Evolutionary Genetics

Evolutionary genetics ibasa rakazara rekutevedzana rakagadzirirwa kupa dudziro yakazara paruzivo rwekushanduka kwezvinhu zvakapihwa zvichibva mukusiyana kwemajini, kusanganisira SNPs, InDels, SVs uye CNVs.Inopa kuongorora kwese kwakakosha kunodiwa pakutsanangura shanduko yekushanduka-shanduka uye maumbirwo emarudzi evanhu, zvakadai sehuwandu hwevanhu, kusiyana kwemajini, hukama hwefilogeny, nezvimwewo. Iinewo zvidzidzo pamusoro pekuyerera kwemajini, izvo zvinopa simba kufungidzira kwehuwandu hwevanhu hunobudirira, nguva yekusiyana.

Taura nesu

Service Details

Demo Results

Nyaya Yokudzidza

Basa Rinobatsira

Takagi et al.,The plant journal, 2013

● Kufungidzira kusiyana kwemarudzi nguva nekumhanya kunoenderana nekusiyana kwema nucleotide nemaamino acids.
● Kuburitsa hukama hwakavimbika hwephylogenetic pakati pezvipenyu zvine simba shoma rekushanduka-shanduka nekushanduka-shanduka
● Kugadzira hukama pakati pekuchinja kwemajini uye phenotypes kufumura maitiro ane hukama
● Kufungidzira kusiyana-siyana kwemavara okugara nhaka, kunoratidza kushanduka-shanduka kwemarudzi
● Kukurumidza Kuchinja Nguva
● Zvakawanda ruzivo: BMK yakaunganidza ruzivo rwakakura muhuwandu hwevanhu uye mapurojekiti ane chekuita nekushanduka-shanduka kwemakore anopfuura gumi nemaviri, achifukidza mazana emarudzi, nezvimwewo uye akabatsira mumapurojekiti anopfuura makumi masere epamusoro-soro anoburitswa muNature Communications, Molecular Plants, Plant Biotechnology Journal, nezvimwewo.

Sevhisi Zvinotsanangurwa

Zvekushandisa:

Kazhinji, vanhu vanosvika vatatu (eg subspecies kana strains) vanokurudzirwa.Huwandu hudiki hwega hwega hunofanirwa kuve nevanhu vasingasviki gumi (Zvirimwa ＞15, zvinogona kudzikiswa kune zvisingawanzo zvisikwa).

Sequencing strategy:

* WGS inogona kushandiswa kumarudzi ane emhando yepamusoro referensi genome, ukuwo SLAF-Seq inoshanda kune zvipenyu zvine kana zvisina referensi genome, kana referensi genome yehurombo.

Inoshanda kune genome size	WGS	SLAF-Tags (×10,000)
≤ 500 Mb	10×/munhu mumwe nomumwe	WGS inokurudzirwa zvakanyanya
500 Mb - 1 Gb		10
1 Gb - 2 Gb		20
≥2 Gb		30

Bioinformatics inoongorora

● Evolutionary analysis

● Kutsvaira kunosarudza

● Kuyerera kwemajini

● Nhoroondo yevanhu

● Nguva yekusiyana

Sample Zvinodiwa uye Delivery

Sample Zvinodiwa:

Zvisikwa	Tissue	WGS-NGS	SLAF
Mhuka	Visceral tishu	0.5~1g	0.5g
	Tsandanyama
	Ropa reMammalian	1.5mL	1.5mL
	Huku/Hove ropa
Plant	Fresh Leaf	1~2g	0.5~1g
	Petal/Stem
	Mudzi/Mbeu
Masero	Cultured sero

gDNA

Concentration
(ng/ul)

Mari

(ug)

OD260/OD280

SLAF

≥35

≥1.6

1.6-2.5

WGS-NGS

≥1

≥0.1

Kuyerera Kwebasa Rebasa

Kuedza kugadzira

Muenzaniso wekutumira

Kuvakwa kweraibhurari

Sequencing

Data analysis

Mushure mekutengesa masevhisi

Zvakapfuura: Bulked Segregant analysis

Zvinotevera: Metabolomics

*Demo mhedzisiro inoratidzwa pano yese kubva kugenomes yakaburitswa neBMKGENE

1.Evolution analysis ine kuvakwa kwe phylogenetic tree, chimiro chevanhu uye PCA inobva pane zvakasiyana-siyana.

