Explore Genetic Variations via Haplotype-Resolved T2T Genome Assembly

In genomic research, incomplete genome maps often limit our understanding of genetic variations and their implications. Haplotype-resolved T2T genome assembly from CD Genomics offers a groundbreaking solution by delivering a gap-free, telomere-to-telomere genome sequence. This approach ensures more precise insight into complex genetic regions, allelic variations, and structural features—key factors in advancing research across a wide array of fields, from drug development to agricultural biotechnology.

With our advanced technology, CD Genomics is able to provide highly accurate genome assemblies, enabling researchers to overcome the challenges presented by incomplete or ambiguous genetic data. This service is an ideal fit for those looking to gain comprehensive insights into genomic structures, variations, and functional elements.

Through this service, we equip our clients with the complete genomic data needed to drive more informed decisions, deeper insights, and ultimately, breakthrough discoveries in their research.

At a glance:

• Why Choose This Service?
• The Advantages of Haplotype-Resolved T2T Genome Assembly
• How Haplotype-Resolved T2T Genome Assembly Solves Key Research Challenges
• Sequencing Strategy
• Applications
• How It Works: Step-by-Step Process
• Project Case Study: Haplotype-Resolved Genome Assembly)
• Frequently Asked Questions (FAQs)
• Demo
• Case Study: Haplotype-Resolved T2T Genome Assembly of the African Catfish (Clarias gariepinus)

Why Choose This Service?

The need for high-resolution, complete genome data is growing, especially in fields like drug development, biotechnology, and agriculture. CD Genomics delivers precisely what researchers need with Haplotype-resolved T2T genome assembly.

This service provides an in-depth genomic map that ensures all complex regions are fully captured—without gaps. Unlike traditional sequencing methods that often miss critical genomic details, our approach guarantees the assembly of entire chromosomes, including challenging repetitive sequences and structural variants.

At CD Genomics, we focus on:

• Comprehensive Genome Coverage: Capturing every part of the genome, from telomere to telomere, without leaving gaps or unresolved regions.
• Haplotype Accuracy: By phasing maternal and paternal alleles separately, we offer unmatched precision in genetic research, which is crucial for studies on inheritance and disease.
• State-of-the-Art Technology: Combining the power of PacBio, Oxford Nanopore, Illumina, and Hi-C, we ensure the highest sequencing accuracy and completeness.

The Advantages of Haplotype-Resolved T2T Genome Assembly

• Haplotype-resolved T2T genome assembly offers critical advantages over traditional methods, ensuring complete, accurate genome mapping with no gaps.
• Complete Chromosome Assembly: Provides a gap-free genome, resolving complex regions like repetitive sequences and structural variants that traditional methods often miss.
• Accurate Haplotype Phasing: Separates maternal and paternal alleles, offering precise data for genetic disease research, population studies, and breeding programs.
• Advanced Technologies: Combining PacBio HiFi, Oxford Nanopore, and Illumina, along with Hi-C phasing, ensures high-quality, high-resolution genomic data.
• Enhanced Structural Variant Detection: Identifies structural variants (SVs) with high precision, providing deeper insights into genome organization and evolution.

How Haplotype-Resolved T2T Genome Assembly Solves Key Research Challenges

Sequencing Strategy

Our Haplotype-resolved T2T genome assembly service employs a combination of advanced sequencing technologies to deliver the most accurate and complete genome assemblies.

This multi-platform approach ensures a comprehensive assembly by combining long-read accuracy with high-throughput precision, covering both short-range details and long-range genome structures. This methodology guarantees the highest standards of sequencing quality and assembly completeness.

Applications

The Haplotype-resolved T2T genome assembly service offers a wide range of applications, providing critical insights for diverse research fields, from genetic studies to biotechnology and agriculture.

How It Works: Step-by-Step Process

Workflow of haplotype-resolved T2T genome assembly.

The assembly integrates ONT ultra-long reads, HiFi reads, and Hi-C data using the Hifiasm assembler. Contigs are scaffolded with Hi-C integration, followed by gap validation and filling, resulting in haplotype-specific T2T genomes. Final evaluation includes assembly statistics, telomere/centromere validation, BUSCO/CEGMA/LAI assessments, and phasing accuracy (switch error and collinearity between haplotypes).

Project Case Study: Haplotype-Resolved Genome Assembly

Frequently Asked Questions (FAQs)

Demo

Case Study: Haplotype-Resolved T2T Genome Assembly of the African Catfish (Clarias gariepinus)

1. Background

The African catfish (Clarias gariepinus) is a critical species in aquaculture due to its rapid growth and resistance to diseases. Understanding its genomic structure is essential for breeding programs aiming to enhance performance traits such as growth rate, disease resistance, and reproductive capabilities. Despite its importance, the lack of a fully resolved genome has hindered research on its genetics. Recent advancements in sequencing technology, including haplotype-resolved T2T genome assembly, provide the potential to unravel the complexities of the catfish genome, enabling more targeted breeding strategies.

2. Methods

In this study, a combination of PacBio HiFi long reads, Oxford Nanopore Technologies (ONT), and Illumina short reads was used to generate a complete haplotype-resolved T2T genome for Clarias gariepinus. The genome was assembled using HiFi sequencing, with both parental genomes resolved using trio binning. To ensure the accuracy of the assembly, the Hi-C technique was employed to aid in scaffolding the genomic regions, allowing the team to obtain a continuous, near-complete genome assembly. Various bioinformatics tools, including Canu, HiFiasm, and wtdbg2, were utilized for different assembly and phasing steps.

3. Results

The resulting genome assembly for the African catfish provided a high-quality reference with a contig N50 value of approximately 15.6 Mb. The genome size was estimated to be approximately 700 Mb. Several key genes involved in growth, disease resistance, and reproductive traits were identified through functional annotation. The haplotype-resolved assembly revealed substantial structural variations between the two parental genomes, which could explain the phenotypic differences observed in hybrids. In particular, candidate genes for disease resistance and growth rate were found to be highly expressed in certain haplotypes, laying the foundation for potential genetic improvements in catfish breeding programs.

Figure 1: Overview of the African Catfish Haplotype-Resolved Genome Assembly Process.

The figure presents a schematic diagram detailing the steps involved in sequencing, assembly, and functional annotation of the catfish genome. This image is adapted from the study's figure illustrating the process of haplotype-resolved assembly and the key findings regarding structural variants.

4. Conclusions

The successful generation of a haplotype-resolved T2T genome for the African catfish provides a comprehensive genomic resource for future research and breeding applications. The high-quality assembly, coupled with the identification of critical genetic markers, will facilitate more precise selection of traits in breeding programs, ultimately leading to improved disease resistance and growth rates. Moreover, the study's approach to using a pangenomic framework sets a precedent for understanding structural variations across populations and their impact on economically important traits.

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