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

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.

Specific Gene Duplication and Loss of Cytochrome P450 in Families 1-3 in Carnivora (Mammalia, Laurasiatheria)

“…UCSC (University of California, Santa Cruz) BLAT (a BLAST-like alignment tool) ( (accessed on 1 October 2022)) was used for additional confirmation of missing genes. The masked palm civet CYP genes were also retrieved and used to fill the gap for Feliformia species from recently assembled and annotated chromosome-level genomic data [ 25 ]…”

Genome assembly and annotation of the king ratsnake, Elaphe carinata

“…Usually, genome-wide repetitive elements are important for eukaryotic evolution [ 35 ] . In E. carinata , the content of repetitive elements in the genome accounted for 42.26%, and the total length reached 621 Mb (Tables 3 and 4 ).…”

The Genome Assembly of the King Ratsnake Elaphe carinata, Helps Reveal Its Biological Characteristics

“…Usually, genome-wide repetitive elements are important for eukaryotic evolution [30]. In E. carinata, the content of repetitive elements in the genome accounted for 38.90%, and the total length reached 621Mb (Tables 2 and 3).…”