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Evolutionary Genetics

Evolutionary genetics is a packed sequencing service designed for providing a comprehensive interpretation on evolutionary information of given materials based on genetic variations, including SNPs, InDels, SVs and CNVs. It provides all fundamental analysis required for describing evolutionary changes and genetic features of populations, such as population structure, genetic diversity, phylogeny relationships, etc. It also contains studies on gene flow, which empowers estimation of effective population size, divergence time.


Service Details

Demo Results

Case Study

Service Advantages

1Evolutionary genetics

Takagi et al., The plant journal, 2013

● Estimating species divergence time and speed based on variations at nucleotide and amino acids level
● Revealing of more reliable phylogenetic relation between species with minimized influence of convergent evolution and parallel evolution
● Constructing links between genetic changes and phenotypes to uncover trait-related genes
● Estimating genetic diversity, which reflects evolutionary potential of species
● Faster Turnaround time
● Extensive experience: BMK has accumulated massive experience in population and evolutionary related projects for over 12 years, covering hundreds of species, etc. and contributed in over 80 high-level projects published in Nature Communications, Molecular Plants, Plant Biotechnology Journal, etc.

Service Specifications

Materials:

Normally, at least three sub-populations (e.g. subspecies or strains) is recommended. Each sub-population should contain no less than 10 individuals (Plants >15, can be reduced for rare species).

Sequencing strategy:

* WGS can be employed for species with high-quality reference genome, while SLAF-Seq is applicable to species either with or without a reference genome, or  reference genome of poor quality.

Applicable to genome size

WGS

SLAF-Tags (×10,000)

≤ 500 Mb

10×/individual

WGS is more recommended

500 Mb - 1 Gb

10

1 Gb - 2 Gb

20

≥2 Gb

30

Bioinformatics analyses

● Evolutionary analysis

● Selective sweep

● Gene flow

● Demographic history

● Divergence time

evolutionary 2

Sample Requirements and Delivery

Sample Requirements:

 

Species

 Tissue

 WGS-NGS

 SLAF

Animal

 

  

 Visceral tissue

 

0.5~1g

 

 

0.5g

 

 

 Muscle tissue

 Mammalian blood

 

1.5mL

 

 

1.5mL

 

 Poultry/Fish blood

Plant

  

  Fresh Leaf    

1~2g

   

0.5~1g

  Petal/Stem
  Root/Seed
 

Cells

  Cultured cell    

 

gDNA

Concentration
(ng/ul)

Amount

(ug)

OD260/OD280

SLAF

≥35

≥1.6

1.6-2.5

WGS-NGS

≥1

≥0.1

-

Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Library Preparation

Library construction

Sequencing

Sequencing

Data analysis

Data analysis

After sale Services

After-sale services


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

    1.Evolution analysis contains construction of phylogenetic tree, population structure and PCA based on genetic variations.

    Phylogenetic tree represents taxonomic and evolutionary relationships among species with common ancestor.
    PCA aims to visualize closeness between sub-populations.
    Population structure shows the presence of genetically distinct sub-population in terms of allele frequencies.

    3-1Phylogenetic-tree 3-2PCA 3-3Population-structure

    Chen, et. al., PNAS, 2020

    2.Selective sweep

    Selective sweep refers to a process by which an advantageous site is selected and frequencies of linked neutral sites are increased and those of unlinked sites are decreased, resulting in reduction of regional.

    Genome-wide detection on selective sweep regions is processed by calculating population genetic index(π,Fst, Tajima’s D) of all SNPs within a sliding window (100 Kb) at certain step (10 Kb).

    Nucleotide diversity(π)
    4Nucleotide-diversity(π)

    Tajima’s D
    5Tajima's-D

    Fixation index(Fst)

    6Fixation-index(Fst)

    Wu, et. al., Molecular Plant, 2018

    3.Gene Flow

    7Gene-flow

    Wu, et. al., Molecular Plant, 2018

    4.Demographic history

    8Demographic-history

    Zhang, et. al., Nature Ecology&Evolution, 2021

    5.Divergence time

    9Divergence-time

    Zhang, et. al., Nature Ecology&Evolution, 2021

    BMK Case

    A genomic variation map provides insights into the genetic basis of Spring Chinese Cabbage(Brassica rapa ssp. Pekinensis) selection 

    Published: Molecular Plant, 2018

    Sequencing strategy:

    Resequencing: sequencing depth: 10×

    Key results

    In this study, 194 Chinese cabbages were processed for re-sequencing with average depth of 10×, which yielded 1,208,499 SNPs and 416,070 InDels. Phylogenetic analysis on these 194 lines shown that these lines can be divided into three ecotypes, spring, summer and autumn. In addition, population structure and PCA analysis indicated that spring Chinese cabbage were originated from an autumn cabbage in Shandong, China. These were subsequently introduced to Korea and Japan, crossed with local lines and some late-bolting varieties of them were introduced back to China and finally became Spring Chinese cabbage.

    Genome-wide scanning on spring Chinese cabbages and autumn cabbages on selection revealed 23 genomic loci that have went through strong selection, two of which were overlapped with bolting-time controlling region based on QTL-mapping. These two regions were found to contain key genes that regulate flowering, BrVIN3.1 and BrFLC1. These two genes were further confirmed to be involved in bolting time by transcriptome study and transgenic experiments.

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

    Population structure analysis on Chinese cabbages

    PB-full-length-RNA-alternative-splicing

    Genetic information on Chinese cabbage selection

     
    Reference

    Tongbing, et al. “A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp.pekinensis)Selection.” Molecular Plants, 11(2018):1360-1376.

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