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#35961775   2022/08/12 To Up

Recent, full-length gene retrocopies are common in canids.

Gene retrocopies arise from the reverse transcription and insertion into the genome of processed mRNA transcripts. Although many retrocopies have acquired mutations that render them functionally inactive, most mammals retain active LINE-1 sequences capable of producing new retrocopies. New retrocopies, referred to as retro copy number variants (retroCNVs), may not be identified by standard variant calling techniques in high-throughput sequencing data. Although multiple functional retroCNVs have been associated with skeletal dysplasias in dogs, the full landscape of canid retroCNVs has not been characterized. Here, retroCNV discovery was performed on a whole-genome sequencing data set of 293 canids from 76 breeds. We identified retroCNV parent genes via the presence of mRNA-specific 30-mers, and then identified retroCNV insertion sites through discordant read analysis. In total, we resolved insertion sites for 1911 retroCNVs from 1179 parent genes, 1236 of which appeared identical to their parent genes. Dogs had on average 54.1 total retroCNVs and 1.4 private retroCNVs. We found evidence of expression in testes for 12% (14/113) of the retroCNVs identified in six Golden Retrievers, including four chimeric transcripts, and 97 retroCNVs also had significantly elevated across dog breeds, possibly indicating selection. We applied our approach to a subset of human genomes and detected an average of 4.2 retroCNVs per sample, highlighting a 13-fold relative increase of retroCNV frequency in dogs. Particularly in canids, retroCNVs are a largely unexplored source of genetic variation that can contribute to genome plasticity and that should be considered when investigating traits and diseases.
Kevin Batcher, Scarlett Varney, Daniel York, Matthew Blacksmith, Jeffrey M Kidd, Robert Rebhun, Peter Dickinson, Danika Bannasch

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#35961570   2022/08/09 To Up

Heterologous spatial distribution of soil polycyclic aromatic hydrocarbons and the primary influencing factors in three industrial parks.

Soil polycyclic aromatic hydrocarbons (PAHs) generated from industrial processes are highly spatially heterologous, with limited quantitative studies on their main influencing factors. The present study evaluated the soil PAHs in three types of industrial parks (a petrochemical industrial park, a brominated flame retardant manufacturing park, and an e-waste dismantling park) and their surroundings. The total concentrations of 16 PAHs in the parks were 340-2.43 × 10, 26.2-2.63 × 10, and 394-2.01 × 10 ng/g, which were significantly higher than those in the surrounding areas by 1-2 orders of magnitude, respectively. The highest soil PAH contamination was observed in the e-waste dismantling park. Nap can be considered as characteristic pollutant in the petrochemical industrial park, while Phe in the flame retardant manufacturing park and e-waste dismantling park. Low molecular weight PAHs (2-3 rings) predominated in the petrochemical industrial park (73.0%) and the surrounding area of brominated flame retardant manufacturing park (80.3%). However, high molecular weight PAHs (4-6 rings) were enriched in the other sampling sites, indicating distinct sources and determinants of soil PAHs. Source apportionment results suggested that PAHs in the parks were mainly derived from the leakage of petroleum products in the petroleum manufacturing process and pyrolysis or combustion of fossil fuels. Contrarily, the PAHs in the surrounding areas could have been derived from the historical coal combustion and traffic emissions. Source emissions, wind direction, and local topography influenced the PAH spatial distributions.
Helong Ren, Peixin Su, Wei Kang, Xiang Ge, Shengtao Ma, Guofeng Shen, Qiang Chen, Yingxin Yu, Taicheng An

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