Evolutionary Genetics
Service Advantages
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
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 |
Amount (ug) |
OD260/OD280 |
|
SLAF |
≥35 |
≥1.6 |
1.6-2.5 |
|
WGS-NGS |
≥1 |
≥0.1 |
- |
Service Work Flow
Experiment design
Sample delivery
Library construction
Sequencing
Data analysis
After-sale services
*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.
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）
Tajima’s D
Fixation index(Fst)
Wu, et. al., Molecular Plant, 2018
3.Gene Flow
Wu, et. al., Molecular Plant, 2018
4.Demographic history
Zhang, et. al., Nature Ecology&Evolution, 2021
5.Divergence 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.
Population structure analysis on Chinese cabbages |
Genetic information on Chinese cabbage selection |
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.