Phylogenetic muti inomiririra taxonomic uye hukama hwekushanduka-shanduka pakati pemarudzi ane madzitateguru akafanana.
PCA ine chinangwa chekuona padhuze pakati pehuwandu hwevanhu.
Population chimiro chinoratidza kuvepo kweiyo genetically distinct sub-population maererano neallele frequencies.

3-1Phylogenetic-muti 3-2PCA 3-3Population-chimiro

Chen, uye.al.,PNAS, 2020

2.Selective tsvaira

Sarudzo yekutsvaira inoreva nzira inosarudzwa saiti inobatsira uye mafambiro enzvimbo dzakabatana asina kwaakarerekera anowedzerwa uye ayo enzvimbo dzisina kubatana anodzikiswa, zvichikonzera kudzikiswa kwedunhu.

Kuonekwa kweGenome-wide pamatunhu akasarudzika anogadziriswa nekuverenga huwandu hwevanhu genetic index (π，Fst, Tajima's D) yeese maSNP mukati mehwindo rinotsvedza (100 Kb) pane imwe nhanho (10 KB).

Nucleotide kusiyana (π)
4Nucleotide-siyana (π)

Tajima's D
5Tajima's-D

Fixation index (Fst)

6Fixation-index(Fst)

Wu, uye.al.,Molecular Plant, 2018

3.Gene Kuyerera

7Gene-kuyerera

Wu, uye.al.,Molecular Plant, 2018

4.Demographic nhoroondo

8Demographic-nhoroondo

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

5.Divergence nguva

9Kusiyana-nguva

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

Nyaya yeBMK

Mepu ye genomic variation inopa nzwisiso muhwaro hwemajini eSpring Chinese Cabbage(Brassica rapa ssp. Pekinensis) sarudzo.

Rakatsikiswa: Molecular Plant, 2018

Sequencing strategy:

Resequencing: kutevedzana kudzika: 10 ×

Mibairo yakakosha

Muchidzidzo ichi, 194 Chinese makabheji akagadziriswa kuti aenzaniswe zvakare neavhareji kudzika kwe10×, iyo yakapa 1,208,499 SNPs uye 416,070 InDels.Kuongorora kwePhylogenetic pamitsara iyi ye194 yakaratidza kuti mitsara iyi inogona kugoverwa kuva ecotypes matatu, chitubu, zhizha uye matsutso.Pamusoro pezvo, chimiro chehuwandu uye kuongororwa kwePCA kwakaratidza kuti chitubu Chinese cabbage yakatanga kubva kumatsutso makabheji muShandong, China.Izvi zvakazounzwa kuKorea neJapan, zvakayambuka nemitsetse yemuno uye mamwe marudzi ekunonoka-bolting awo akadzoserwa kuChina uye akazova Spring Chinese cabbage.

Genome-wide scanning pamatsutso eChinese makabheji uye mumatsutso makabheji pakusarudza kwakaratidza 23 genomic loci dzakapfuura nekusarudzwa kwakasimba, maviri acho aipindirana nenzvimbo yekudzora-nguva yekutonga zvichienderana neQTL-mepu.Matunhu maviri aya akawanikwa aine majini akakosha anodzora kutumbuka, BrVIN3.1 uye BrFLC1.Aya majini maviri akasimbiswa zvakare kuve akabatanidzwa mukuvhara nguva nekudzidza kwezvinyorwa uye transgenic kuyedza.

PB-yakazara-kureba-RNA-Sequencing-case-study

Population structure analysis paChinese cabbage

PB-yakazara-kureba-RNA-alternative-splicing

Ruzivo rweGenetic pakusarudza kweChinese kabichi

Reference

Tongbing, et al."A Genomic Variation Mepu Inopa Insights muGenetic Basis yeChitubu Chinese Cabbage (Brassica rapa ssp.pekinensis)Sarudzo."Molecular Plants,11(2018):1360-1376.