Development of sequencing platforms and bioinformatics in de novo genome assembly
(Amarasinghe S L et al., Genome Biology, 2020)
● Constructing novel genomes and improving existing reference genomes for species of interest.
● Higher accuracy, continuity and completeness in assembly
● Constructing fundamental resource for research in sequence polymorphism, QTLs, gene editing, breeding, etc.
● Equipped with full spectrum of third-generation sequencing platforms: one-stop genome assembly solution
● Flexible sequencing and assembling strategies fulfilling diverse genomes with different features
● Highly skilled bioinformatician team with great experience in complex genome assemblies, including polyploids, giant genomes, etc.
● Over 100 successful cases with an accumulative published impact factor of over 900
● Turn-around-time as fast as 3 months for chromosome-level genome assembly.
● Solid technical support with a series of patents and software copyrights in both experimental side and bioinformatics.
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) |
Nanopore |
20-50 kb |
Simple genome ≥ 100 X Complex genome ≥ 150 X |
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 |
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.
*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
Wang M et al., Molecular Biology and Evolution, 2021
2.Statistics of Weining rye 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
Fu A et al., Horticulture Research, 2021
4.Identification of intact long terminal repeats in three cotton genomes
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%)
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.
![]() Circos diagram on genomic features of Weining rye genome |
![]() Evolutionary and chromosome synteny analyses of the rye genome |
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