Haplotype-Resolved Genome Sequencing & Assembly Service
Service Highlights
Conventional assemblies blur allelic differences, leading to incomplete or misleading interpretations. Haplotype-resolved genome sequencing and assembly separates parental haplotypes, delivering chromosome-level accuracy that empowers reliable studies of genetic variation, trait inheritance, and genome evolution.
Request a QuoteWhy Haplotype-Resolved Genome Assembly Is Essential for Modern Genomics
The Limitation of Conventional Assemblies
- Traditional genome assemblies collapse homologous chromosomes into a single consensus sequence.
- This oversimplification masks allelic variation, distorts structural complexity, and reduces the accuracy of functional interpretation.
- Key biological features such as allele-specific expression (ASE), structural rearrangements, and heterozygosity are frequently lost.
How Haplotype-Resolved Assembly Changes the Picture
- Preserves both parental or homologous chromosome sequences rather than merging them.
- Produces chromosome-level haplotype assemblies that reflect the true genetic diversity of diploid and polyploid genomes.
- Enables accurate detection of structural variants and allele-specific regulation.
- Provides a biologically faithful foundation for downstream functional and evolutionary studies.
Research Value and Applications
- Agricultural genomics → uncover the genetic basis of hybrid vigor, fertility, and crop adaptation.
- Functional genomics → investigate allele-specific expression and regulatory mechanisms.
- Evolutionary biology → trace ancestry, divergence, and genome evolution in complex species.
- Comparative genomics → reveal differences between haplotypes and across populations.
Our Approach at CD Genomics
At CD Genomics, we integrate HiFi long-read sequencing, Hi-C scaffolding, and advanced phasing strategies to generate chromosome-level haplotype assemblies. Our service delivers high-quality, publication-ready data that captures allelic complexity and empowers reliable downstream analyses in functional, agricultural, and evolutionary genomics.
Advantages of Haplotype-Resolved Genome Sequencing
Allele-Aware Resolution
Unlike consensus assemblies that merge homologous chromosomes, haplotype-resolved assembly preserves each parental or homologous sequence. This enables precise analysis of allele-specific variation and prevents misinterpretation of functional differences.
Chromosome-Level Accuracy
By integrating HiFi long-read sequencing with Hi-C scaffolding, we generate assemblies that reach chromosome-scale continuity. This level of detail provides a more faithful representation of diploid and polyploid genomes.
Structural Variant Detection
Our approach captures complex genomic features often missed in conventional assemblies, including nested inversions, duplications, and translocations. These insights are critical for understanding genome evolution and functional consequences.
Broad Applicability Across Genomes
Whether working with diploid species, hybrid crops, or highly complex polyploid organisms, our service provides tailored strategies that adapt to the unique challenges of each genome type.
Functional and Evolutionary Insights
Haplotype-resolved assemblies open new avenues for studying trait inheritance, hybrid vigor, allele-specific expression, and evolutionary divergence—making them invaluable across agriculture, functional genomics, and population genetics.
Publication-Ready Deliverables
We provide assemblies and annotations that meet international research standards, ensuring your datasets are ready for publication, downstream analysis, and integration into comparative studies.
Service Workflow — From Sample to Assemblies
1. Sample QC
Assess DNA quality and integrity to ensure suitability for long-read sequencing.
2. Sequencing Design
Choose strategy based on genome type and parental data availability:
- With parents → accurate phasing using parent reads + HiFi + Hi-C.
- Without parents → SNP phasing with HiFi and Hi-C.
- Polyploids → hybrid strategies with reference support.
3. Sequencing & Assembly
Generate haplotype-resolved chromosome-level assemblies that reflect true genetic diversity.
4. Annotation
Identify repeats, coding genes, ncRNAs, pseudogenes, and perform functional annotation (KEGG, GO, Pfam, InterPro).
5. Analysis & Delivery
Provide structural variant detection, allele-specific expression, comparative genomics, and evolutionary insights, with publication-ready datasets.
Technical Route: How Haplotype-Resolved Assembly Is Performed
Sample Requirements for High-Quality Haplotype-Resolved Assembly
To obtain reliable haplotype-resolved assemblies, samples should meet the following requirements:
Genome Survey (short-read platform)
- Sample type: genomic DNA
- Input amount: ≥0.2 μg for short-insert libraries
- Concentration: ≥5 ng/μl
- Purity: OD260/280 = 1.8–2.2; OD260/230 = 0.8–2.5
- Quality: intact DNA, clear main band, no degradation or contamination
Genome de novo Assembly (HiFi long-read platform)
- DNA amount: ≥6 μg (HiFi)
- Concentration: ≥30 ng/μl
- Integrity: high molecular weight DNA with fragments ≥30 kb
- Purity: OD260/280 ≥1.5; OD260/230 ≥1.2; QC/NC = 0.5–2.0
Genome Annotation (Iso-Seq)
- At least six samples from different tissues or developmental stages recommended
- Iso-Seq long-read sequencing suggested for comprehensive transcriptome coverage
Hi-C Sequencing (optional for scaffolding)
- Fresh tissues cross-linked with formaldehyde
- One Hi-C library requires ~5 ml of fresh blood or ~1 g of tissue (2–3 g recommended for optimal results)
For detailed guidance and tailored requirements, please contact our scientists to ensure optimal project design and accurate results.
Deliverables — What You Receive
Upon completion of the haplotype-resolved genome sequencing and assembly project, you will receive:
- Chromosome-level haplotype assemblies
Separate parental or homologous sequences reconstructed with high continuity.
