Whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the Black Bengal goat
| Autor: | Md. Abdul Jalil, MP Choudhury, Md. Shamsul Alam Bhuiyan, M.A.M. Yahia Khandoker, Nure Hasni Desha, Gautam Kumar Deb, Md. Bazlur R. Mollah |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Whole genome sequencing Genetics General Immunology and Microbiology Genome-wide association study Single-nucleotide polymorphism General Medicine Biology Quantitative trait locus Genome General Biochemistry Genetics and Molecular Biology Breed 03 medical and health sciences 030104 developmental biology 0302 clinical medicine Capra hircus General Pharmacology Toxicology and Pharmaceutics Indel 030217 neurology & neurosurgery |
| Zdroj: | F1000Research. 8:318 |
| ISSN: | 2046-1402 |
| DOI: | 10.12688/f1000research.18316.1 |
| Popis: | The Black Bengal goat (BBG) is a dwarf sized heritage goat (Capra hircus) breed from Bangladesh, and is well known for its high fertility, excellent meat and skin quality. Here we present the first whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the BBG. A total of 833,469,900 raw reads consisting of 125,020,485,000 bases were obtained by sequencing one male BBG sample. The reads were aligned to the San Clemente and the Yunnan black goat genome which resulted in 98.65% (properly paired, 94.81%) and 98.50% (properly paired, 97.10%) of the reads aligning, respectively. Notably, the estimated sequencing coverages were 48.22X and 44.28X compared to published San Clemente and the Yunnan black goat genomes respectively. On the other hand, a total of 9,497,875 high quality SNPs (Q ≥ 20) along with 1,023,359 indels, and 8,746,849 high quality SNPs along with 842,706 indels were identified in BBG against the San Clemente and Yunnan black goat genomes respectively. The dataset is publicly available from NCBI BioSample (SAMN10391846), Sequence Read Archive (SRR8182317, SRR8549413 and SRR8549904), with BioProject ID PRJNA504436. These data might be useful genomic resources in conducting genome wide association studies, identification of quantitative trait loci (QTLs) and functional genomic analysis of the Black Bengal goat. |
| Databáze: | OpenAIRE |
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