The assembled and annotated genome of the masked palm civet (Paguma larvata)

Abstract

Background: The masked palm civet (Paguma larvata) acts as an intermediate host of severe acute respiratory syndrome coronavirus (SARS-CoV), which caused SARS, and transfered this virus from bats to humans. Additionally, P. larvata has the potential to carry a variety of zoonotic viruses that may threaten human health. However, genome resources for P. larvata have not been reported to date.

Findings: A chromosome-level genome assembly of P. larvata was generated using PacBio sequencing, Illumina sequencing, and Hi-C technology. The genome assembly was 2.44 Gb in size, of which 95.32% could be grouped into 22 pseudochromosomes, with contig N50 and scaffold N50 values of 12.97 Mb and 111.81 Mb, respectively. A total of 21,582 protein-coding genes were predicted, and 95.20% of the predicted genes were functionally annotated. Phylogenetic analysis of 19 animal species confirmed the close genetic relationship between P. larvata and species belonging to the Felidae family. Gene family clustering revealed 119 unique, 243 significantly expanded, and 58 significantly contracted genes in the P. larvata genome. We identified 971 positively selected genes in P. larvata, and one known human viral receptor gene PDGFRA is positively selected in P. larvata, which is required for human cytomegalovirus infection.

Conclusions: This high-quality genome assembly provides a valuable genomic resource for exploring virus-host interactions. It will also provide a reliable reference for studying the genetic bases of the morphologic characteristics, adaptive evolution, and evolutionary history of this species.

Keywords: Hi-C proximity mapping; gene family evolution; genome assembly; masked palm civet; phylogeny; positive selection.

Figure 1:

(a) Synteny of corresponding chromosomes and gene density across the Paguma larvata genome. (b) Comparison of copy numbers in gene clusters that reside in the genomes of P. larvata and 18 other animals. Single-copy orthologs denote that the family can have only one gene for each species, and multicopy orthologs denote that the family clustered more than one gene for each species. Other orthologs denote the family can have any number of genes for each species except the single-copy and multicopy orthologs. Unique paralogs denote species-specific gene families, and unclustered genes denote species-specific genes that cannot cluster with any other genes. (c) Phylogenetic relationship of 19 animal genomes based on the maximum likelihood method. The black numbers indicate estimated divergent times as the number of years (millions) ago, while green and red numbers denote gene families subject to expansion and contraction for each species, respectively.

Figure 2:

Phylogenetic relationships of known human virus receptor of PDGFRA under positive selection and ACE2 receptor in P. larvata and other species.