Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n=50)

被引：37

作者：

Williams, John L. ^{[1
]}

Iamartino, Daniela ^{[2
]}

Pruitt, Kim D. ^{[3
]}

Sonstegard, Tad ^{[4
]}

Smith, Timothy P. L. ^{[5
]}

Low, Wai Yee ^{[1
]}

Biagini, Tommaso ^{[6
]}

Bomba, Lorenzo ^{[7
,28
]}

Capomaccio, Stefano ^{[7
]}

Castiglioni, Bianca ^{[8
]}

Coletta, Angelo ^{[9
]}

Corrado, Federica ^{[10
]}

Ferre, Fabrizio ^{[11
]}

Iannuzzi, Leopoldo ^{[12
]}

Lawley, Cynthia ^{[13
]}

Macciotta, Nicolo ^{[14
]}

McClure, Matthew ^{[15
,29
]}

Mancini, Giordano ^{[16
]}

Matassino, Donato ^{[17
]}

Mazza, Raffaele ^{[2
]}

Milanesi, Marco ^{[7
]}

Moioli, Bianca ^{[18
]}

Morandi, Nicola ^{[19
]}

Ramunno, Luigi ^{[20
]}

Peretti, Vincenzo ^{[21
]}

Pilla, Fabio ^{[22
]}

Ramelli, Paola ^{[23
]}

Schroeder, Steven ^{[15
]}

Strozzi, Francesco ^{[23
,24
]}

Thibaud-Nissen, Francoise ^{[3
]}

Zicarelli, Luigi ^{[22
]}

Ajmone-Marsan, Paolo ^{[7
]}

Valentini, Alessio ^{[25
]}

Chillemi, Giovanni ^{[26
]}

Zimin, Aleksey ^{[27
]}

机构：

[1] Univ Adelaide, Sch Anim & Vet Sci, Davies Res Ctr, Roseworthy, SA 5371, Australia

[2] AIA, LGS, Via Bergamo 292, I-26100 Cremona, CR, Italy

[3] Natl Ctr Biotechnol Informat, NIH, Natl Lib Med, Bethesda, MD 20894 USA

[4] Recombinet, 1246 Univ Ave W, St Paul, MN 55104 USA

[5] USDA ARS, US Meat Anim Res Ctr, 844 Rd 313, Clay Ctr, NE 68933 USA

[6] IRCCS, Casa Sollievo Sofferenza, Bioinformat Unit, San Giovanni Rotondo, Italy

[7] Univ Cattolica Sacro Cuore, Via Emilia Parmense 84, I-29122 Piacenza, PC, Italy

[8] CNR, Ist Biol Biotecnol Agraria, Via Einstein, I-26900 Lodi, Italy

[9] ANASB, Caserta, Italy

[10] IZSM, Via Salute, I-280055 Portici, NA, Italy

[11] Univ Bologna Alma Mater, Dept Pharm & Biotechnol FaBiT, Via Belmeloro 8-2, I-40126 Bologna, Italy

[12] CNR, Ist Sistema Produz Anim Ambiente Mediterra 2, Via Argine 1085, I-80147 Naples, Italy

[13] Illumina Inc, 499 Illinois St,Suite 210, San Francisco, CA 94158 USA

[14] Univ Sassari, Piazza Univ 21, I-07100 Sassari, Italy

[15] USDA, ARS, Anim Genom & Improvement Lab, Bldg 306 BARC East, Beltsville, MD 20705 USA

[16] Scuola Normale Super Pisa, Piazza Cavalieri 7, I-56125 Pisa, Italy

[17] Consorzio Sperimentazione, Div Applicaz Biotecniche Innovat, ConSDABI, Benevento, BN, Italy

[18] CRA Ctr Ric Produz Carni Miglioramento Genet, Via Salaria 31, I-00015 Monterotondo, Italy

[19] Merial Italia, Via Lorenzini 8, I-20139 Milan, Italy

[20] Univ Naples Federico II, Dipartimento Agraria, Via Univ 100, I-80055 Portici, NA, Italy

[21] Univ Naples Federico II, Dept Vet Med & Anim Prod, Via Delpino 1, I-80137 Naples, Italy

[22] Univ Molise, Dept Agr Environm & Food, Campobasso, Italy

[23] Parco Tecnol Padano, Via Einstein, I-26500 Lodi, Italy

[24] Enterome, 94-96 Ave Ledru Rollin, F-75011 Paris, France

[25] Univ Tuscia, Via S Camillo Lellis, I-01100 Viterbo, Italy

[26] Cineca, SCAI Super Comp Applicat & Innovat Dept, Via Tizii 6, I-00185 Rome, Italy

[27] Univ Maryland, College Pk, MD 20742 USA

[28] Wellcome Trust Sanger Inst, Human Genet, Genome Campus, Hinxton 10 1HH, CB, England

[29] Irish Cattle Breeding Federat, Highfield House, Cork P72 X050, Ireland

来源：

GIGASCIENCE | 2017年 / 6卷 / 10期

关键词：

Water buffalo; genome assembly; transcriptome; annotation; SEQUENCE; DATABASE;

D O I：

10.1093/gigascience/gix088

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 (2n = 50) and the swamp (2n = 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.

引用

页数：6

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