Probing the genomic limits of de-extinction in the Christmas Island rat

Lin, Jianqing; Duchêne, David A.; Carøe, Christian; Smith, Oliver; Ciucani, Marta Maria; Niemann, Jonas; Richmond, Douglas J.; Greenwood, Alex D.; MacPhee, R. D. E.; Gopalakrishnan, Shyam; Gilbert, M. Thomas P.

doi:10.1016/j.cub.2022.02.027

Cited by 13 publications

(4 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Molecular de-extinction is the resurrection of extinct molecules of life: nucleic acids, proteins, and other compounds no longer encoded by living organisms. While the societal benefit of organismal de-extinction is still unknown and contentious, technical challenges like incomplete genomic coverage remain significant (1,2). By synthesizing only isolated compounds, molecular de-extinction circumvents many of the ethical and technical problems posed by whole-organism de-extinction.…”

Section: Introductionmentioning

confidence: 99%

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning

Maasch

Torres

Melo

et al. 2023

Cell Host & Microbe

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning

Maasch

Torres

Melo

et al. 2023

Cell Host & Microbe

View full text Add to dashboard Cite

“…Finally, while attempts at species "de-extinction" face formidable hurdles (cf. Lin et al 2022;Richmond, Sinding, and Gilbert 2016), the potential to generate true de novo reference genomes, to examine the three-dimensional structure of ancient genomes from samples preserved in permafrost, and to explore epigenetic patterns genome-wide may -when combined with developments in the study of ancient RNA (e.g. Fromm et al 2020;Smith et al 2019;Fordyce et al 2013) and proteins (e.g.…”

Section: Discussionmentioning

confidence: 99%

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

Sandoval-Velasco

Dudchenko

Rodríguez

et al. 2023

Preprint

View full text Add to dashboard Cite

Ancient DNA (aDNA) sequencing analysis typically involves alignment to a modern reference genome assembly from a related species. Since aDNA molecules are fragmentary, these alignments yield information about small-scale differences, but provide no information about larger features such as the chromosome structure of ancient species. We report the genome assembly of a female Late Pleistocene woolly mammoth (Mammuthus primigenius) with twenty-eight chromosome-length scaffolds, generated using mammoth skin preserved in permafrost for roughly 52,000 years. We began by creating a modified Hi-C protocol, dubbed PaleoHi-C, optimized for ancient samples, and using it to map chromatin contacts in a woolly mammoth. Next, we developed "reference-assisted 3D genome assembly," which begins with a reference genome assembly from a related species, and uses Hi-C and DNA-Seq data from a target species to split, order, orient, and correct sequences on the basis of their 3D proximity, yielding accurate chromosome-length scaffolds for the target species. By means of this reference-assisted 3D genome assembly, PaleoHi-C data reveals the 3D architecture of a woolly mammoth genome, including chromosome territories, compartments, domains, and loops. The active (A) and inactive (B) genome compartments in mammoth skin more closely resemble those observed in Asian elephant skin than the compartmentalization patterns seen in other Asian elephant tissues. Differences in compartmentalization between these skin samples reveal sequences whose transcription was potentially altered in mammoth. We observe a tetradic structure for the inactive X chromosome in mammoth, distinct from the bipartite architecture seen in human and mouse. Generating chromosome-length genome assemblies for two other elephantids (Asian and African elephant), we find that the overall karyotype, and this tetradic Xi structure, are conserved throughout the clade. These results illustrate that cell-type specific epigenetic information can be preserved in ancient samples, in the form of DNA geometry, and that it may be feasible to perform de novo genome assembly of some extinct species.

show abstract

“…To further explore how the genomic divergence can influence our genome reconstruction success, we undertook a similar approach as the genome of the Christmas Island rat 54 , and explored the chromosomal regions in the G. alexis reference that were significantly depleted of Xerces DNA reads. We used bedtools 31 and some in-home bash scripting to calculate the mean coverage per gene of the G. alexis genome for Xerces Blue sequencing DNA reads.…”

Section: Methodsmentioning

confidence: 99%

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

de-Dios

Fontsere

Renom

et al. 2021

Preprint

View full text Add to dashboard Cite

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. To explore the demographic history of this iconic butterfly and to better understand why it went extinct, we sequenced at medium coverage the genomes of four 80 to 100-year-old Xerces Blue specimens and seven historic specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, we show that both species experienced population growth during the MIS 7 interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. In addition, the Xerces Blue carried a higher proportion of derived, putatively deleterious amino acid-changing alleles than the Silvery Blue. These results demonstrate that the Xerces Blue experienced more than 100 thousand years of population decline, prior to its human-induced final extinction.

show abstract

Probing the genomic limits of de-extinction in the Christmas Island rat

Cited by 13 publications

References 53 publications

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning

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

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

Contact Info

Product

Resources

About