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Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution.
Lan, Tianming; Fang, Dongming; Li, Haimeng; Sahu, Sunil Kumar; Wang, Qing; Yuan, Hao; Zhu, Yixin; Yang, Zipeng; Zhang, Le; Yang, Shangchen; Lu, Haorong; Han, Lei; Zhang, Shaofang; Yu, Jieyao; Mahmmod, Yasser S; Xu, Yanchun; Hua, Yan; He, Fengping; Yuan, Ziguo; Liu, Huan.
  • Lan T; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Fang D; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Li H; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Sahu SK; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
  • Wang Q; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Yuan H; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Zhu Y; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
  • Yang Z; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
  • Zhang L; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
  • Yang S; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Lu H; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
  • Han L; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
  • Zhang S; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
  • Yu J; College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.
  • Mahmmod YS; College of Life Sciences, Zhejiang University, Hangzhou, China.
  • Xu Y; China National GeneBank, BGI-Shenzhen, Shenzhen, China.
  • Hua Y; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China.
  • He F; College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.
  • Yuan Z; China National GeneBank, BGI-Shenzhen, Shenzhen, China.
  • Liu H; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China.
Front Genet ; 12: 819493, 2021.
Article in English | MEDLINE | ID: covidwho-1674328
ABSTRACT
The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has been particularly concerned about this species. Here, we present the first genome of the P. larvata, comprising 22 chromosomes assembled using single-tube long fragment read (stLFR) and Hi-C technologies. The genome length is 2.41 Gb with a scaffold N50 of 105.6 Mb. We identified the 107.13 Mb X chromosome and one 1.34 Mb Y-linked scaffold and validated them by resequencing 45 P. larvata individuals. We predicted 18,340 protein-coding genes, among which 18,333 genes were functionally annotated. Interestingly, several biological pathways related to immune defenses were found to be significantly expanded. Also, more than 40% of the enriched pathways on the positively selected genes (PSGs) were identified to be closely related to immunity and survival. These enriched gene families were inferred to be essential for the P. larvata for defense against the pathogens. However, we did not find a direct genomic basis for its adaptation to omnivorous diet despite multiple attempts of comparative genomic analysis. In addition, we evaluated the susceptibility of the P. larvata to the SARS-CoV-2 by screening the RNA expression of the ACE2 and TMPRSS2/TMPRSS4 genes in 16 organs. Finally, we explored the genome-wide heterozygosity and compared it with other animals to evaluate the population status of this species. Taken together, this chromosome-scale genome of the P. larvata provides a necessary resource and insights for understanding the genetic basis of its biological characteristics, evolution, and disease transmission control.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Language: English Journal: Front Genet Year: 2021 Document Type: Article Affiliation country: Fgene.2021.819493

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Language: English Journal: Front Genet Year: 2021 Document Type: Article Affiliation country: Fgene.2021.819493