PGD: a pangolin genome hub for the research community.

Tze King Tan,Aini Mohamed Yusoff,Stephen J O'Brien,Siew Woh Choo,Guat Jah Wong,Warren E Johnson,Naresh V.R Mutha,Ian C Paterson,Ksenia Krasheninnikova,Pavel Dobrynin,Wesley C Warren,Mike Rayko,Ka Yun Tan,Aleksey Komissarov,Cheuk Chuen Siow,Ranjeev Hari,Gaik Tamazian

doi:10.1093/database/baw063

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

Highlights

Pangolins are ancient creatures whose ancestors are thought to be members of a suborder of Palaeanodonta from some 60 million years ago [1]
These hard scales are used as a protective layer; when threatened, pangolins quickly roll up into a tight ball and the scales act as a shield
We have recently sequenced the genomes of two pangolin species, the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla) from Malaysia and Taiwan, respectively, using high-throughput next-generation sequencing (NGS) approaches

Summary

Introduction

Pangolins are ancient creatures whose ancestors are thought to be members of a suborder of Palaeanodonta from some 60 million years ago [1]. PGD provides interactive and user-friendly web interfaces for users to search, browse, retrieve, visualize and analyze pangolin genomic and transcriptomic data and information. We annotated the entire genome of both pangolin species using a well-established MAKER pipeline, which was designed for the annotation of emerging model genomes using evidence from ab initio gene prediction, sequence homology approach and the transcriptomic data from Malayan pangolin [10].

Results

Conclusion