Creating the first graphical pan-genome map of sheep based on HiFi sequencing

Pan-genome refers to the entire gene sequence present in a species

With the advent of PacBio HiFi sequencing technology, genome assembly no longer consumes a lot of manpower and material resources, and high-quality genome assembly can often be completed within a few days

As an important scientific research team in the study of animal genomes in China, Professor Jiang Yu's team from Northwest A&F University will publish the first high-quality reference genome Saanen_v1 of Saanen dairy goat in 2021 in Genetics Selection Evolution, a top journal in the field of animal genetics and breeding ¹ , the study used high-depth Pacbio sequencing and Hi-C-assisted assembly technology, and its Contig N50 reached 46Mb

Recently, Prof.

13 sheep breeds with high-quality haplotype genome assembly

In this study, the authors used PacBio HiFi sequencing technology to perform whole genome sequencing on a total of 13 sheep breeds from Europe, Asia, the Middle East and Africa.

Among them, the most complete assembly of the FRI1 genome, the Contig N50 representing the assembly continuity has reached 85.

Pan-genome construction and variant analysis

With the construction of a total of 26 sets of high-quality haplotype genomes for 13 breeds, the authors further analyzed structural variation, and constructed a complex graph-based pan-genome of sheep based on structural variation, single base polymorphisms

Through the analysis, the variants classified as SINES were concentrated at 150 bp in size, the LTR-related variants were concentrated at around 1,300 bp, and the larger LINE-related variants were at 7,750 bp (Fig.

Insertional variants were predicted to encompass 588 genes, while deletion variants likely affected 1920 genes, including their exonic regions

Genes associated with tail traits in sheep and their variants

In the follow-up analysis of structural variation, the authors further discovered genes and their variants that are highly related to sheep tail traits, including a 169 bp insert in the HOXB13 gene that affects its expression, and structures in BMP2, HAO1, PDGFD Variation and single base variation

Compared with resequencing, graphical pan-genome research has far-reaching implications

Genome-wide analysis of genomic structural variation across breeds is critical to understand the full extent of genetic diversity and to pinpoint its association with phenotypic traits

PacBio HiFi sequencing can achieve haplotype assembly analysis of 13 samples in a short time, laying a solid foundation for high-quality pan-genome construction
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It also further provides solid data support for the analysis of functional genomes
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Related Literature
1.
Li, Ran, et al.
"A near complete genome for goat genetic and genomic research.
" Genetics Selection Evolution 53.
1 (2021): 1-17.

2.
Li, Ran, et al.
"The first sheep graph pan-genome reveals the spectrum of structural variations and their effects on different tail phenotypes.
" bioRxiv (2021).

3.
Davenport, Kimberly M.
, et al.
"An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome.
" GigaScience 11 (2022).

4.
Oar_rambouillet_v1.
0, https://