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Overview

Major Livestock and Poultry such as cattle, goat, sheep, chicken and duck are five representative animals providing meat, milk and wool in our daily lives. Until now, these animals formed nearly thousands of breeds with various traits. So it’s beneficial for us to study causative variations under phenotype. However, a single genome is insufficient to represent the genomic content of one specie, since many common sequences might be absent in the sequenced individual. So we construct four pan-genomes of Caprini, Bos, Pig and Chicken with NCBI published genomes and our de novo genome assemblies. We also used re-sequencing data to obtain the distribution of presence-absence variations (PAVs) of the dispensable-genome. This project will help to reveal the natural evolution and artificial domestication history in domestic animals and provide dominant functional loci and target for the downstream breeders.

User Manual

1. Home

Home page shows the basic information and statistical results of Caprini pan-genome. Users can switch the sample distribution map of goats and sheep by clicking on the forward button.

2. Search

The livestock and poultry pan-genome database provides three retrieval methods:

Search by a gene:Type a gene name into the "search term" box, then press "search" to obtain gene basic information, and Presence-absence variations (PAVs) of the dispensable-genome in the re-sequencing samples. Users can click "view" button to get graphical results.

Search by a position:Use the "Position Search" box to obtain basic information of the included genes, and PAV distributions.

Search localization for dispensable sequences:Type a gene name or position to obtain localization of dispensable sequences.

3. Genome table

Users can get genome information, assembly and pan-genome construction information from Genome table.

4. Tools

Gbrowse: View gene annotation, dispensable sequence localization, CNVs, and expression.

Blat: Alignment sequences to a pan-genome database.

Blast: Alignment sequences to a pan-genome database.

5. Download

Caprini, Bos, Pig and Chicken pan-genome reference sequences, and gene annotation were provided in ftp server of download page.

Contract

If you have any questions, please contact us by email: yu.jiang@nwafu.edu.cn.