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Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked long reads

https://doi.org/10.1101/195180

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Factors influencing the hunting success of an African wild dog pack

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Sex-biased dispersal in African wild dogs,Lycaon pictus

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Pup production, sex ratios, and survivorship in African wild dogs, Lycaon pictus

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Genome-wide SNPs reveal low effective population size within confined management units of the highly vagile Galapagos shark (Carcharhinus galapagensis)

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Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

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Genomic Flatlining in the Endangered Island Fox

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SNPs in ecology, evolution and conservation

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Genomics and the challenging translation into conservation practice

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Inverse density dependence and the Allee effect

inferredcites →https://doi.org/10.1017/s1367943000001001openalex-snapshot

Multipack dynamics and the Allee effect in the African wild dog, Lycaon pictus

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Initial sequencing and analysis of the human genome

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Technology: The $1,000 genome

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Inference of human population history from individual whole-genome sequences

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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

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Rapid evolutionary response to a transmissible cancer in Tasmanian devils

inferredcites →https://doi.org/10.1038/ng.3015openalex-snapshot

Inferring human population size and separation history from multiple genome sequences

inferredcites →https://doi.org/10.1038/ng.3254openalex-snapshot

Exploring population size changes using SNP frequency spectra

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Coming of age: ten years of next-generation sequencing technologies

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Genotype and SNP calling from next-generation sequencing data

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Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype

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Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus)

inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

inferredcites →https://doi.org/10.1093/beheco/arv100openalex-snapshot

Opposing effects of group size on reproduction and survival in African wild dogs

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot

QUAST: quality assessment tool for genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btu356openalex-snapshot

Toward better understanding of artifacts in variant calling from high-coverage samples

inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

inferredcites →https://doi.org/10.1093/jhered/esp031openalex-snapshot

Highly Endangered African Wild Dogs (Lycaon pictus) Lack Variation at the Major Histocompatibility Complex

inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a111371openalex-snapshot

Molecular Genetic and Morphological Analyses of the African Wild Dog (Lycaon pictus)

inferredcites →https://doi.org/10.1101/128348openalex-snapshot

Improved de novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low Cost

inferredcites →https://doi.org/10.1101/gr.111120.110openalex-snapshot

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

inferredcites →https://doi.org/10.1101/gr.157388.113openalex-snapshot

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

inferredcites →https://doi.org/10.1101/gr.193474.115openalex-snapshot

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot

Direct determination of diploid genome sequences

inferredcites →https://doi.org/10.1111/eva.12178openalex-snapshot

A field guide to whole‐genome sequencing, assembly and annotation

inferredcites →https://doi.org/10.1111/j.0021-8901.2004.00936.xopenalex-snapshot

Molecular techniques, wildlife management and the importance of genetic population structure and dispersal: a case study with feral pigs

inferredcites →https://doi.org/10.1111/j.1095-8312.1999.tb01157.xopenalex-snapshot

Non-invasive genetic sampling and individual identification

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05477.xopenalex-snapshot

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

inferredcites →https://doi.org/10.1111/j.1469-1795.1998.tb00220.xopenalex-snapshot

Six ecological factors that may limit African wild dogs, Lycaon pictus

inferredcites →https://doi.org/10.1126/sciadv.1400253openalex-snapshot

Accelerated modern human–induced species losses: Entering the sixth mass extinction

inferredcites →https://doi.org/10.1126/sciadv.1700299openalex-snapshot

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

inferredcites →https://doi.org/10.1126/science.1236573openalex-snapshot

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

inferredcites →https://doi.org/10.1126/science.1246752openalex-snapshot

The biodiversity of species and their rates of extinction, distribution, and protection

inferredcites →https://doi.org/10.1126/science.280.5372.2126openalex-snapshot

Edge Effects and the Extinction of Populations Inside Protected Areas

inferredcites →https://doi.org/10.1146/annurev-animal-031412-103636openalex-snapshot

Conservation Genomics of Threatened Animal Species

inferredcites →https://doi.org/10.1159/000084979openalex-snapshot

Repbase Update, a database of eukaryotic repetitive elements

inferredcites →https://doi.org/10.1186/1471-2105-12-491openalex-snapshot

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

inferredcites →https://doi.org/10.1186/1741-7007-10-12openalex-snapshot

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot

ANGSD: Analysis of Next Generation Sequencing Data

inferredcites →https://doi.org/10.1186/s12864-016-3368-9openalex-snapshot

Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus)

inferredcites →https://doi.org/10.1186/s13059-015-0837-4openalex-snapshot

Genomic legacy of the African cheetah, Acinonyx jubatus

inferredcites →https://doi.org/10.1186/s13059-016-1090-1openalex-snapshot

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

inferredcites →https://doi.org/10.1371/journal.pone.0037558openalex-snapshot

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

inferredcites →https://doi.org/10.1371/journal.pone.0091172openalex-snapshot

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

inferredcites →https://doi.org/10.1371/journal.pone.0105015openalex-snapshot

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

inferredcites →https://doi.org/10.1534/g3.116.038208openalex-snapshot

De NovoGenome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-019-44772-5openalex-snapshot

Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus)

inferred← citeshttps://doi.org/10.1093/gigascience/giy124openalex-snapshot

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads

inferred← citeshttps://doi.org/10.1093/gigascience/giy168openalex-snapshot

New de novo assembly of the Atlantic bottlenose dolphin ( Tursiops truncatus ) improves genome completeness and provides haplotype phasing

inferred← citeshttps://doi.org/10.1101/349472openalex-snapshot

Empowering conservation practice with efficient and economical genotyping from poor quality samples

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