimin</name><affiliation wicri:level="4"><nlm:affiliation>University of Maryland, College Park, MD 20742, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Maryland, College Park, MD 20742</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></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><idno type="wicri:Area/PubMed/Curation">000252</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000252</idno><idno type="wicri:Area/PubMed/Checkpoint">000252</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000252</idno><idno type="wicri:Area/Ncbi/Merge">005066</idno><idno type="wicri:Area/Ncbi/Curation">005066</idno><idno type="wicri:Area/Ncbi/Checkpoint">005066</idno><idno type="wicri:Area/Main/Merge">000B61</idno><idno type="wicri:Area/Main/Curation">000B66</idno><idno type="wicri:Area/Main/Exploration">000B66</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 wicri:level="1"><nlm:affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371</wicri:regionArea><wicri:noRegion>SA 5371</wicri:noRegion></affiliation></author><author><name sortKey="Iamartino, Daniela" sort="Iamartino, Daniela" uniqKey="Iamartino D" first="Daniela" last="Iamartino">Daniela Iamartino</name><affiliation wicri:level="1"><nlm:affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR)</wicri:regionArea><wicri:noRegion>26100 Cremona (CR)</wicri:noRegion></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 wicri:level="2"><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Sonstegard, Tad" sort="Sonstegard, Tad" uniqKey="Sonstegard T" first="Tad" last="Sonstegard">Tad Sonstegard</name><affiliation wicri:level="2"><nlm:affiliation>Recombinetics, 1246 University Ave W, St Paul, MN 55104, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Recombinetics, 1246 University Ave W, St Paul, MN 55104</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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 wicri:level="2"><nlm:affiliation>USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></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 wicri:level="1"><nlm:affiliation>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371</wicri:regionArea><wicri:noRegion>SA 5371</wicri:noRegion></affiliation></author><author><name sortKey="Biagini, Tommaso" sort="Biagini, Tommaso" uniqKey="Biagini T" first="Tommaso" last="Biagini">Tommaso Biagini</name><affiliation wicri:level="1"><nlm:affiliation>IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, S. Giovanni Rotondo, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, S. Giovanni Rotondo</wicri:regionArea><wicri:noRegion>S. Giovanni Rotondo</wicri:noRegion></affiliation></author><author><name sortKey="Bomba, Lorenzo" sort="Bomba, Lorenzo" uniqKey="Bomba L" first="Lorenzo" last="Bomba">Lorenzo Bomba</name><affiliation wicri:level="1"><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC</wicri:regionArea><wicri:noRegion>29122 Piacenza PC</wicri:noRegion></affiliation></author><author><name sortKey="Capomaccio, Stefano" sort="Capomaccio, Stefano" uniqKey="Capomaccio S" first="Stefano" last="Capomaccio">Stefano Capomaccio</name><affiliation wicri:level="1"><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC</wicri:regionArea><wicri:noRegion>29122 Piacenza PC</wicri:noRegion></affiliation></author><author><name sortKey="Castiglioni, Bianca" sort="Castiglioni, Bianca" uniqKey="Castiglioni B" first="Bianca" last="Castiglioni">Bianca Castiglioni</name><affiliation wicri:level="1"><nlm:affiliation>CNR, Istituto di Biologia e Biotecnologia Agraria Via Einstein, 26900 Lodi, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>CNR, Istituto di Biologia e Biotecnologia Agraria Via Einstein, 26900 Lodi</wicri:regionArea><wicri:noRegion>26900 Lodi</wicri:noRegion></affiliation></author><author><name sortKey="Coletta, Angelo" sort="Coletta, Angelo" uniqKey="Coletta A" first="Angelo" last="Coletta">Angelo Coletta</name><affiliation wicri:level="1"><nlm:affiliation>ANASB Associazione Nazionale Allevatori Specie Bufalina, Centuran, Caserta, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>ANASB Associazione Nazionale Allevatori Specie Bufalina, Centuran, Caserta</wicri:regionArea><wicri:noRegion>Caserta</wicri:noRegion></affiliation></author><author><name sortKey="Corrado, Federica" sort="Corrado, Federica" uniqKey="Corrado F" first="Federica" last="Corrado">Federica Corrado</name><affiliation