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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling.

Camille Eché¹, Carole Iampietro¹, Clément Birbes²

¹INRAE, US 1426, GeT-PlaGe, Genotoul, France Genomique, Université Fédérale de Toulouse, Castanet-Tolosan, France.

Scientific Data

|June 8, 2023

Summary

We generated high-quality, haplotyped reference genomes for a Charolais heifer using multiple sequencing technologies. This bovine pangenome contribution enhances insights into sequencing methods and variant detection.

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Area of Science:

Genomics
Comparative Genomics
Bioinformatics

Background:

The Genome in a Bottle project established a precedent for creating high-quality reference genomes.
Comprehensive genomic data is crucial for advancing cattle breeding and genetic research.

Purpose of the Study:

To create a high-quality, haplotyped reference genome for the Charolais cattle breed.
To evaluate and compare various next-generation sequencing technologies for genome assembly.
To contribute to the development of a comprehensive bovine pangenome.

Main Methods:

Sequencing a Charolais heifer and its parents using Illumina, Oxford Nanopore, Pacific Biosciences (HiFi and CLR), 10X Genomics, and Hi-C technologies.
Generating haplotyped assemblies using trio binning and advanced bioinformatic pipelines.
Performing quality assessment using BUSCO scores and identifying structural variants.

Main Results:

Two haplotyped reference genomes and a consensus assembly were generated, with PacBio HiFi assembly reaching 3.2 Gb.
The consensus assembly achieved a BUSCO completeness score of 95.8% for conserved mammalian genes.
Over 35,000 structural variants larger than 50 base pairs were identified.

Conclusions:

The generated reference genomes provide a valuable resource for the Charolais breed and the broader bovine pangenome initiative.
The study demonstrates the utility of integrating multiple sequencing technologies for robust genome assembly and variant discovery.
These datasets will facilitate further research in SNP, indel, and structural variant calling, as well as de novo assembly in cattle.