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Contamination in ancient faunal datasets

ABSTRACT: Low coverage shotgun sequencing of woolly mammoth and ancient canid samples.

PROVIDER: PRJEB41038 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR4778300_1.fastq.gz	Fastqsanger.gz
	ERR4778300_2.fastq.gz	Fastqsanger.gz
	ERR4778310_1.fastq.gz	Fastqsanger.gz
	ERR4778310_2.fastq.gz	Fastqsanger.gz
	ERR4778320_1.fastq.gz	Fastqsanger.gz

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Project description:Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

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