Dataset Information

The Caribou (Rangifer tarandus) Genome.

ABSTRACT: Rangifer tarandus, known as caribou or reindeer, is a widespread circumpolar species which presents significant variability in their morphology, ecology, and genetics. A genome was sequenced from a male boreal caribou (R. t. caribou) from Manitoba, Canada. Both paired end and Chicago libraries were constructed and sequenced on Illumina platforms. The final assembly consists of approximately 2.205 Gb, and has a scaffold N50 of 11.765 Mb. BUSCO (Benchmarking Universal Single-Copy Orthologs) reconstructed 3820 (93.1%) complete mammalian genes, and genome annotation identified the locations of 33,177 protein-coding genes. An alignment to the bovine genome was carried out, indicating sequence coverage on all bovine chromosomes. A high-quality reference genome will be invaluable for evolutionary research and for conservation efforts for the species. Further information about the genome, including a FASTA file of the assembly and the annotation files, is available on our caribou genome website. Raw sequence data is available at the National Centre for Biotechnology Information (NCBI), under the BioProject accession number PRJNA549927.

SUBMITTER: Taylor RS

PROVIDER: S-EPMC6678279 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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The Caribou (Rangifer tarandus) Genome.

Taylor Rebecca S RS Horn Rebekah L RL Zhang Xi X Golding G Brian GB Manseau Micheline M Wilson Paul J PJ

Genes 20190717 7

Rangifer tarandus, known as caribou or reindeer, is a widespread circumpolar species which presents significant variability in their morphology, ecology, and genetics. A genome was sequenced from a male boreal caribou (R. t. caribou) from Manitoba, Canada. Both paired end and Chicago libraries were constructed and sequenced on Illumina platforms. The final assembly consists of approximately 2.205 Gb, and has a scaffold N50 of 11.765 Mb. BUSCO (Benchmarking Universal Single-Copy Ort ...[more]

PMID: 31319535

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Project description:The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision-making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re-sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θπ and estimated the coalescent or ancestral effective population size (Ne), which ranged from 12,030 to 15,513. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. In contrast, values of contemporary Ne, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral Ne and Tajima's D into management decisions.

Project description:BackgroundDevelopment of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species.ResultsFrom a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip.ConclusionThis design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

Project description:In-situ oil sands development (ISD) involves a network of facilities, wells, roads and pipelines to extract and transport subsurface bitumen. This technology is rapidly expanding and there is uncertainty whether ISDs restrict animal movement, leading to increased extinction probabilities for some wide-ranging species. Here we test for effects of simulated future (i.e., 50 years from now) and current ISDs on simulated movements of woodland caribou (Rangifer tarandus), a threatened species across North America. In simulations of future scenarios, we varied the spacing and permeability of ISDs and the presence/absence of protected areas. Permeability was measured as the number of times simulated caribou crossed ISDs with different levels of modelled permeability. We estimated the effects of these factors on caribou step length and annual home range size, key metrics of small and large spatiotemporal scales of movement, respectively. Current caribou crossings of above-ground pipeline features of ISDs were measured using camera traps and compared to expected caribou crossing rates based on present-day caribou movement simulations. Current crossing rates were evaluated within the context of predicted future crossing success rates necessary to maintain caribou step lengths and home ranges. With few exceptions, permeability across ISDs was the main factor affecting caribou movement, more so than spacing between developments or the presence of protected areas. However, minimal permeability (crossing rates of c. 15% to 60%, relative to an undisturbed site was needed to maintain existing home range size and step lengths. The effect of permeability on home range size and step length was non-linear, suggesting that small increases in permeability would provide a disproportionately greater benefit to caribou movement. Our predictions demonstrate that maintaining permeability across ISDs is more important than spacing between leases or including protected areas, and thus provides clear direction for mitigation efforts for features that will exist on the landscape for decades to come.

Project description:Background:Caribou (Rangifer tarandus) is the top dietary source of iron and several micronutrients necessary for red blood cell production (erythropoiesis) in the contemporary diet of Inuit adults across Canada. Many caribou populations across the circumpolar north, however, have experienced dramatic declines in recent decades. Restricted access to caribou may negatively impact the nutrition and health of Inuit communities. Methods:We used data from the Inuit Health Survey, a cross-sectional survey of 2550 Inuit adults in thirty-six communities across northern Canada (conducted in 2007-2008) to examine the relationship between caribou consumption, hemoglobin (Hb), and blood biomarkers of nutrient intake and contaminant exposure. Multivariable linear regression was used to investigate the potential public health impact of a theoretical restriction in caribou consumption, by estimating the response of Hb concentrations (and the attendant change in anemia prevalence), to theoretical changes in caribou consumption (with and without substitution of caribou with other country food meat). Results:Mean (95% CI) daily caribou meat consumption differed by an order of magnitude 4.3 (3.9-4.7), 51.1 (48.5-53.8), and 236.7 (224.7-248.7) grams/day between tertiles of caribou consumption. Mean (95% CI) hemoglobin levels increased from 129.1 (128.1-130.2) g/L to 132.5 (131.3-133.7) g/L between the highest and lowest tertiles of caribou consumption. In multivariable regression analyses, average daily caribou meat consumption was positively associated (P<?0.001) with hemoglobin levels. This relationship translated into approximately 4?g/L hemoglobin increase in participants in the third tertile of caribou consumption. The overall prevalence of anemia observed in the study population was 26.5% (24.5 - 28.3%) and a modelled restriction in caribou consumption (i.e. caribou?=?0) increased the overall prevalence of anemia by approximately 6%. The maximum negative effect of caribou restrictions was related to a complete restriction on caribou consumption, coupled with the substitution of caribou with other country food meat (35.4% prevalence). Conclusions:Given the importance of caribou to Inuit culture, health and wellbeing, and the high price of healthful market foods in remote northern communities, strategies to promote the sustainable harvest of country foods are urgently required to ensure the health and nutrition security of the Inuit, in the context of rapidly changing Arctic environments and ecosystems.

Dataset Information

The Caribou (Rangifer tarandus) Genome.

Publications

The Caribou (<i>Rangifer tarandus</i>) Genome.

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