wicri:level="1"><nlm:affiliation>IZSM, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2-80055, Portici (NA), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IZSM, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2-80055, Portici (NA)</wicri:regionArea><wicri:noRegion>Portici (NA)</wicri:noRegion></affiliation></author><author><name sortKey="Ferre, Fabrizio" sort="Ferre, Fabrizio" uniqKey="Ferre F" first="Fabrizio" last="Ferré">Fabrizio Ferré</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 8/2, 40126 Bologna, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 8/2, 40126 Bologna</wicri:regionArea><wicri:noRegion>40126 Bologna</wicri:noRegion></affiliation></author><author><name sortKey="Iannuzzi, Leopoldo" sort="Iannuzzi, Leopoldo" uniqKey="Iannuzzi L" first="Leopoldo" last="Iannuzzi">Leopoldo Iannuzzi</name><affiliation wicri:level="1"><nlm:affiliation>CNR, Istituto Per Il Sistema Produzione Animale In Ambiente Mediterraneo, Via Argine, 1085, 80147 Napoli, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>CNR, Istituto Per Il Sistema Produzione Animale In Ambiente Mediterraneo, Via Argine, 1085, 80147 Napoli</wicri:regionArea><wicri:noRegion>80147 Napoli</wicri:noRegion></affiliation></author><author><name sortKey="Lawley, Cynthia" sort="Lawley, Cynthia" uniqKey="Lawley C" first="Cynthia" last="Lawley">Cynthia Lawley</name><affiliation wicri:level="2"><nlm:affiliation>Illumina, Inc. 499 Illinois St. Suite 210, San Francisco, CA 94158, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Illumina, Inc. 499 Illinois St. Suite 210, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Macciotta, Nicol" sort="Macciotta, Nicol" uniqKey="Macciotta N" first="Nicol" last="Macciotta">Nicol Macciotta</name><affiliation wicri:level="1"><nlm:affiliation>Università degli Studi di Sassari, Piazza Università 21, 07100 Sassari, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Università degli Studi di Sassari, Piazza Università 21, 07100 Sassari</wicri:regionArea><wicri:noRegion>07100 Sassari</wicri:noRegion></affiliation></author><author><name sortKey="Mcclure, Matthew" sort="Mcclure, Matthew" uniqKey="Mcclure M" first="Matthew" last="Mcclure">Matthew Mcclure</name><affiliation wicri:level="2"><nlm:affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Mancini, Giordano" sort="Mancini, Giordano" uniqKey="Mancini G" first="Giordano" last="Mancini">Giordano Mancini</name><affiliation wicri:level="1"><nlm:affiliation>Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Matassino, Donato" sort="Matassino, Donato" uniqKey="Matassino D" first="Donato" last="Matassino">Donato Matassino</name><affiliation wicri:level="1"><nlm:affiliation>ConSDABI, Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Contrada Piano Cappelle, Benevento (BN), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>ConSDABI, Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Contrada Piano Cappelle, Benevento (BN)</wicri:regionArea><wicri:noRegion>Benevento (BN)</wicri:noRegion></affiliation></author><author><name sortKey="Mazza, Raffaele" sort="Mazza, Raffaele" uniqKey="Mazza R" first="Raffaele" last="Mazza">Raffaele Mazza</name><affiliation wicri:level="1"><nlm:affiliation>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR)</wicri:regionArea><wicri:noRegion>26100 Cremona (CR)</wicri:noRegion></affiliation></author><author><name sortKey="Milanesi, Marco" sort="Milanesi, Marco" uniqKey="Milanesi M" first="Marco" last="Milanesi">Marco Milanesi</name><affiliation wicri:level="1"><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC</wicri:regionArea><wicri:noRegion>29122 Piacenza PC</wicri:noRegion></affiliation></author><author><name sortKey="Moioli, Bianca" sort="Moioli, Bianca" uniqKey="Moioli B" first="Bianca" last="Moioli">Bianca Moioli</name><affiliation wicri:level="1"><nlm:affiliation>CRA Centro di Ricerca per la Produzione delle Carni ed il Miglioramento Genetico, Via Salaria 31, 00015, Montorotondo, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>CRA Centro di Ricerca per la Produzione delle Carni ed il Miglioramento Genetico, Via Salaria 31, 00015, Montorotondo</wicri:regionArea><wicri:noRegion>Montorotondo</wicri:noRegion></affiliation></author><author><name sortKey="Morandi, Nicola" sort="Morandi, Nicola" uniqKey="Morandi N" first="Nicola" last="Morandi">Nicola Morandi</name><affiliation wicri:level="1"><nlm:affiliation>Merial Italia, via Lorenzini 8, 20139 Milano, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Merial