Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution

Tianming Lan; Dongming Fang; Haimeng Li; Sunil Kumar Sahu; Qing Wang; Hao Yuan; Yixin Zhu; Zipeng Yang; Le Zhang; Shangchen Yang; Haorong Lu; Lei Han; Shaofang Zhang; Jieyao Yu; Yasser S Mahmmod; Yanchun Xu; Yan Hua; Fengping He; Ziguo Yuan; Huan Liu

doi:10.3389/fgene.2021.819493

Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution

Front Genet. 2022 Jan 21:12:819493. doi: 10.3389/fgene.2021.819493. eCollection 2021.

Authors

Tianming Lan¹, Dongming Fang¹, Haimeng Li^{1

2}, Sunil Kumar Sahu¹, Qing Wang^{1

2}, Hao Yuan^{3

4}, Yixin Zhu^{1

2}, Zipeng Yang^{3

4}, Le Zhang⁵, Shangchen Yang⁶, Haorong Lu^{7

8}, Lei Han⁵, Shaofang Zhang^{7

8}, Jieyao Yu^{7

8}, Yasser S Mahmmod^{9

10}, Yanchun Xu⁵, Yan Hua¹¹, Fengping He¹², Ziguo Yuan^{3

4}, Huan Liu^{1

8}

Affiliations

¹ State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
² College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
³ College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
⁴ Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
⁵ College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.
⁶ College of Life Sciences, Zhejiang University, Hangzhou, China.
⁷ China National GeneBank, BGI-Shenzhen, Shenzhen, China.
⁸ Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China.
⁹ Department of Veterinary Sciences, Faculty of Health Sciences, Higher Colleges of Technology, Al Ain, United Arab Emirates.
¹⁰ Division of Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.
¹¹ Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.
¹² College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.

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.

Keywords: SARS-CoV-2; genetic diversity; genome assembly; immune system; masked palm civet; omnivorous diet.