Sequencing and de novo genome assembly of a nelore (Bos indicus) bull.

Bos indicus cattle breeds have been extensively used for dairy and beef production in tropical climates and present several natural adaptations to biotic and abiotic stresses found in these regions of the world. As breeder associations stride towards incorporating genomic tools into ongoing genetic evaluations and breeding programs to improve productivity and beef and milk quality traits, a (B. indicus) genome assembly represents an essential tool which will be vital to help identify and understand the underlying genetic variations that distinguish taurine and indicine cattle, which have diverged >250,000 years ago. DNA obtained from semen from a Nelore bull born in 1987, with an estimated cumulative inbreeding coefficient of 29.4%, and that can be traced to animals imported from India, was used to produce 100bp paired-end sequences from short (300 and 700bp) and long insert (3, 5 and 10 kbp) libraries, with an Illumina HiSeq platform. A total of 120Gbp were sequenced, corresponding to 45x raw coverage of the genome. The SOAP de novo assembler was used to build contigs and scaffolding. Several parameters sets were evaluated to obtain the best assembly based on the number of scaffolds, number of bases in scaffolds, N50, and total gap length. The best assembly obtained so far contains 2.7Gbp, 15,103 scaffolds with N50 of 649Kbp, and 756Mbp of gaps. Current results are being used to target additional sequencing of specific libraries to improve scaffold assembly. In addition, different sequencing technologies are also under evaluation for generating additional data to improve sequence assembly quality before comparisons with the reference (B. taurus) sequence are performed.

Bibliographic Details

Main Authors:	CINTRA, L. C., ZERLOTINI, A., LOBO, F. P., SILVA, F. R. da, GIACHETTO, P. F., KUSER-FALCÃO, P. R., SILVA, L. O. C. da, EGITO, A. A. do, SIQUEIRA, F., SILVA, N. M. A. da, PAIVA, S. R., YAMAGISHI, M. E. B., CAETANO, A. R.
Other Authors:	LEANDRO CARRIJO CINTRA, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA; FELIPE RODRIGUES DA SILVA, CNPTIA; POLIANA FERNANDA GIACHETTO, CNPTIA; PAULA REGINA KUSER FALCAO, CNPTIA; LUIZ OTAVIO CAMPOS DA SILVA, CNPGC; ANDREA ALVES DO EGITO, CNPGC; FABIANE SIQUEIRA, CNPGC; NAIARA MILAGRES AUGUSTO DA SILVA, CENARGEN; SAMUEL REZENDE PAIVA, Cenargen; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; ALEXANDRE RODRIGUES CAETANO, CENARGEN.
Format:	Anais e Proceedings de eventos biblioteca
Language:	English eng
Published:	2014-01-02
Subjects:	Sequenciamento de genoma, Bioinformática., Bos Indicus., Genome assembly, Bioinformatics, Nellore.,
Online Access:	http://www.alice.cnptia.embrapa.br/alice/handle/doc/974758
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