TY - JOUR
T1 - Draft genome of the reindeer (Rangifer tarandus)
AU - Li, Zhipeng
AU - Lin, Zeshan
AU - Ba, Hengxing
AU - Chen, Lei
AU - Yang, Yongzhi
AU - Wang, Kun
AU - Qiu, Qiang
AU - Wang, Wen
AU - Li, Guangyu
N1 - Publisher Copyright:
© The Author(s) 2017.
PY - 2017/12/1
Y1 - 2017/12/1
N2 - 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.
AB - 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.
KW - Annotation
KW - Assembly
KW - Caribou
KW - Genomics
KW - Rangier tarandus
KW - Reindeer
KW - Whole genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85042362003&partnerID=8YFLogxK
U2 - 10.1093/gigascience/gix102
DO - 10.1093/gigascience/gix102
M3 - 文章
C2 - 29099922
AN - SCOPUS:85042362003
SN - 2047-217X
VL - 6
SP - 1
EP - 5
JO - GigaScience
JF - GigaScience
IS - 12
ER -