Nroj / Tsiaj De Novo Genome Sequencing
Kev Pabcuam Zoo
Kev loj hlob ntawm sequencing platforms thiab bioinformatics nyob rau hauvde novgenome sib dhos
(Amarasinghe SL thiab al.,Genome Biology, 2020)
● Tsim cov genomes tshiab thiab txhim kho cov genomes uas twb muaj lawm siv rau hom kev nyiam.
● Ntau dua qhov tseeb, txuas ntxiv thiab ua tiav hauv kev sib dhos
● Tsim cov peev txheej tseem ceeb rau kev tshawb fawb hauv cov kab ke polymorphism, QTLs, gene editing, yug me nyuam, thiab lwm yam.
● Nruab nrog tag nrho spectrum ntawm thib peb-tiam sequencing platforms: ib-nres genome los ua ke daws
● Yooj yim sib txuas thiab sib sau cov tswv yim ua kom tiav ntau hom genomes nrog cov yam ntxwv sib txawv
● Pab pawg kws tshaj lij bioinformatician nrog cov kev paub zoo hauv kev sib koom ua ke ntawm genome, suav nrog polyploids, genomes loj, thiab lwm yam.
● Ntau tshaj 100 qhov teeb meem ua tiav nrog cov ntawv tshaj tawm cuam tshuam ntau dua 900
● Tig-ib puag ncig-lub sij hawm sai li 3 lub hlis rau chromosome-theem genome los ua ke.
● Cov kev txhawb nqa muaj zog nrog ntau cov patents thiab software copyrights nyob rau hauv ob qho tib si sim thiab bioinformatics.
Service Specifications
|
Cov ntsiab lus
|
Platform
|
Nyeem Length
|
Kev pab them nqi
|
| Kev Tshawb Fawb Genome
| Illumina NovaSeq
| PEB 150
| ≥ 50 X
|
| Genome Sequence
| PacBio Revio: koj puas xav tau ntau tus thwjtim?
| 15 kb HiFi nyeem ntawv
| ≥ 30 X
|
| Nyob zoo-C
| Illumina NovaSeq
| PEB 150
| ≥100X
|
Kev khiav haujlwm
Sample Requirements thiab Delivery
Cov Qauv Xav Tau:
| Hom | Cov ntaub so ntswg | Rau PacBio | Rau Nanopor |
| Tsiaj | Cov kab mob visceral (lub siab, tus po, thiab lwm yam) | Yog '> 1.0 g | Yog '> 3.5 g |
| Cov leeg | Yog '> 1.5 g | Yog '> 5.0 g | |
| Cov ntshav ntawm cov tsiaj | ≥ 1.5 mL | ≥ 5.0 mL | |
| Ntshav ntses los yog noog | ≥ 0.2 mL | ≥ 0.5 mL | |
| Nroj tsuag | Cov nplooj tshiab | Yog '> 1.5 g | Yog '> 5.0 g |
| Petal los yog qia | Yog '> 3.5 g | Yog '> 10.0 g | |
| Roots los yog noob | Yog '> 7.0 g | Yog '> 20.0 g | |
| Cells | Cell kab lis kev cai | ≥ 3 × 107 | ≥ 1 × 108 |
Pom zoo coj mus kuaj
Ntim: 2 ml centrifuge tube (Tin foil tsis pom zoo)
Rau feem ntau ntawm cov qauv, peb pom zoo kom tsis txhob khaws cia hauv ethanol.
Sample labeling: Cov qauv yuav tsum tau sau kom meej meej thiab zoo ib yam rau xa cov qauv ntaub ntawv.
Kev Thauj Khoom: Dry-ice: Cov qauv yuav tsum tau ntim rau hauv hnab ua ntej thiab muab faus rau hauv cov dej khov qhuav.
