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Plant/Animal De novo Genome Sequencing

De novo sequencing refers to construction of a species’ whole genome using sequencing technologies, e.g. PacBio, Nanopore, NGS, etc., in absence of a reference genome. The remarkable improvement in read length of third generation sequencing technologies has brought new opportunities in assembling complex genomes, such as those with high heterozygosity, high ratio of repetitive regions, polyploids, etc. With read length at tens of kilobases level, these sequencing reads enables resolving of repetitive elements, regions with abnormal GC contents and other highly complex regions.

Platform: PacBio Sequel II /Nanopore PromethION P48/ Illumina NovaSeq6000


Service Details

Demo Results

Case Study

Service Advantages

1Development-of-sequencing-and-bioinformatics-in-de-novo-genome-assembly

Development of sequencing platforms and bioinformatics in de novo genome assembly

(Amarasinghe S L et al., Genome Biology, 2020)

Ø Constructing novel genomes and improving existing reference genome for species of interest.
Ø Higher accuracy, continuity and completeness in assembly
Ø Constructing fundamental resource for research in sequence polymorphism, QTLs, gene editing, breeding, etc.
Ø Equipped by full spectrum of third-generation sequencing platforms: one-stop genome assembly solution
Ø Flexible sequencing and assembling strategies fulfilling diverse genomes with different features
Ø Highly skilled bioinformatician team with great experience in complex genome assemblies, including polyploids, giant genomes, etc.
Ø Over 100 successful cases with accumulative published impact factor of over 900
Ø Turn-around-time as fast as 3 months for chromosome-level genome assembly.
Ø Solid technical support with a series of patents and software copyrights in both experimental side and bioinformatics.

Service Specifications

Sequencing Mode

Library

Recommended depth

Estimated turn-around time

Assembly

PacBio HiFi

15 to 30 kb

Simple genome ≥ 30 X

Complex genome ≥ 60 X

3 -6 months for assembly and genome annotation (Depending on species)

Contig N50 ≥ 2 Mb (Depending on species)

PacBio CLR

20 kb, 30 kb

Simple genome ≥ 100 X

Complex genome ≥ 150 X

Nanopore

20-50 kb

Bioinformatics analyses

ü genome resequencing
ü Base Calling
ü Quality Control and error correction
ü De novo assembly
ü Assembly refinement
ü Gene prediction
ü Genome annotation
ü Downstream analyses

2Plant-or-Animal-De-novo-genome-assembly-work-flow

Sample Requirements and Delivery

Sample Requirements:

Species

Tissue

For PacBio

For Nanopore

Animals

Visceral organs(liver, spleen, etc.)

≥ 1.0 g

≥ 3.5 g

Muscle

≥ 1.5 g

≥ 5.0 g

Blood of mammals

≥ 1.5 mL

≥ 5.0 mL

Blood of fish or birds

≥ 0.2 mL

≥ 0.5 mL

Plants

Fresh leaves

≥ 1.5 g

≥ 5.0 g

Petal or stem

≥ 3.5 g

≥ 10.0 g

Roots or seeds

≥ 7.0 g

≥ 20.0 g

Cells

Cell culture

≥ 3×107

≥ 1×108

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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DNA extraction

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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.Circos on chromosome-level genome assembly of G. rotundifolium by Nanopore sequencing platform

    3Circos-on-genomic-features-of-cotton-genome

    Wang M et al., Molecular Biology and Evolution, 2021 

    2.Statistics of Weining rye genome assembly and annotation

    4Statistics-of-genome-assembly-and-annotation

    Li G et al., Nature Genetics, 2021

    3.Gene prediction of Sechium edule genome, derived from three prediction methods: De novo prediction, Homology-based prediction and RNA-Seq data based prediction

    5Gene-prediction

    Fu A et al., Horticulture Research, 2021

    4.Identification of intact long terminal repeats in three cotton genomes

    6Identification-of-genome-repetitive-elements

    Wang M et al., Molecular Biology and Evolution, 2021

    5.Hi-C heat map of the C. acuminata genome showing genome-wide all-by-all interactions. Intensity of Hi-C interactions is proportional to linear distance between contigs. A clean straight line on this heat map indicates a highly accurate anchoring of contigs on chromosomes. (Contig anchoring ratio: 96.03%) 

    7Hi-C-heat-map-on-assembled-sequencing-anchoring

    kang M et al., Nature Communications, 2021

     

    BMK Case

    A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

    Published: Nature Genetics, 2021

    Sequencing strategy:

    Genome assembly: PacBio CLR mode with 20 kb library (497 Gb, approx. 63×)
    Sequence correction: NGS with 270 bp DNA library (430 Gb, approx. 54×) on Illumina platform
    Contigs anchoring: Hi-C library(560 Gb, approx. 71×) on Illumina platform
    Optical map: (779.55 Gb, approx. 99×) on Bionano Irys

    Key results

    1.An assembly of Weining rye genome was published with total genome size of 7.74 Gb(98.74% of estimated genome size by flow cytometry). Scaffold N50 of this assembly achieved 1.04 Gb. 93.67% of contigs were successfully anchored on 7 pseudo-chromosomes. This assembly was evaluated by linkage map, LAI and BUSCO, which resulted in high scores in all evaluations.

    2.Further studies on comparative genomics, genetic linkage map, transcriptomics studies were performed on base of this genome. A series of traits related genomic features were revealed including genome-wide gene duplications and their impact on starch biosynthesis genes; physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye.

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

    Circos diagram on genomic features of Weining rye genome 

    PB-full-length-RNA-alternative-splicing

    Evolutionary and chromosome synteny analyses of the rye genome

    Reference

    Li, G., Wang, L., Yang, J. et al. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes. Nat Genet 53, 574–584 (2021).

    https://doi.org/10.1038/s41588-021-00808-z

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