caprini

Welcome to Livestock and Poultry Pan-genome Database

Livestock and Poultry, such as cattle, goat, sheep, chicken and duck are five representative animals providing human daily living equipment of meat, milk and wool. However, some causal mutations associated with economic traits or some breed-specific variations couldn't be effectively discovered due to the limited single individual genome. The pan-genome outperform the traditional reference assembly by incorporating a core genome shared among individuals and partially shared dispensable genome. Therefore, we construct four pan-genomes of Caprini, Bos, Pig and Chicken containing NCBI published genomes and our de novo genome assemblies, which will provided an avenue for studying the degree of dispensable genomes within a tribe or breeds and explaining the functional and evolutionary consequences of dispensable genome and their importance in shaping the genome flexibility. Livestock and Poultry pan-genome will not only deepen our understanding their speciation history but also help explain how genomic adaptions have conferred flexibility in various environments and what roles have human played in modifying animal behavior and phenotype.


This database provides:

  • Search
  • Search a gene symbol to obtain its basic information and Presence-absence variations (PAVs) of the dispensable-genome in the re-sequencing samples.
  • Search a position located on any chromosomes or scaffolds of the pan-genome to obtain genes included and PAV distributions.
  • Genome Table:
  • Genome information, assembly and Pan-genome construction information.
  • Tools:
  • GBrowse: View gene annotation, dispensable sequence localization, CNVs, and expression.
  • Blat: Alignment sequences to pan-genome.
  • Blast: Alignment sequences to pan-genome.
  • Download:
  • Providing pan-genome fasta sequences and gene annotation in ftp server.