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.
Highlights
The masked palm civet (Paguma larvata) (Carnivora: Viverridae) attracted public concern in 2003 when the severe acute respiratory syndrome (SARS)-associated coronavirus (SARSCoV) was identified by Guan et al from several P. larvata individuals from a Shenzhen (China) market (Guan et al, 2003)
The genome size of the P. larvata was estimated to be 2.46 Gb, with a heterozygosity rate of 0.635% (Supplementary Figure S1), by calculating the frequency of 17-mer using 82.08 Gb short reads generated by DNBSEQ-T1 sequencer
The guanine and cytosine (GC) content of this genome is 42.1%, which was very similar to 42.5% of its closely related species, Paradoxurus hermaphroditus (GCA_004024585.1)
Summary
The masked palm civet (Paguma larvata) (Carnivora: Viverridae) attracted public concern in 2003 when the severe acute respiratory syndrome (SARS)-associated coronavirus (SARSCoV) was identified by Guan et al from several P. larvata individuals from a Shenzhen (China) market (Guan et al, 2003) This small carnivore is the only species in the genus of Paguma. The masked palm civet was found to hibernate slightly during the winter in the northern area (Zhang et al, 1991; Kang et al, 1997) It has been introduced in Japan as an alien species (Nawa, 1965; Torii, 2009). This species is nocturnal, arboreal, and basically solitary They live in a variety of habitats, including forests, rainforest, parks, fruit orchards, and gardens. There are 15 subspecies according to body color and facial pattern (Wozencraft, 2005), but the genetic difference among different populations is low (Patou et al, 2009), indicating the need for taxonomic revision for this species
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