Draft genome of the reindeer (Rangifer tarandus)

GigaScience
Zhipeng LiGuangyu Li

Abstract

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. 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 taur...Continue Reading

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Citations

Jul 16, 2019·PLoS Biology·David G Hazlerigg, Nicholas J C Tyler
May 30, 2020·Molecular Biology and Evolution·Jaelle C BrealeyKaterina Guschanski
Dec 14, 2019·Genome Biology and Evolution·João P MarquesJosé Melo-Ferreira
Aug 6, 2020·Animals : an Open Access Journal From MDPI·Veronika KharzinovaNatalia Zinovieva
Nov 4, 2017·GigaScience·Zhipeng LiGuangyu Li
Jul 20, 2019·Genes·Rebecca S TaylorPaul J Wilson
Sep 6, 2021·Molecular Ecology·Rebecca S TaylorPaul J Wilson

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Methods Mentioned

BETA
whole genome shotgun

Key Resources (RRID) Mentioned

SCR_014986
SCR_015026
SCR_015008
SCR_015247
SCR_015027
SCR_012902
SCR_002654
SCR_008417
SCR_011822
SCR_005829

Software Mentioned

TBLASTN
BLASTP
SOAPdenovo
Benchmarking Universal Single - Copy Orthologs ( BUSCO
Augustus
RepeatModeler
RepeatMasker
InterProScan
GenScan
PRANK

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