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Updated: May 13, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Constructing a draft Indian cattle pangenome using short-read sequencing.

Sarwar Azam^1,2, Abhisek Sahu¹, Naveen Kumar Pandey¹

¹National Institute of Animal Biotechnology, Hyderabad, India.

Communications Biology

|April 13, 2025

Summary

This summary is machine-generated.

Indian desi cattle genomics is better understood with a new pangenome. This reveals novel genetic variants unique to the breed, improving our understanding of their adaptability and traits.

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Area of Science:

Genomics
Animal Genetics
Bioinformatics

Background:

Indian desi cattle possess significant genetic diversity and adaptability.
A single reference genome inadequately represents the full genetic variation within desi cattle populations.
Understanding this variation is crucial for genetic resource conservation and trait improvement.

Purpose of the Study:

To construct a comprehensive pangenome for Indian desi cattle.
To identify and characterize non-reference novel sequences (NRNS) within the desi cattle population.
To explore the functional implications and origins of these novel genetic variants.

Main Methods:

Sequencing of 68 desi cattle genomes across seven breeds.
Utilizing the PanGenome Analysis (PanGA) pipeline for NRNS identification.
Comparative analysis with existing Bos indicus pangenomes.

Main Results:

Identification of 13,065 NRNS, totaling approximately 41 Mbp, with significant population-specific variation.
Most identified NRNS were unique to Indian desi cattle, showing limited overlap with Chinese indicine pangenomes.
Approximately 40% of NRNS were found in genic regions and linked to quantitative trait loci for traits like milk production.

Conclusions:

The desi cattle pangenome provides a more complete representation of their genetic diversity.
The identified NRNS offer insights into breed-specific adaptations and economically important traits.
Pangenome approaches enhance genomic analysis accuracy and uncover novel genetic insights in cattle.