Evolutionary noob caj noob ces
Kev Pabcuam Zoo
Takagi et al.,Phau ntawv cog lus, xyoo 2013
● Kev kwv yees hom kev sib txawv lub sij hawm thiab ceev raws li qhov sib txawv ntawm nucleotide thiab amino acids qib
● Kev nthuav tawm ntawm kev txhim kho kev sib raug zoo ntawm phylogenetic ntawm cov tsiaj nrog txo qis kev cuam tshuam ntawm kev hloov pauv hloov pauv thiab kev hloov pauv sib luag
● Tsim kev sib txuas ntawm cov kev hloov pauv caj ces thiab cov phenotypes los nthuav tawm cov noob caj noob ces
● Kev kwv yees muaj ntau haiv neeg, uas qhia txog kev muaj peev xwm hloov pauv ntawm hom
● Lub sijhawm hloov pauv sai dua
● Kev paub dav dav: BMK tau sau ntau qhov kev paub hauv cov pej xeem thiab cov kev hloov pauv uas muaj feem xyuam rau ntau tshaj 12 xyoo, suav nrog ntau pua hom, thiab lwm yam thiab tau pab ntau tshaj 80 cov haujlwm siab tshaj tawm hauv Nature Communications, Molecular Plants, Plant Biotechnology Journal, thiab lwm yam.
Service Specifications
Khoom siv:
Feem ntau, tsawg kawg yog peb pawg neeg (xws li subspecies lossis hom kab mob) raug pom zoo.Txhua sub-population yuav tsum tsis pub tsawg tshaj 10 tus neeg (Nroj tsuag ＞ 15, tuaj yeem txo qis rau hom tsawg).
Sequence Strategy:
* WGS tuaj yeem ua haujlwm rau cov tsiaj uas muaj kev siv genome zoo, thaum SLAF-Seq muaj feem xyuam rau hom tsiaj nrog lossis tsis muaj kev siv genome, lossis siv cov genome ntawm cov khoom tsis zoo.
| Muaj feem xyuam rau genome loj | WGS | SLAF-Tag (×10,000) |
| ≤ 500 Mb | 10 × / tus kheej | WGS tau pom zoo ntau dua |
| 500 Mb - 1 Gb | 10 | |
| 1 Gb - 2 Gb | 20 | |
| ≥ 2 Gb | 30 |
Bioinformatics tsom xam
● Evolutionary tsom xam
● Xaiv cheb
● Gene ntws
● Keeb kwm ntawm pej xeem
● Lub sijhawm sib txawv
Sample Requirements thiab Delivery
Cov Qauv Xav Tau:
| Hom | Cov ntaub so ntswg | WGS-NGS | SLAF |
| Tsiaj
| Visceral ntaub so ntswg |
0.5-1g
|
0,5g ib
|
| Cov nqaij mos | |||
| Mammalian ntshav | 1.5 ml yog '
| 1.5 ml yog '
| |
| Nqaij qaib / Ntses ntshav | |||
| Nroj tsuag
| Nplooj tshiab | 1 ~ 2g | 0.5-1g |
| Nplooj / qia | |||
| Hauv paus / noob | |||
| Cells | Cultivated cell |
| gDNA ua | Nco ntsoov | Tus nqi (ug) | OD 260/OD 280 |
| SLAF | ≥35 | ≥1.6 | 1.6-2.5 Nws |
| WGS-NGS | ≥1 | ≥0.1 | - |
Kev Pabcuam Ua Haujlwm Flow
Kev sim tsim
Qauv xa tuaj
Kev tsim kho tsev qiv ntawv
Sequencing
Cov ntaub ntawv tsom xam
Kev pab cuam tom qab muag
*Cov txiaj ntsig tau pom ntawm no yog tag nrho los ntawm genomes luam tawm nrog BMKGENE
1.Evolution tsom xam muaj kev tsim kho ntawm tsob ntoo phylogenetic, pej xeem cov qauv thiab PCA raws li kev hloov pauv caj ces.
Phylogenetic ntoo sawv cev rau taxonomic thiab evolutionary kev sib raug zoo ntawm cov tsiaj nrog cov poj koob yawm txwv.
