PGD: a pangolin genome hub for the research community

Abstract

Pangolins (order Pholidota) are the only mammals covered by scales. We have recently sequenced and analyzed the genomes of two critically endangered Asian pangolin species, namely the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla). These complete genome sequences will serve as reference sequences for future research to address issues of species conservation and to advance knowledge in mammalian biology and evolution. To further facilitate the global research effort in pangolin biology, we developed the Pangolin Genome Database (PGD), as a future hub for hosting pangolin genomic and transcriptomic data and annotations, and with useful analysis tools for the research community. Currently, the PGD provides the reference pangolin genome and transcriptome data, gene sequences and functional information, expressed transcripts, pseudogenes, genomic variations, organ-specific expression data and other useful annotations. We anticipate that the PGD will be an invaluable platform for researchers who are interested in pangolin and mammalian research. We will continue updating this hub by including more data, annotation and analysis tools particularly from our research consortium.Database URL: http://pangolin-genome.um.edu.my

Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences

“…Although this paper was in review following revision, the pangolin genome ( Tan et al 2016 ) was released and cleared its 12-month embargo period. This gives us an opportunity to incorporate the pangolin data into our analyses.…”

From bats to pangolins: new insights into species differences in the structure and function of the immune system

“…Among these efforts is the creation of the Pangolin Gene Database, as well as the work of Zang et al, 2020 and others. 6,67 Pangolins, like bats, have been identified as a possible natural reservoir and source of SARS-CoV2. 6,68 It has been determined that pangolin-CoV is ∼90% identical to SARS-CoV-2 receptor binding domain and is its second closest relative.…”

Comprehensive genome analysis of a pangolin-associatedParaburkholderia fungorumprovides new insights into its secretion systems and virulence

“…The genome sequence of pangolin Pf (accession numbers: CP028829-CP028832) can be downloaded from the GenBank database at the National Center for Biotechnology Information (NCBI) website. It was assembled from the previous pangolin genome data (accession numbers: SRR3949798, SRR3949787, SRR3949728, SRR3949765, and SRR11935558) generated from the genome sequencing of an infected female Malayan pangolin (Tan et al, 2016b;Choo et al, 2020). Briefly, the raw reads generated from three P. fungorum-infected tissues (cerebrum, cerebellum and fetus) of the Malayan pangolin (manuscript in preparation) were pooled and assembled by mapping the reads to the reference genome, Paraburkholderia fungorum ATCC BAA-463 (Accession numbers: CP010024-CP010027) downloaded from NCBI using CLC Assembly Cell software with default parameters (D'Cruze et al, 2011).…”

“…In a previous genome sequencing project, we sequenced the genomes of the infected cerebellum and cerebrum of a female pregnant Malayan pangolin (Manis javanica) and its infected fetus (Tan et al, 2016b;Choo et al, 2016b). A bacterium genome was identified in the pangolin genome data and identified as a Paraburkholderia species (hereto referred to as pangolin Pf).…”