caprini

Welcome to The Caprini Pan-genome Database

Goats and sheep are the earliest domestic animals providing meat, milk, wool and other animal products for humans. Until now, it formed nearly two thousands of breeds with various traits. We collected a large number of re-sequencing data containing goat and sheep to search the major genes and causal mutations related economic traits. However, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. Therefore, we constructed a goat based Caprini Pan-genome according to 10 Caprini genomes that have been published or de novo assembled in our laboratory. This pan-genome contains ~2.9 Gbp latest goat reference sequence (RefSeq accession: GCF_001704415.1) and ~312 Mbp non-redundant sequences. Meanwhile, we also constructed a detailed variation database using thousands of sequencing data of goats and sheep. The construction of Caprini pan-genome and genetic variation database will help to reveal the natural evolution and artificial domestication history of Caprinae, promote the genetic breeding research and application, and provide dominant functional loci and target for the downstream breeders.

This database provides:

  1. Sequences and gene annotations for Caprini pan-genome
  2. Basic information of 10 Caprini genomes and re-sequencing samples
  3. Presence-absence variations (PAVs) of the dispensable-genome in the re-sequencing samples
  4. Variations including SNPs, Indels and CNVs for the re-sequencing samples
  5. Expression profiles in different tissues for goats and sheep

Information in this database can be accessed in the following ways:

  1. Search
    • Search a single gene to obtain its basic information, variation distributions, PAV, gene functions and expressions
    • Search a position located on any chromosomes or scaffolds of the pan-genome, to obtain variation distributions, PAV, gene functions and expressions
    • Search species-specific and breeds-specific sequences of goats and sheep
  2. Tools:
    • JBrowse: View gene annotation, frequency, SNPs, and expression
    • Blast: Alignment sequences to goat based Caprini pan-genome.

Goat-based Pan-genome

Genome composition

Fragment distribution

Pan-Genome pipeline

Statistics

Genome Novel Sequence Size Novel Gene Number
CHIR_2.0 7.7 M 8,106
CapAeg_1.0 17 M 17,661
Caeg1 2.3 M 1,884
CI_1.0 77 M 88,130
Oori1 11 M 12,170
Oar_v4.0 63 M 55,988
Pn_1.0 85 M 37,657
Al_1.0 52 M 24,113
Total 312 M 245,709
Genome Novel Sequence Size Novel Gene Number
CHIR_2.0 7.7 M 8,106
CapAeg_1.0 17 M 17,661
Caeg1 2.3 M 1,884
CI_1.0 77 M 88,130
Oori1 11 M 12,170
Oar_v4.0 63 M 55,988
Pn_1.0 85 M 37,657
Al_1.0 52 M 24,113
Total 312 M 245,709
Genome Novel Sequence Size Novel Gene Number
CHIR_2.0 7.7 M 8,106
CapAeg_1.0 17 M 17,661
Caeg1 2.3 M 1,884
CI_1.0 77 M 88,130
Oori1 11 M 12,170
Oar_v4.0 63 M 55,988
Pn_1.0 85 M 37,657
Al_1.0 52 M 24,113
Total 312 M 245,709

Sheep-based Pan-genome

Genome composition

Fragment distribution

Pan-Genome pipeline

Statistics

Genome Novel Sequence Size Novel Gene Number
CHIR_2.0 7.7 M 8,106
CapAeg_1.0 17 M 17,661
Caeg1 2.3 M 1,884
CI_1.0 77 M 88,130
Oori1 11 M 12,170
Oar_v4.0 63 M 55,988
Pn_1.0 85 M 37,657
Al_1.0 52 M 24,113
Total 312 M 245,709
Genome Novel Sequence Size Novel Gene Number
CHIR_2.0 7.7 M 8,106
CapAeg_1.0 17 M 17,661
Caeg1 2.3 M 1,884
CI_1.0 77 M 88,130
Oori1 11 M 12,170
Oar_v4.0 63 M 55,988
Pn_1.0 85 M 37,657
Al_1.0 52 M 24,113
Total 312 M 245,709
Genome Novel Sequence Size Novel Gene Number
CHIR_2.0 7.7 M 8,106
CapAeg_1.0 17 M 17,661
Caeg1 2.3 M 1,884
CI_1.0 77 M 88,130
Oori1 11 M 12,170
Oar_v4.0 63 M 55,988
Pn_1.0 85 M 37,657
Al_1.0 52 M 24,113
Total 312 M 245,709