PCA lub hom phiaj kom pom kev sib ze ntawm cov neeg nyob sab nraud.
Cov qauv pej xeem qhia pom muaj qhov sib txawv ntawm cov noob caj noob ces nyob rau hauv cov nqe lus ntawm allele frequencies.
Chen, thiab.al.,PNAS, xyoo 2020
2.Selective sweep
Kev xaiv cheb yog hais txog cov txheej txheem los ntawm qhov chaw zoo yog xaiv thiab zaus ntawm cov chaw nruab nrab txuas ntxiv tau nce thiab cov chaw tsis sib txuas tau raug txo qis, ua rau txo qis hauv cheeb tsam.
Kev tshawb nrhiav genome-wide ntawm cov cheeb tsam xaiv cheb yog ua tiav los ntawm kev suav cov pej xeem genetic index (π, Fst, Tajima's D) ntawm tag nrho SNPs nyob rau hauv lub qhov rais swb (100 Kb) ntawm qee cov kauj ruam (10 Kb).
Nucleotide diversity (π)
Tajima's D
Fixation index (Fst)
Wu, et.al.,Molecular Cog, xyoo 2018
3.Gene Flow
Wu, et.al.,Molecular Cog, xyoo 2018
4.Demographic keeb kwm
Zhang, thiab.al.,Nature Ecology & Evolution, 2021 ib
5. Lub sijhawm sib txawv
Zhang, thiab.al.,Nature Ecology & Evolution, 2021 ib
BMK Cas
Daim ntawv qhia kev hloov pauv genomic muab kev nkag siab rau hauv cov noob caj noob ces ntawm Spring Chinese Cabbage (Brassica rapa ssp. Pekinensis) xaiv
Luam tawm: Molecular Cog, xyoo 2018
Sequence Strategy:
Resequencing: sequencing qhov tob: 10 ×
Cov txiaj ntsig tseem ceeb
Hauv txoj kev tshawb no, 194 Suav cabbages tau ua tiav rau kev rov ua dua nrog qhov nruab nrab qhov tob ntawm 10 ×, uas tau txais 1,208,499 SNPs thiab 416,070 InDels.Phylogenetic tsom xam ntawm 194 kab no qhia tau hais tias cov kab no tuaj yeem muab faib ua peb hom ecotypes, caij nplooj ntoos hlav, caij ntuj sov thiab caij nplooj zeeg.Tsis tas li ntawd, cov qauv pej xeem thiab PCA tsom xam tau qhia tias lub caij nplooj ntoo hlav suav suav tau los ntawm lub caij nplooj zeeg zaub qhwv hauv Shandong, Suav.Cov no tau tom qab qhia rau Kaus Lim Kauslim thiab Nyij Pooj, hla nrog cov kab hauv zos thiab qee qhov lig-bolting ntau yam ntawm lawv tau qhia rov qab mus rau Tuam Tshoj thiab thaum kawg los ua Spring Suav cabbage.
Genome-wide scanning ntawm lub caij nplooj ntoos hlav Suav cabbages thiab lub caij nplooj zeeg cabbages ntawm kev xaiv tau qhia 23 genomic loci uas tau mus los ntawm kev xaiv muaj zog, ob ntawm cov uas tau sib tshooj nrog bolting-lub sij hawm tswj cheeb tsam raws li QTL-mapping.Ob thaj chaw no tau pom tias muaj cov noob tseem ceeb uas tswj cov paj, BrVIN3.1 thiab BrFLC1.Ob lub noob no tau lees paub ntxiv tias yuav koom nrog hauv lub sijhawm bolting los ntawm kev kawm transcriptome thiab kev sim hloov pauv.
 Kev txheeb xyuas pej xeem cov qauv ntawm Suav cabbages |  Cov ntaub ntawv keeb kwm ntawm Suav cabbage xaiv |
Tongbing, et al."Genomic Variation Map muab kev nkag siab rau hauv Genetic Basis ntawm Spring Chinese Cabbage (Brassica rapa ssp.pekinensis) Kev xaiv."Molecular Nroj Tsuag,11 (2018): 1360-1376.
