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Plant/Animal Whole Genome Sequencing

Whole Genome Sequencing (WGS) is technique used to determine the entirely of the DNA sequence of an organism’s genome at a single time.

Usually, the service is divided into two different groups depending on the existence of a reference genome:

De novo whole genome sequencing. In this situation, the genome to be sequenced doesn’t have a reference genome available, and for that reason, the objective of this sequencing is to generate it (or to improve an existing one). This technique needs to use both, Illumina data and long-read sequencing to enhance the genome assembly by creating an overlap between reads.
Re-sequencing. It 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.

Service Details

Bioinformatics

Demo Result

Featured Publications

Service Features

De novo

This technique is particularly useful with challenging genomes such as those with high degree of heterozygosity, repetitive regions, polypoloid genomes, abnormal CG contents etc.

Our one-stop solution provides integrated sequencing services and bioinformatic analysis that deliver a high-quality de novo assembled genome. An initial genome survey with Illumina provides estimations of genome size and complexity, and this information is used to guide the next step of long-read sequencing with PacBio HiFi, followed by de novo assembly of contigs. The subsequent use of HiC assembly enables anchoring of the contigs to the genome, obtaining a chromosome-level assembly. Finally, the genome is annotated by gene prediction and by sequencing expressed genes, resorting to transcriptomes with short and long reads.

-- Integration of multiple sequencing and bioinformatic services in a one-stop solutionService suitable for the constructing novel
-- genomes or improvement of existing reference genomes for species of interest.

Resequencing

-- Library preparation can be standard or PCR-free
-- Available in 4 sequencing platforms: Illumina NovaSeq, MGI T7, Nanopore Promethion P48 or PacBio Revio.
-- Bioinformatic analysis focused on variant calling: SNP, InDel, SV and CNV

Service Advantages

● Extensive Expertise and Publication Record: For de novo services, we have accumulated massive experience in high-quality genome assembly of diverse species, including diploid genomes and highly complex genomes of polyploid and allopolyploid species. Since 2018, we have contributed to over 300 high-impact publications, and 20+ of them are published in Nature Genetics. On genome re-sequecning, we accumulated over 1000 species, which resulted in over 1000 published cases with a cumulative impact factor of over 5000.

● One-stop Solution: On de novo sequencing, our integrated approach combines multiple sequencing technologies and bioinformatic analyses into a cohesive workflow, delivering a high-quality assembled genome.

● Tailored to Your Needs: Our service workflow is customizable, allowing adaptation for genomes with diverse features and specific research needs.

● Highly Skilled Bioinformatics and Laboratorial Team: Whether it is for de novo sequencing or re-sequencing, our team has a skilled set of tools and knowledge to guarantee the project success. This can be corroborated with the series of patents and software copyrights they’ve developed.

● 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 Bioinformatics Analysis: Including variation calling and function annotation.

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

Service Specifications

Variants to be identified	Sequencing strategy	Recommended depth
SNP and InDel	Illumina NovaSeq PE150 or MGI T7	10x
SV and CNV (less accurate)	Illumina NovaSeq PE150 or MGI 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/MGI

Nanopore

PacBio

Animal Viscera

0.5-1 g

≥ 3.5 g

Animal Muscle

≥ 5 g

Mammalian Blood

1.5 mL

≥ 0.5 mL

≥ 5 mL

Poultry/Fish Blood

≥ 0.1 mL

≥ 0.5 mL

Plant- Fresh Leaf

1-2 g

≥ 2 g

≥ 5 g

Cultured Cells

≥ 1x10⁷

≥ 1x10⁸

Insect soft tissue/Individual

0.5-1 g

≥ 1 g

≥ 3 g

Extracted DNA

Concentration: ≥ 1 ng/ µL

Amount: ≥ 30 ng

Limited or no degradation or contamination

Concentration

Amount

OD260/280

OD260/230

Limited or no degradation or contamination

≥ 40 ng/ µL

4 µg/flow cell/sample

1.7-2.2

≥1.5

Concentration

Amount

OD260/280

OD260/230

Limited or no degradation or contamination

≥ 50 ng/ µL

10 µg/flow cell/sample

1.7-2.2

1.8-2.5

PCR-free Library Preparation:

Concentration≥ 40 ng/ µL

Amount≥ 500 ng

Service Work Flow

Sample delivery

DNA extraction

Library construction

Sequencing

Data analysis

Data delivery

Previous: 10x Genomics Visium Spatial Transcriptome

Next: Single- nuclei RNA Sequencing

De novo bioinformatics pipeline

If you want to see an overview of our different pipelines for the assembly:

Complete bioinformatic analysis, separated in 4 steps:

1. Genome survey, based on k-mer analysis with NGS reads. It will give us information on:

Estimation of genome size
Estimation of heterozygosity
Estimate of repetitive regions

2. Genome Assembly with PacBio HiFi. Using long reads will give us:

De novo assembly
Assembly assessment: including BUSCO analysis for genome completeness and mapping back of NGS and PacBio HiFi reads

3. Hi-C assembly. Once we have the assembly, having information on the genome 3D structure will deepen the knowledge and enrich the reference genome we are building.

Hi-C library QC to estimate valid Hi-C interactions.
Hi-C assembly. We will do the clustering of contigs in groups, followed by contig ordering within each group and assigning contig orientation.
Hi-C evaluation

4. Genome annotation:

Non-coding RNA prediction
Repetitive sequences identification (transposons and tandem repeats)
Gene prediction
- De novo: ab initio algorithms
- Based on homology
- Based on transcriptome, with long and short reads: reads are de novo assembled or mapped to the draft genome
- Annotation of predicted genes with multiple databases

Re-sequencing bioinformatics pipeline

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, C. et al. (2021) ‘Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution’, Nature Communications, 12(1). doi: 10.1038/S41467-021-21379-X.

Li, Y. et al. (2023) ‘Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis)’, Molecular Biology and Evolution, 40(1). doi: 10.1093/MOLBEV/MSAD006.

Tian, T. et al. (2023) ‘Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm’, Nature Genetics 2023 55:3, 55(3), pp. 496–506. doi: 10.1038/s41588-023-01297-y.

Zhang, F. et al. (2023) ‘Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family’, Nature Communications 2023 14:1, 14(1), pp. 1–18. doi: 10.1038/s41467-023-37133-4.

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.

Challenging case-studies:

Telomere-to-telomere assembly: Fu, A. et al. (2023) ‘Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics’, Horticulture Research, 10(1). doi: 10.1093/HR/UHAC228.

Haplotype assembly: Hu, W. et al. (2021) ‘Allele-defined genome reveals biallelic differentiation during cassava evolution’, Molecular Plant, 14(6), pp. 851–854. doi: 10.1016/j.molp.2021.04.009.

Giant genome assembly: Yuan, J. et al. (2022) ‘Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii’, Nature Communications 2022 13:1, 13(1), pp. 1–16. doi: 10.1038/s41467-022-35063-1.

Polyploid genome assembly: Zhang, Q. et al. (2022) ‘Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum’, Nature Genetics 2022 54:6, 54(6), pp. 885–896. doi: 10.1038/s41588-022-01084-1.