![]() ![]() The cell's state is regulated at different levels, such as DNA, RNA and protein, by complex interplay of intrinsic molecules existing in the organism and extrinsic stimuli such as local environment. The fast-developing sequencing methods now enable unbiased, high-throughput and high-resolution view of the heterogeneity from individual cell within a population, in terms of its fate decisions, identity and function. Molecular Biology and Evolution, 29(12), 712.In recent years, single cell assays have made exciting progresses, overcoming the issue of heterogeneity associated with bulk populations. Aquatic adaptation and depleted diversity: A deep dive into the genomes of the sea otter and giant otter. C., Koepfli, K.-P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., … Wayne, R. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. Repbase Update, a database of repetitive elements in eukaryotic genomes. From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline. O., Hartl, C., Poplin, R., del Angel, G., Levy-Moonshine, A., … DePristo, M. Genomics and the future of conservation genetics. Molecular Ecology Resources published by John Wiley & Sons Ltd.Īllendorf, F. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.ġ0X Chromium Hi-C PSMC conservation genomics single nucleotide polymorphism (SNP) whole genome resequencing. ![]() Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Additionally, the level of diversity across populations varied according to management strategy. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large-scale and long-term reintroduction project. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. Genetic information is therefore considered a critical aspect of conservation management. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Petersburg, Russia.Ĭaptive populations provide a valuable insurance against extinctions in the wild. 13 Computer Technologies Laboratory, ITMO University, St. ![]() ![]() 12 Environment Agency, Abu Dhabi, United Arab Emirates.11 Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.10 Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.9 Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.8 The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.7 Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.6 Terrestrial & Marine Biodiversity Sector, Environment Agency, Abu Dhabi, United Arab Emirates.5 RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK.4 Theodosius Dobzhansky Center for Genome Bioinformatics, St.3 Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA.2 Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.1 Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK. ![]()
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