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Mammuthus primigenius

ABSTRACT: The woolly mammoth is an extinct mammal and a subject for paleogenomic studies

PROVIDER: PRJNA68357 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR058709.fastq.gz	Fastqsanger.gz
	DRR058710_1.fastq.gz	Fastqsanger.gz
	DRR058710_2.fastq.gz	Fastqsanger.gz
	DRR058711.fastq.gz	Fastqsanger.gz
	DRR058712.fastq.gz	Fastqsanger.gz

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Proteomics of muscle and bone marrow samples from the 28,000-year-old remains of a woolly mammoth (Mammuthus primigenius).

Project description:The 28,000-year-old remains of a woolly mammoth, named ‘Yuka’, were found in Siberian permafrost. We performed proteomic analyses of muscle and bone marrow samples obtained from the remains to gain information about the repertoire and modifications of proteins.

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Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius.

Project description:Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.

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Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

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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Proteomic Analysis of the Shandrin Mammoth by EVA Technology and High-Resolution Mass Spectrometry: What is its Gut Telling Us?

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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Project description:Sequencing of woolly mammoth environmental sample

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