HGFDB: a collective database of helmeted guinea fowl genomics.

Xuzhen Li,Shengchang Duan,Yunfei Li,Zhaocheng Ma,Shanshan Chen,Zetan Xu,Yuan Du,Quankuan Shen,Yunbin Pan,Yang Dong,Xiao Dong,Zhi Li

doi:10.1093/database/baaa116

Abstract

As a vigorous and hardy and an almost disease-free game bird, the domestic helmeted guinea fowl (Numida meleagris, hereafter HGF) has attracted considerable attention in a large number of genetic study projects. However, none of the current/recent avian databases are related to this agriculturally and commercially important poultry species. To address this data gap, we developed Helmeted Guinea Fowl Database (HGFDB), which manages and shares HGF genomic and genetic data. By processing the data of genome assembly, sequencing reads and genetic variations, we organized them into eight modules, which correspond to ‘Home’, ‘Genome’, ‘Re-sequence’, ‘Gene’, ‘Variation’, ‘Download’, ‘Tools’ and ‘Help’, HGFDB provides the most comprehensive view of the HGF genome to date and will be relevant for future studies on HGF structural and functional genomics and genetic improvement. Database URL: http://hgfdb.ynau.edu.cn/

Highlights

The domestic helmeted guinea fowl (Numida meleagris, NCBI Taxonomy ID: 8996, hereafter HGF), under the family of Galliformes, is an agriculturally important poultry species
Much effort has been taken on exploration of the genetic variation of poultry species, which serves as an important first step to reveal the uniqueness and to identify valuable genetic resources
It was not until 2019 that the first draft HGF genome assembly obtained by short sequencing reads was published [10]

Summary

Introduction

The domestic helmeted guinea fowl (Numida meleagris, NCBI Taxonomy ID: 8996, hereafter HGF), under the family of Galliformes, is an agriculturally important poultry species. HGF is important, little genetic study has been experimented on it, especially when compared to chicken. Only a handful of papers have been published on genetic diversity of HGF, mainly by microsatellite markers [7] or mtDNA [8, 9]. It was not until 2019 that the first draft HGF genome assembly obtained by short sequencing reads was published [10]. We have discovered a tremendous number of single nucleotide polymorphism and InDel markers for 129 re-sequenced samples, which provides a foundation for developing future sustainable genetic improvement and conservation programs

Methods

Results

Conclusion