Products

Plant/Animal Whole Genome Sequencing

Whole Genome Sequencing (WGS), also known as resequencing, refers to the whole genome sequencing of different individuals of species with known reference genomes. On this basis, the genomic differences of individuals or populations can be further identified. WGS enables the identification of Single Nucleotide Polymorphism (SNP), Insertion Deletion (InDel), Structure variation (SV), and Copy Number Variation (CNV). SVs comprise a larger portion of the variation base than SNPs and have a greater impact on the genome, substantially affecting living organisms. While short-read resequencing is effective in identifying SNPs and InDels, long-read resequencing allows for more precise identification of large fragments and complicated variations.

Service Details

Bioinformatics

Demo Result

Featured Publications

Service features

● Library preparation can be standard or PCR-free

● Available in 4 sequencing platforms: Illumina NovaSeq, BGI T7, Nanopore Promethion P48, or PacBio Revio.

● Bioinformatic analysis focused on the detection of variants: SNP, InDel, SV and CNV

Service Advantages

● Extensive Expertise and Publication Records: Accumulated experience in genome sequencing for over 1000 species has resulted in over 800 published cases with a cumulative impact factor of over 4000.

● Comprehensive Bioinformatics Analysis: Including variation calling and function annotation

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

● Comprehensive Annotation: We use multiple databases to functionally annotate the genes with identified variations and perform the corresponding enrichment analysis, providing insights on multiple research projects.

Service Specifications

Variants to be identified	Sequencing strategy	Recommended depth
SNP and InDel	Illumina NovaSeq PE150 or BGI T7	10x
SV and CNV (less accurate)	Illumina NovaSeq PE150 or BGI T7	30x
SV and CNV (more accurate)	Nanopore Prom P48	20x
SNPs, Indels, SV and CNV	PacBio Revio	10x

Sample Requirements

Tissue or extracted nucleic acids	Illumina/BGI	Nanopore	PacBio
Animal Viscera	0.5-1g	≥3.5g	≥3.5g
Animal Muscle	0.5-1g	≥5g	≥5g
Mammalian Blood	1.5 mL	≥5 mL	≥5 mL
Poultry/Fish Blood	1.5 mL	≥0.5 mL	≥0.5 mL
Plant- Fresh Leaf	1-2g	≥5g	≥5g
Plant -Petal/Stem		≥10g	≥10g
Plant - Root/Seed		≥20g	≥20g
Cultured Cells		≥1x10⁸	≥1x10⁸
Extracted DNA	Concentration: ≥1 ng/ µL Amount: 30ng Limited or no degradation or contamination	Concentration: ≥40 ng/ µL Amount: 4 µg/flow cell OD260/280=1.7-2.2 OD260/23 ≥1.5 Limited or no degradation or contamination	Concentration: ≥50 ng/ µL Amount: 410µg/flow cell OD260/280=1.7-2.2 OD260/23=1.8-2.5 Limited or no degradation or contamination

Service Work Flow

Sample delivery

DNA extraction

Library construction

Sequencing

Data analysis

Data delivery

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Includes the following analysis:

Raw Data Quality Control
Statistics of alignment to reference genome
Variant identification: SNP, InDel, SV and CNV
Functional annotation of variants

Statistics of alignment to reference genome – sequencing depth distribution

SNP calling among multiple samples

InDel identification – statistics of the InDel length in the CDS region and the genome-wide region

Variant distribution across the genome – Circos plot

Functional annotation of genes with identified variants – Gene Ontology

Chai, Q. et al. (2023) ‘A glutathione S‐transferase GhTT19 determines flower petal pigmentation via regulating anthocyanin accumulation in cotton’, Plant Biotechnology Journal, 21(2), p. 433. doi: 10.1111/PBI.13965.

Cheng, H. et al. (2023) ‘Chromosome-level wild Hevea brasiliensis genome provides new tools for genomic-assisted breeding and valuable loci to elevate rubber yield’, Plant Biotechnology Journal, 21(5), pp. 1058–1072. doi: 10.1111/PBI.14018.

Li, A. et al. (2021) ‘Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity’, Communications Biology 2021 4:1, 4(1), pp. 1–12. doi: 10.1038/s42003-021-02823-6.

Zeng, T. et al. (2022) ‘Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation’, Communications Biology, 5(1), pp. 1–12. doi: 10.1038/s42003-022-03907-7.