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Hi-C based Genome Assembly

Hi-C is a method designed to capture chromosome configuration by combining probing proximity-based interactions and high-throughput sequencing. The intensity of these interactions are believed to be negatively correlated with physical distance on chromosomes. Therefore, Hi-C data could guide the clustering, ordering and orienting of assembled sequences in a draft genome and anchoring those onto certain number of chromosomes. This technology empowers a chromosome-level genome assembly in absence of population-based genetic map. Every single genome needs a Hi-C.

Platform:Illumina NovaSeq6000 / DNBSEQ


Service Details

Demo Results

Case Study

Service Advantages

1Principle-of-Hi-C-sequencing

Overview of Hi-C
(Lieberman-Aiden E et al., Science, 2009)

Ø No need in constructing genetic population for contig anchoring
Ø Higher marker density leading to higher contigs anchoring ratio at above 90%;
Ø Enables evaluation and corrections on existing genome assemblies;
Ø Shorter turn-around time with higher accuracy in genome assembly;
Ø Abundant experienced with over 1000 Hi-C library constructed for over 500 species;
Ø Over 100 successful cases with accumulative published impact factor of over 760;
Ø Hi-C based genome assembly for polyploid genome, 100% anchoring rate was achieved in previous project.
Ø In-house patents and software copyrights for Hi-C experiments and data analysis
Ø Self-developed visualized data tuning software, enables manual block moving, reversing, revoking and redo.

Service Specifications

Sequencing Platform

Library

Recommended depth

Estimated turn-around time

Assembly

Illumina

300-350 bp

Simple genome ≥ 100 ×

Complex genome ≥ 150 ×

3 months

(Depending on species)

Anchoring ratio ≥ 90% (Depending on species)

Bioinformatics analyses

ü Raw data quality control

ü Hi-C library quality control

ü Hi-C based genome assembly

ü Post-assembly evaluation

2Hi-C-based-genome-assembly

Sample Requirements and Delivery

Sample Requirements:

For animals:
1.Muscle (Frozen): ≥ 2 g;
2.Whole blood (Non-frozen): ≥ 2 ml (for 3 libraries)

For plants:
1.Seedlings (e.g. young seedlings cultivated from seeds, tissue culture seedingling, etc) : collect all leaves and young stem;
2.Mature plant: collect stem tip and the first 1 or 2 new leaves close to stem tip.
* Recommended amount for each sample ≥ 4 g. (Theoretical usage for library construction is 1 g per library).

Recommended Sample Delivery

Container: 2 ml centrifuge tube (Tin foil is not recommended)
For most of samples, we recommend not to preserve in ethanol.
Sample labeling: Samples need to be clearly labeled and identical to submitted sample information form.
Shipment: Dry-ice: Samples need to be packed in bags first and buried in dry-ice.

Service Work Flow

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Experiment design

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Sample delivery

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Hi-C experiment

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Library construction

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Sequencing

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Data analysis

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After-sale services


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  • *Demo results shown here are all from genomes published with Biomarker Technologies

    1.Hi-C interaction heat map of Camptotheca acuminata genome. As shown on the map, the intensity of interactions is negatively correlated with the linear distance, which indicates a highly-accurate chromosome-level assembly. (Anchoring ratio: 96.03%)

    3Hi-C-interaction-heatmap-showing-contigs-anchoring-in-genome-assembly

    Kang M et al., Nature Communications, 2021

     

    2.Hi-C facilitated the validation of inversions between Gossypium hirsutum L. TM-1 A06 and G. arboreum Chr06

    4Hi-C-heatmap-facilitate-revealing-of-inversions-between-genomes

    Yang Z et al., Nature Communications, 2019

     

     

    3.Assembly and biallelic differentiation of the cassava genome SC205. Hi-C heatmap shown clear split in homologous chromosomes. 

    5Hi-C-heatmap-showing-homologous-chromosomes

    Hu W et al., Molecular Plant, 2021

     

     

    4.Hi-C heatmap on two Ficus species genome assembly: F.microcarpa (anchoring ratio: 99.3%) and F.hispida (anchoring ratio: 99.7%) 
    6Hi-C-heatmap-showing-contig-anchoring-of-Ficus-genomes

    Zhang X et al., Cell, 2020

     

     

    BMK Case

    Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution 

    Published: Cell, 2020

    Sequencing strategy:

    F. microcarpa genome: Approx. 84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)

    F. hispida genome: Approx. 97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)

    Eupristina verticillata genome: Approx. 170 X PacBio RSII (65 Gb)

    Key results

    1.Two banyan tree genomes and one pollinator wasp genome were constructed using PacBio sequencing, Hi-C and linkage map.
    (1)F. microcarpa genome: An assembly of 426 Mb (97.7% of estimated genome size) was established with contig N50 of 908 Kb, BUSCO score of 95.6%. In total of 423 Mb sequences were anchored to 13 chromosomes by Hi-C. Genome annotation yielded 29,416 protein-coding genes.
    (2)F. Hispida genome: An assembly of 360 Mb (97.3% of estimated genome size) were yield with contig N50 of 492 Kb and BUSCO score of 97.4%. A total of 359 Mb sequences were anchored on 14 chromosomesby Hi-C and highly identical to high-density linkage map.
    (3)Eupristina verticillata genome: An assembly of 387 Mb (Estimated genome size: 382 Mb) were established with contig N50 of 3.1 Mb and BUSCO score of 97.7%.

    2.Comparative genomics analysis revealed great number of structure variations between two Ficus genomes, which provided invaluable genetic resource for adaptive evolution studies. This study, for the first time, provided insights into Fig-wasp coevolution at genomic-level.

    PB-full-length-RNA-Sequencing-case-study

    Circos diagram on genomic features of two Ficus genomes, including chromosomes, segmental duplications (SDs), transposons(LTR, TEs, DNA TEs), gene expression and synteny

    PB-full-length-RNA-alternative-splicing

    Identification of the Y chromosome and sex determination candidate gene

    Reference

    Zhang, X. , et al. “Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution.” Cell 183.4(2020).

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