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Comparative Genomics

Comparative genomics literally means comparing the complete genome sequences and structures of different species. This discipline aims at revealing species evolution, gene function, gene regulatory mechanism at genome level by identifying the sequence structures and elements that conserved or differentiated across different species. Typical comparative genomics study includes analyses in gene family, evolutionary development, whole genome duplication, selective pressure, etc.

Service Details

Demo Results

Case Study

Service Advantages


● Comprehensive analyses package, containing the eight most commonly required analyses

● High reliability in analysis with detailed and easily understandable interpretation on results

● Well-designed ready-to-publish figures

● Highly-skilled bioinformatics team fulfills diverse personalized analysis demands

● Shorter turn-around time with higher accuracy in analysis

● Abundant experience with over 90 successful cases with accumulative published impact factor of over 900

Service Specifications

Estimated turn-around time

Number of species


30 working days

6 - 12

 Gene family clustering

Gene family expansion and contraction

Phylogenetic tree construction

Divergence time estimation(Fossil calibration required)

LTR insertion time (For plants)

Whole genome duplication (For plants)

Selective pressure

Synteny analysis

Bioinformatics analyses

● Gene family

● Phylogenetics

● Divergence time

● Selective pressure

● Synteny analysis

流程图Comparative Genomics

Sample Requirements and Delivery

Sample Requirements:

Tissue or DNA for genome sequencing and assembly

For Tissue




PacBio CCS


Visceral tissue

0.5 ~ 1g

≥ 3.5g

Muscle tissue

≥ 5.0g

≥ 5.0mL

Mammalian blood

≥ 0.5mL

Poultry/Fish blood


Fresh Leaf

1 ~ 2g

≥ 5.0g



1 ~ 2g

≥ 10.0g



1 ~ 2g

≥ 20.0g


Cultured cell


≥ 1 x 108


Genome sequence files(.fasta) and annotation files (.gff3) of closely related species

Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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

    1.LTR insert time estimation: The figure shown a unique bimodal distribution in LTR-RTs insertion times in Weining rye genome, compared to other species. The most recent peak appeared around 0.5 million years ago.


    Li Guang et al., Nature Genetics, 2021



    2.Phylogeny and gene family analysis on chayote (Sechium edule) : By analyzing chayote and the other 13 related species in gene family, Chayote was found to be most closely related with snake gourd (Trichosanthes anguina). Chayote derived from snake gourd in around 27-45 Mya and whole genome duplication(WGD) was observed in chayote in 25±4 Mya, which is the third WGD event in cucuibitaceae. 


    Fu A et al., Horticulture Research, 2021



    3.Synteny analysis: Some genes related to phytohormones in fruit development were found in chayote, snake gourd and squash. Correlation between chayote and squash is slightly higher than that between chayote and snake gourd. 


    Fu A et al., Horticulture Research, 2021



    4.Gene family analysis: KEGG enrichment on gene family expansion and contraction in G.thurberi and G.davidsonii genomes shown that steroid biosynthesis and brassinosteroid biosynthesis related genes were expanded. 


    Yang Z et al., BMC Biology, 2021



    5.Whole genome duplication analysis: 4DTV and Ks distribution analysis shown whole genome duplication event. Peaks of intraspecies shown duplication events. Peaks of interspecies shown speciation events. The analysis indicated that comparing with the other three closely related species, O. europaea went through a large scale gene duplication more recently.


    Rao G et al., Horticulture Research, 2021

    BMK Case

    Rose without prickle: genomic insights linked to moisture adaptation 

    Published: National Science Review, 2021

    Sequencing strategy:

    ‘Basye’s Thornless’ (R. Wichurainan) genome:
    Approx. 93 X PacBio + approx. 90 X Nanopore + 267 X Illumina

    Key results

    1.High quality R.wichuraiana genome was constructed using long-read sequencing techniques, which yield an assembly of 530.07 Mb (Estimated genome size was approximately 525.9 Mb by flow cytometry and 525.5 by genome survey; Heterozygosity was around 1.03%). BUSCO estimated score was 93.9%. Comparing with “Old blush” (haploOB), the quality and completeness of this genome was confirmed by base single-base accuracy and LTR assembly index (LAI=20.03). R.wichuraiana genome contains 32,674 protein coding genes.

    2.Multi-omics joint analysis, consisting of comparative genomics, transcriptomics, QTL analysis of genetic population, revealed the crucial speciation between R. wichuraiana and Rosa chinensis. Also, expression variation of related genes in QTL were likely to be associated with stem prickle patterning.


    Comparative genomics anaysis between Basye;s Thornless and Rosa chinensis including synteny analysis, gene family cluster, expansion and contraction analysis, revealed large number of variations, which related to crucial traits in roses. The unique expansion in NAC and FAR1/FRS gene family was very likely to be associated with resistance to black spot.

    81Comparative-genomics-analyses-between-BT-and-OB 82Comparative-genomics-analyses-between-BT-and-OB 83Comparative-genomics-analyses-between-BT-and-OB

    Comparative genomics analysis between BT and haploOB genomes.


    Zhong, M. , et al. “Rose without prickle: genomic insights linked to moisture adaptation” National Science Review, 2021;, nwab092.

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