Draft genome of the reindeer (Rangifer tarandus)
文献类型: 外文期刊
第一作者: Li, Zhipeng
作者: Li, Zhipeng;Ba, Hengxing;Li, Guangyu;Lin, Zeshan;Chen, Lei;Yang, Yongzhi;Wang, Kun;Qiu, Qiang;Wang, Wen
作者机构:
关键词: Rangier tarandus;reindeer;caribou;genomics;whole genome sequencing;assembly;annotation
期刊名称:GIGASCIENCE ( 影响因子:6.524; 五年影响因子:8.702 )
ISSN: 2047-217X
年卷期: 2017 年 6 卷 12 期
页码:
收录情况: SCI
摘要: Background: The reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and it is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer, as well as males, regularly grow cranial appendages (antlers, the defining characteristics of cervids). Moreover, reindeer milk contains more protein and less lactose than bovids' milk. A high-quality reference genome of this species will assist efforts to elucidate these and other important features in the reindeer. Findings: We obtained 615 Gb (Gigabase) of usable sequences by filtering the low-quality reads of the raw data generated from the Illumina Hiseq 4000 platform, and a 2.64-Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21 555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1339 snRNA, and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus and ancestors of Bos taurus and Capra hircus is estimated to be about 29.5 million years ago. Conclusions: Our results provide the first high-quality reference genome for the reindeer and a valuable resource for studying the evolution, domestication, and other unusual characteristics of the reindeer.
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