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Updated: Jul 2, 2025
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
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Pig pangenome graph reveals functional features of non-reference sequences
Jian Miao1, Xingyu Wei1, Caiyun Cao1
1College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Journal of Animal Science and Biotechnology
|February 23, 2024
Summary
This study introduces a pig pangenome graph, revealing numerous non-reference sequences (NRSs) and their links to pig immunity and heat tolerance, advancing genetic variation understanding.
Area of Science:
- Animal Genomics
- Bioinformatics
- Population Genetics
Background:
- Understanding genetic variation in animals is limited by single linear reference genomes.
- Non-reference sequences (NRSs) remain understudied, hindering comprehensive genetic analysis.
Purpose of the Study:
- To construct a pig pangenome graph to explore genetic variation beyond the reference genome.
- To identify and characterize non-reference sequences (NRSs) in pig populations.
- To investigate the functional implications of NRSs in relation to pig traits.
Main Methods:
- Construction of a pig pangenome graph utilizing 21 pig assemblies.
- Identification and analysis of non-reference sequences (NRSs).
- Association studies between NRSs and genetic divergence, coding sequences, immune-related terms, and heat tolerance.
Main Results:
- A pig pangenome graph identified 23,831 NRSs (105 Mb total length).
- NRS prevalence correlated with genetic divergence; insertions were enriched in immune-related terms and associated with novel genes.
- Significant differences in NRS frequencies between Eastern and Western pigs were observed, with heat-resistant pigs showing specific NRS insertions.
Conclusions:
- A graph genome approach effectively reveals functional insights into NRSs in pig populations.
- NRSs play a role in pig immune capacity and adaptation traits like heat tolerance.
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