- Genome annotation files
Comprehensive annotation of repeats, coding genes, non-coding RNAs, and pseudogenes.
- Functional analysis results
Pathway and ontology assignments through databases such as KEGG, GO, Pfam, and InterPro.
- Variant and expression analysis
Structural variant profiles and allele-specific expression analysis where applicable.
- Comparative and evolutionary insights
Optional outputs including phylogenetic relationships, haplotype comparisons, and asymmetric evolution.
- Visualization and reports
Publication-ready figures (heatmaps, Circos plots, phylogenetic trees) and a detailed analysis report.
- Raw and processed data files
Complete datasets with quality control results for transparency and further analysis.
Service Description — Haplotype-Resolved Genome Assembly Strategies
| Service Type | Suitable Samples | Sequencing Strategy | Notes & Standards |
|---|---|---|---|
| ADPA (Diploid Phasing Assembly with Parents) | Diploid or allopolyploid genomes with parental data | - Parental short reads: ≥50× (PE150, ~350 bp) - Offspring HiFi long reads: ≥30× (15–20 kb) - Offspring Hi-C data: ≥100× |
Parental data enables highly accurate phasing of haplotypes and reliable chromosome-level assemblies. |
| AUPPA (Assembly without Parents) | Diploid genomes without parental data | - Offspring HiFi long reads: ≥30× (15–20 kb) - Offspring Hi-C data: ≥100× |
Haplotype separation achieved by SNP-based phasing; Hi-C improves accuracy of scaffolding and phasing. |
| ATPA (Tetraploid Phasing Assembly) | Highly homologous tetraploid genomes | - Reference from closely related diploid genome(s) recommended - Parental short reads: ≥30× (PE150, optional but preferred) - Offspring HiFi long reads: ≥30× (15–20 kb) - Offspring Hi-C data: ≥100× |
Reference-assisted strategies improve resolution of homologous subgenomes; optional parental data further increases accuracy. |
Applications of Haplotype-Resolved Genome Assembly
- Agricultural genomics
Enables precise discovery of allelic variation linked to hybrid vigor, fertility, and environmental adaptation, supporting the development of improved crop and livestock traits. - Functional genomics
Provides the resolution needed to detect allele-specific expression and regulatory differences, helping clarify how genetic variation drives phenotypic outcomes. - Evolutionary biology
Reveals ancestral lineages, divergence patterns, and adaptive events with higher accuracy than consensus assemblies. - Comparative genomics
Facilitates detailed comparisons of haplotype structures across individuals and populations, offering a clearer view of genetic diversity and inheritance. - Population genetics
Delivers accurate information on heterozygosity, recombination, and allelic networks, forming a solid foundation for advanced statistical and modeling studies.
Case Studies
Title: High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry
Journal: Horticulture Research | Methods: PacBio HiFi sequencing, Hi-C scaffolding, haplotype phasing
Using the strawberry cultivar "Yanli" (Fragaria × ananassa), researchers obtained a chromosome-level haplotype-resolved genome comprising 56 chromosomes, split into two haplotypes—Hap1 (825 Mb, contig N50 ~26.7 Mb) and Hap2 (808 Mb, contig N50 ~27.5 Mb). They identified a ~10 Mb inversion and translocation on chromosome 2-1 and annotated over 100,000 protein-coding genes in each haplotype. Structural diversity and complex allele-specific expression were uncovered in anthocyanin biosynthesis genes, demonstrating functional heterogeneity among haplotypes. This high-continuity assembly provides a robust foundation for exploring gene function and genome evolution in cultivated strawberry.
Overview of the haplotype-resolved genome assembly of the "Yanli" (Fragaria × ananassa) genome.
Frequently Asked Questions — Answers to Your Haplotype Assembly Concerns
1. Why use haplotype-resolved assembly over conventional consensus assembly?
Consensus assemblies merge homologous chromosomes into a single representation, often concealing essential differences such as allelic variation, structural rearrangements, and allele-specific expression. Haplotype-resolved assembly preserves each chromosome independently, enabling accurate detection of these critical biological features—essential for meaningful genomic analysis.
2. Can I run a parent-guided assembly if only one parent's data is available?
Yes—though less ideal, one parent's data can still enhance phasing accuracy. Without full parental information, we default to SNP-mode phasing combined with Hi-C data. While this approach may not reach the level of parent-guided phasing, it still significantly improves assembly accuracy compared to traditional methods.
3. Is this service suitable for polyploid genomes (e.g., tetraploid or allopolyploid)?
Absolutely. We employ tailored strategies—such as reference-assisted phasing, combined with HiFi reads and Hi-C scaffolding—to separate homologous sub-genomes effectively, even in highly homologous polyploids. Optional parental or closely related reference data further strengthens assembly quality.
4. Will the data you provide be easy to use for downstream analysis and publication?
Yes. We deliver annotated haplotype assemblies, structural variant maps, allele-specific expression profiles, and visualization-ready figures (e.g., heatmaps, Circos plots). Everything is provided in standard formats, so you can immediately integrate them into manuscripts, comparative studies, or functional analyses.
5. What if my sample quality is below recommended standards—what then?
If your sample doesn't initially meet the criteria, we will offer personalized advice for improvement—such as additional purification or re-extraction. Our goal is to ensure your sample performs well through sequencing and assembly, aligning with the high-quality standards necessary for reliable results.
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