Kev Pabcuam Ua Haujlwm Flow
Kev sim tsim
Qauv xa tuaj
DNA rho tawm
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 Biomarker Technologies
1.Circos ntawm chromosome-theem genome los ua ke ntawmG. rotundifoliumlos ntawm Nanopore sequencing platform
Wang M et al.,Molecular Biology thiab Evolution, 2021 ib
2.Statistics ntawm Weining rye genome los ua ke thiab annotation
Li G et al.,Nature Genetics, 2021 ib
3.Gene twv ua ntej ntawmSechium edulegenome, muab los ntawm peb txoj kev kwv yees:De novkev twv ua ntej, Homology-raws li kev twv ua ntej thiab RNA-Seq cov ntaub ntawv raws li kev twv ua ntej
Fu A et al.,Kev Tshawb Fawb Txog Kev Tshawb Fawb, 2021 ib
4.Kev txheeb xyuas qhov tsis zoo ntawm lub davhlau ya nyob twg rov ua dua hauv peb cov paj rwb genomes
Wang M et al.,Molecular Biology thiab Evolution, 2021 ib
5.Hi-C tshav kub daim ntawv qhia ntawm lubC. acuminatagenome qhia genome-wide tag nrho-los-txhua yam kev sib cuam tshuam.Kev siv ntawm Hi-C kev sib cuam tshuam yog proportional rau linear nrug ntawm contigs.Ib txoj kab ncaj nraim ntawm daim ntawv qhia tshav kub no qhia tau hais tias muaj qhov tseeb ntawm kev sib txuas ntawm chromosomes.(Contig anchoring ratio: 96.03%)
Kang M et al.,Nature Communications,2021
BMK Cas
Kev sib sau ua ke genome zoo qhia txog rye genomic yam ntxwv thiab cov noob tseem ceeb agronomically
Luam tawm: Nature Genetics, 2021 ib
Sequence Strategy:
Genome los ua ke: PacBio CLR hom nrog 20 kb tsev qiv ntawv (497 Gb, kwv yees 63 ×)
Kev kho ib ntus: NGS nrog 270 bp DNA tsev qiv ntawv (430 Gb, kwv yees 54 ×) ntawm Illumina platform
Contigs anchoring: Hi-C tsev qiv ntawv (560 Gb, kwv yees 71 ×) ntawm Illumina platform
Optical map: (779.55 Gb, kwv yees 99 ×) ntawm Bionano Irys
Cov txiaj ntsig tseem ceeb
1.Ib lub rooj sib txoos ntawm Weining rye genome tau luam tawm nrog tag nrho cov genome loj ntawm 7.74 Gb (98.74% ntawm kwv yees genome loj los ntawm ntws cytometry).Scaffold N50 ntawm lub rooj sib txoos no ua tiav 1.04 Gb.93.67% ntawm contigs tau ua tiav ntawm 7 pseudo-chromosomes.Lub rooj sib txoos no tau soj ntsuam los ntawm daim ntawv qhia kev sib txuas, LAI thiab BUSCO, uas ua rau cov qhab nia siab hauv txhua qhov kev ntsuam xyuas.
2.Cov kev tshawb fawb ntxiv ntawm kev sib piv genomics, daim ntawv qhia kev sib txuas ntawm caj ces, kev tshawb fawb transcriptomics tau ua los ntawm lub hauv paus ntawm cov genome no.Ib tug series ntawm cov yam ntxwv muaj feem xyuam rau genomic nta tau tshwm sim nrog rau genome-wide gene duplications thiab lawv cuam tshuam rau starch biosynthesis noob;Lub cev lub koom haum ntawm complex prolamin loci, gene qhia nta lub hauv paus ntsiab lus ntawm kev coj zoo thiab putative domestication-ssociated chromosomal regions thiab loci nyob rau hauv rye.
 Circos daim duab ntawm genomic nta ntawm Weining rye genome |  Evolutionary thiab chromosome synteny tsom xam ntawm rye genome |
Li, G., Wang, L., Yang, J.ua al.Kev sib sau ua ke ntawm genome zoo qhia txog cov yam ntxwv ntawm rye genomic thiab cov noob tseem ceeb agronomically.Nat Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