Italia, via Lorenzini 8, 20139 Milano</wicri:regionArea><wicri:noRegion>20139 Milano</wicri:noRegion></affiliation></author><author><name sortKey="Ramunno, Luigi" sort="Ramunno, Luigi" uniqKey="Ramunno L" first="Luigi" last="Ramunno">Luigi Ramunno</name><affiliation wicri:level="1"><nlm:affiliation>Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA)</wicri:regionArea><wicri:noRegion>80055 Portici (NA)</wicri:noRegion></affiliation></author><author><name sortKey="Peretti, Vincenzo" sort="Peretti, Vincenzo" uniqKey="Peretti V" first="Vincenzo" last="Peretti">Vincenzo Peretti</name><affiliation wicri:level="1"><nlm:affiliation>Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Napoli, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Napoli</wicri:regionArea><wicri:noRegion>80137 Napoli</wicri:noRegion></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><wicri:noCountry code="subField">University of Molise</wicri:noCountry></affiliation></author><author><name sortKey="Ramelli, Paola" sort="Ramelli, Paola" uniqKey="Ramelli P" first="Paola" last="Ramelli">Paola Ramelli</name><affiliation wicri:level="1"><nlm:affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Parco Tecnologico Padano, Via Einstein, 26500, Lodi</wicri:regionArea><wicri:noRegion>Lodi</wicri:noRegion></affiliation></author><author><name sortKey="Schroeder, Steven" sort="Schroeder, Steven" uniqKey="Schroeder S" first="Steven" last="Schroeder">Steven Schroeder</name><affiliation wicri:level="2"><nlm:affiliation>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Strozzi, Francesco" sort="Strozzi, Francesco" uniqKey="Strozzi F" first="Francesco" last="Strozzi">Francesco Strozzi</name><affiliation wicri:level="1"><nlm:affiliation>Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Parco Tecnologico Padano, Via Einstein, 26500, Lodi</wicri:regionArea><wicri:noRegion>Lodi</wicri:noRegion></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 wicri:level="2"><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></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><wicri:noCountry code="subField">University of Molise</wicri:noCountry></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 wicri:level="1"><nlm:affiliation>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC</wicri:regionArea><wicri:noRegion>29122 Piacenza PC</wicri:noRegion></affiliation></author><author><name sortKey="Valentini, Alessio" sort="Valentini, Alessio" uniqKey="Valentini A" first="Alessio" last="Valentini">Alessio Valentini</name><affiliation wicri:level="1"><nlm:affiliation>Universit à della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Universit à della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo</wicri:regionArea><wicri:noRegion>01100 Viterbo</wicri:noRegion></affiliation></author><author><name sortKey="Chillemi, Giovanni" sort="Chillemi, Giovanni" uniqKey="Chillemi G" first="Giovanni" last="Chillemi">Giovanni Chillemi</name><affiliation wicri:level="3"><nlm:affiliation>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185, Rome.</nlm:affiliation><country>Italie</country><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName><wicri:orgArea>SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185</wicri:orgArea></affiliation></author><author><name sortKey="Zimin, Aleksey" sort="Zimin, Aleksey" uniqKey="Zimin A" first="Aleksey" last="Zimin">Aleksey Zimin</name><affiliation wicri:level="4"><nlm:affiliation>University of Maryland, College Park, MD 20742, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Maryland, College Park, MD 20742</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></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><affiliations><list><country><li>Australie</li><li>Italie</li><li>États-Unis</li></country><region><li>Californie</li><li>Latium</li><li>Maryland</li><li>Minnesota</li><li>Nebraska</li><li>Toscane</li></region><settlement><li>College Park (Maryland)</li><li>Pise</li><li>Rome</li></settlement><orgName><li>Université du Maryland</li></orgName></list><tree><noCountry><name sortKey="Pilla, Fabio" sort="Pilla, Fabio" uniqKey="Pilla F" first="Fabio" last="Pilla">Fabio Pilla</name><name sortKey="Zicarelli, Luigi" sort="Zicarelli, Luigi" uniqKey="Zicarelli L" first="Luigi" last="Zicarelli">Luigi Zicarelli</name></noCountry><country name="Australie"><noRegion><name sortKey="Williams, John L" sort="Williams, John L" uniqKey="Williams