Genome Assembly and Analysis of the North American Mountain Goat (<i>Oreamnos americanus</i>) Reveals Species-Level Responses to Extreme Environments

Martchenko, Daria; Chikhi, Rayan; Shafer, Aaron B. A.

doi:10.1534/g3.119.400747

Cited by 15 publications

(17 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We explored the possible phylogenetic position of the reads that aligned to the Oar_v3.1 genome within the Ovis and Capra genus. In order to determine the SNPs to compare to SAT29, we built a dataset with individuals from all the available species of the genus Ovis and Capra : Ovis vignei (Nextgen project: https://projects.ensembl.org/nextgen/), Ovis aries (Nextgen project: https://projects.ensembl.org/nextgen/), Ovis canadensis (Kardos et al, 2015), Ovis ammon (Yang et al, 2017b), Ovis orientalis (Nextgen project: https://projects.ensembl.org/nextgen/), Ovis nivicola (Upadhyay et al, 2020) Capra hircus (Nextgen Project: https://projects.ensembl.org/nextgen/), C. caucasica (Zheng et al, 2020), C. ibex (Grossen et al, 2020), C. aegagrus (Alberto et al, 2018) and Oreamnos americanus as an outgroup (Martchenko et al, 2020). We downloaded the available VCF files of the following genomes: 75 Ovis aries genomes, 4 Ovis vignei genomes, 14 Ovis orientalis genomes and one Capra hircus.…”

Section: Methods Detailsmentioning

confidence: 99%

“…Oreamnos americanus as an outgroup (Martchenko et al, 2020) . We downloaded the As the available VCF files does not cover all species we wanted to include, we downloaded the FASTQ files of one Ovis canadensis, one Ovis nivicola, one Ovis ammon, one C caucasica, one Capra ibex, one C sibirica, two C aegagrus and one Oreamnos americanus to produce additional VCF files for downstream analyses.…”

Section: Ovis Genomic Analysismentioning

confidence: 99%

See 1 more Smart Citation

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Gelabert

Sawyer

Bergström

et al. 2021

Preprint

View full text Add to dashboard Cite

SummaryArchaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history.HighlightsWe demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remainsA single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomesWe show that sediment ancient DNA can reveal important aspects of the human and faunal pastEvidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum∼0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species

show abstract

Section: Methods Detailsmentioning

confidence: 99%

Section: Ovis Genomic Analysismentioning

confidence: 99%

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Gelabert

Sawyer

Bergström

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…The genome of B. taurus (ARS-UCD1.2) (Rosen et al 2020) was selected as reference, and that of O. americanus (ASM975805v1) (Martchenko et al 2020),O. aries(Oar rambouillet v1.0),C. hircus (ARS1) (Worley 2017),P. hodgsonii (PHO1.0) (Ge et al 2013),A.…”

Section: Phylogenetic Analysis and Divergence Time Estimationmentioning

confidence: 99%

Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity

Yang

et al. 2022

Preprint

View full text Add to dashboard Cite

The takin (Budorcas taxicolor) is one of the largest bovid herbivores across caprinae subfamily. The takin is at high risk of extinction, however, its taxonomic status is still unclear. In this study, we constructed the first reference genome of B. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb and a scaffold N50 of 101.27 Mb, which were anchored onto 25+XY chromosomes. Compared to the common ancestral karyotype of bovidae (2n=60), we found the takin (2n=52) experienced four chromosome fusions and one large translocation. We also found that the takin was most closely related to muskox, not other caprinae species. Further, we re-sequenced nine golden takins from the main distribution area, Qinling Mountains, and identified 3.3 million SNPs. The genetic diversity of takin was very low (θπ=0.00028 and heterozygosity=0.00038), which was among the lowest detected in the domestic and wild mammals. We also found takin genomes showed high inbreeding coefficient (FROH=0.217) suggesting severe inbreeding depression. The genome analysis show that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into its evolution.

show abstract

“…ensembl.org/nextgen/), Ovis canadensis, 120 Ovis ammon, 121 Ovis orientalis (Nextgen project: https://projects.ensembl.org/ nextgen/), Ovis nivicola 122 Capra hircus (Nextgen Project: https://projects.ensembl.org/nextgen/), C. caucasica, 123 C. ibex, 124 C. aegagrus 125 and Oreamnos americanus as an outgroup. 126 We downloaded the available VCF files of the following genomes: 75 Ovis aries genomes, 4 Ovis vignei genomes, 14 Ovis orientalis genomes and one Capra hircus. This dataset consists of 48,870,177 SNPs in the autosomal chromosomes of the Ovis aries genome.…”

Section: Ovis Genomic Analysismentioning

confidence: 99%

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

et al. 2021

View full text Add to dashboard Cite

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment Highlights d A single shotgun-sequenced Pleistocene sediment yielded genomic data of three mammals d Sediment genome sequencing can produce data comparable to that from skeletal remains d A pre-LGM human lineage from the Caucasus was an ancestral component of West Eurasia d 0.01X wolf and bison environmental genomes, suggesting reshaping of populations

show abstract

Genome Assembly and Analysis of the North American Mountain Goat (Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments

Cited by 15 publications

References 52 publications

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Contact Info

Product

Resources

About