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Fossil metagenome

ABSTRACT: Metagenome of the woolly mammoth calf Lyuba

PROVIDER: PRJNA395646 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5875720_1.fastq.gz	Fastqsanger.gz
	SRR5875720_2.fastq.gz	Fastqsanger.gz
	SRR5875730_1.fastq.gz	Fastqsanger.gz
	SRR5875730_2.fastq.gz	Fastqsanger.gz
	SRR5875721_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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Project description:The investigation about archaeological samples, which are of inestimable value, requires minimally destructive or nondestructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. This paper reports the results of the first-ever analysis of proteins extracted from the EVA film applied to a tissue sample some 40000 years old. In particular, the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), via a shotgun MS-based approach was investigated. Proteomic and peptidomic analysis allowed the exploration of the mammoth dietary plants and its gut bacteria. The results were validated through the level of deamidation and other post-translational modifications of the peptides of the samples, which were used to discrimitate the “original” endogenous peptides from contaminant ones. Overall, the results of the metaproteomic analysis here reported are in accordance with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth.

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