J" first="John L" last="Williams">John L. Williams</name></noRegion><name sortKey="Low, Wai Yee" sort="Low, Wai Yee" uniqKey="Low W" first="Wai Yee" last="Low">Wai Yee Low</name></country><country name="Italie"><noRegion><name sortKey="Iamartino, Daniela" sort="Iamartino, Daniela" uniqKey="Iamartino D" first="Daniela" last="Iamartino">Daniela Iamartino</name></noRegion><name sortKey="Ajmone Marsan, Paolo" sort="Ajmone Marsan, Paolo" uniqKey="Ajmone Marsan P" first="Paolo" last="Ajmone-Marsan">Paolo Ajmone-Marsan</name><name sortKey="Biagini, Tommaso" sort="Biagini, Tommaso" uniqKey="Biagini T" first="Tommaso" last="Biagini">Tommaso Biagini</name><name sortKey="Bomba, Lorenzo" sort="Bomba, Lorenzo" uniqKey="Bomba L" first="Lorenzo" last="Bomba">Lorenzo Bomba</name><name sortKey="Capomaccio, Stefano" sort="Capomaccio, Stefano" uniqKey="Capomaccio S" first="Stefano" last="Capomaccio">Stefano Capomaccio</name><name sortKey="Castiglioni, Bianca" sort="Castiglioni, Bianca" uniqKey="Castiglioni B" first="Bianca" last="Castiglioni">Bianca Castiglioni</name><name sortKey="Chillemi, Giovanni" sort="Chillemi, Giovanni" uniqKey="Chillemi G" first="Giovanni" last="Chillemi">Giovanni Chillemi</name><name sortKey="Coletta, Angelo" sort="Coletta, Angelo" uniqKey="Coletta A" first="Angelo" last="Coletta">Angelo Coletta</name><name sortKey="Corrado, Federica" sort="Corrado, Federica" uniqKey="Corrado F" first="Federica" last="Corrado">Federica Corrado</name><name sortKey="Ferre, Fabrizio" sort="Ferre, Fabrizio" uniqKey="Ferre F" first="Fabrizio" last="Ferré">Fabrizio Ferré</name><name sortKey="Iannuzzi, Leopoldo" sort="Iannuzzi, Leopoldo" uniqKey="Iannuzzi L" first="Leopoldo" last="Iannuzzi">Leopoldo Iannuzzi</name><name sortKey="Macciotta, Nicol" sort="Macciotta, Nicol" uniqKey="Macciotta N" first="Nicol" last="Macciotta">Nicol Macciotta</name><name sortKey="Mancini, Giordano" sort="Mancini, Giordano" uniqKey="Mancini G" first="Giordano" last="Mancini">Giordano Mancini</name><name sortKey="Matassino, Donato" sort="Matassino, Donato" uniqKey="Matassino D" first="Donato" last="Matassino">Donato Matassino</name><name sortKey="Mazza, Raffaele" sort="Mazza, Raffaele" uniqKey="Mazza R" first="Raffaele" last="Mazza">Raffaele Mazza</name><name sortKey="Milanesi, Marco" sort="Milanesi, Marco" uniqKey="Milanesi M" first="Marco" last="Milanesi">Marco Milanesi</name><name sortKey="Moioli, Bianca" sort="Moioli, Bianca" uniqKey="Moioli B" first="Bianca" last="Moioli">Bianca Moioli</name><name sortKey="Morandi, Nicola" sort="Morandi, Nicola" uniqKey="Morandi N" first="Nicola" last="Morandi">Nicola Morandi</name><name sortKey="Peretti, Vincenzo" sort="Peretti, Vincenzo" uniqKey="Peretti V" first="Vincenzo" last="Peretti">Vincenzo Peretti</name><name sortKey="Ramelli, Paola" sort="Ramelli, Paola" uniqKey="Ramelli P" first="Paola" last="Ramelli">Paola Ramelli</name><name sortKey="Ramunno, Luigi" sort="Ramunno, Luigi" uniqKey="Ramunno L" first="Luigi" last="Ramunno">Luigi Ramunno</name><name sortKey="Strozzi, Francesco" sort="Strozzi, Francesco" uniqKey="Strozzi F" first="Francesco" last="Strozzi">Francesco Strozzi</name><name sortKey="Valentini, Alessio" sort="Valentini, Alessio" uniqKey="Valentini A" first="Alessio" last="Valentini">Alessio Valentini</name></country><country name="États-Unis"><region name="Maryland"><name sortKey="Pruitt, Kim D" sort="Pruitt, Kim D" uniqKey="Pruitt K" first="Kim D" last="Pruitt">Kim D. Pruitt</name></region><name sortKey="Lawley, Cynthia" sort="Lawley, Cynthia" uniqKey="Lawley C" first="Cynthia" last="Lawley">Cynthia Lawley</name><name sortKey="Mcclure, Matthew" sort="Mcclure, Matthew" uniqKey="Mcclure M" first="Matthew" last="Mcclure">Matthew Mcclure</name><name sortKey="Schroeder, Steven" sort="Schroeder, Steven" uniqKey="Schroeder S" first="Steven" last="Schroeder">Steven Schroeder</name><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><name sortKey="Sonstegard, Tad" sort="Sonstegard, Tad" uniqKey="Sonstegard T" first="Tad" last="Sonstegard">Tad Sonstegard</name><name sortKey="Thibaud Nissen, Francoise" sort="Thibaud Nissen, Francoise" uniqKey="Thibaud Nissen F" first="Francoise" last="Thibaud-Nissen">Francoise Thibaud-Nissen</name><name sortKey="Zimin, Aleksey" sort="Zimin, Aleksey" uniqKey="Zimin A" first="Aleksey" last="Zimin">Aleksey Zimin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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