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Overview

Goats and sheep of Caprini are a major source of meat, milk and fiber in our daily lives. 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. This website was to construct a Caprini pan-genome based on 10 Caprini genomes including 4 de novo genome assemblies (Pseudois nayaur, Ammotragus lervia, Capra ibex and Ovis ammon) and 6 NCBI published genomes (ARS1 and CHIR_2.0 of domestic goat, Oar4.0 of domestic sheep, CapAeg1.0 and Caeg1 of wild goat, Ooril of wild sheep). We also used re-sequencing data from nearly one thousand goats and sheep samples to build a detailed variation database. This project shows a great advantage over a single reference assembly in exploring genomic variations and expands our understanding of environment adaptation.

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 Caprini pan-genome database provides three retrieval methods:

A. Search by a gene:Type a gene name into the "search term" box, then press "search" to obtain gene basic information, variations distribution in different goat/sheep breeds and gene expressions. Users can click "view" button to get graphical results.

B. Search by a position:Use the "Position Search" box to obtain basic information of the included genes, all variations information in this region and gene expression information in babies and adults.

C. Search specific sequences by species and breeds:Choose Caprinae species and each goat/sheep breed from the drop-down list, then press "Search" to obtain species-specific and breeds-specific sequences of goats and sheep.

3. Sample table

Users can query sample breeds or sample distribution region to filter the sample information.

4. Expression

The expression data mainly shows the RPKM value of tissue samples, which can be linked to jbrowse page for visualization.

5. Tools

A. Jbrowse: View gene annotation, frequency, SNPs and gene expression.

B. Blast: Alignment sequences to reference genome or Caprini pan-genome.

6. Download

Caprini pan-genome reference sequences, annotation, and resequencing data were provided in ftp server of download page.

Contract

If you have any questions, please contact us by email: jiangyu96@163.com.