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Nroj / Tsiaj De Novo Genome Secencing

Nroj / tsiaj de novo genome excome excening duab

De novoCov ua ntu zus rau kev tsim kho ntawm hom 'Genome uas siv cov ntu thev naus laus zis nyob rau hauv qhov tsis muaj ntsuas genome. Kev qhia thiab thoob plaws kev kawm qib thib peb-tiam, muaj cov lus txhawb siab ntev dua, tau txhim kho Genria los ua ke los ntawm kev nce sib tshooj ntawm kev nyeem. Txoj kev txhim kho no tshwj xeeb yog qhov cuam tshuam nrog cov cheeb tsam uas tau rov qab, thiab cov kab ke nrog cov kev sib sau ua ke uas feem ntau sib sau ua ke siv cov lus luv luv nyob ib leeg.

Peb qhov kev daws teeb meem ib qho muab cov kev pab cuam sib xyaw thiab kev tshawb xyuas Bioinformic thiab kev tshawb xyuas Bioinformic uas xa cov txiaj ntsig zoo ntawm novo ua ke genome. Qhov kev kuaj xyuas genina thawj zaug nrog Genina muaj kev kwv yees genome thiab nyuaj, thiab cov ntaub ntawv no tau siv los coj cov kauj ruam tom ntej ntawm ntev nyeem nrog pacbio hieci, ua rawsde novoLos ua ke ntawm contigs. Qhov kev siv ntawm HIC tom ntej no ua rau kev sib dhos ntawm cov contigs mus rau genome, tau txais ib lub chaw ua si chromosome-qib Chromosome-tau txais ib lub rooj sib txoos chromosome-tau Thaum kawg, lub genome no yog tshaj tawm los ntawm cov ntaus cim twv ua ntej thiab los ntawm kev nthuav tawm cov noob, chaw ua haujlwm nrog cov ntawv xa mus nrog luv luv thiab ntev nyeem.

Tiv Tauj Peb

Cov Lus Qhia Pab

Bioinformformic

Demo Cov Ntsiab Lus

Cov Ntawv Tshaj Tawm Tshwj Xeeb

Cov Nta

● Kev sib xyaw ua ke ntawm ntau yam ua ntu zus thiab cov kev pabcuam bioinformic hauv ib qho kev daws teeb meem:

Daim ntawv ntsuam xyuas genome nrog allina los kwv yees g genome loj thiab phau ntawv qhia tom ntej cov kauj ruam;

Ntev nyeem cov qib raude novosib dhos ntawm crossigs;

Hi-c sib npaug rau chromosome anchoring;

mws mws ua ntu zus rau cov cim ntawm cov noob;

Siv tau ntawm lub rooj sib txoos.

● Kev pabcuam rau kev tsim kho cov tshiab genomes los yog txhim kho cov kev siv cov genomes uas twb muaj lawm rau hom kev txaus siab.

Kev Pabcuam Zoo

1Development-of-of-of-of-bioinformatics-hauv-de-NOVO-GAENTO-KOOM

Kev loj hlob ntawm cov platforms thiab bioinformics hauvde novoGenome Sib Dhia

(Amarasinghe sl li al.,Txoj Kev Genome, 2020)

●Kev txawj ntse thiab cov ntaub ntawv tshaj tawm: Bmkgene tau sau ntau cov genome sib dhos ntawm cov hom decroid, nrog rau cov diploid genomes thiab ntau txoj kev polyploid thiab Allopolyploid hom. Txij xyoo 2018, peb tau pab txhawb rau300 Cov Ntawv Tshaj Tawm High-Kev Cuam Tshuam, thiab 20+ ntawm lawv tau tshaj tawm hauv cov noob caj noob cesCov.

● Ib qho kev daws teeb meem: Peb txoj kev sib koom tes sib txuas ntxiv cov kev sib txuas ua ke ntau ntu thiab cov tshuaj ntsuam xyuas mus rau hauv cov khoom siv sib xyaw ua ke, xa cov txiaj ntsig zoo ntawm cov khoom siv gorge.

●Ua rau koj cov kev xav tau: Peb cov kev pabcuam ua haujlwm yog customizable, cia kev yoog raws genomes nrog ntau yam kev xav tau. Qhov no suav nrog kev pab tau giant menomes, polyploid genomes, zoo heterozygous genomes, thiab ntau dua.

●Cov kws txawj ntse heev hauv pab pawg thiab pab neeg saib xyuas: Nrog rau kev paub zoo hauv kev sim thiab bioinformformy pem hauv ntej ntawm cov gentre sib dhos thiab cov duab patents thiab software luam tawm.

●Kev txhawb nqa tom qab:Peb cov lus cog tseg txuas ntxiv nthuav tawm cov phiaj xwm ua tiav nrog 3-hli tom qab muag lub sijhawm pabcuam. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

Kev Pabcuam Tshwj Xeeb

Ntsuam Xyuas

Genome Sib Dhia

Chromosome-qib

Genome Annotation

50 x ICAINEQ PE150

30x Pacbio CCS HIFI nyeem

100 x hi-c

RNA-SEQ IFFINA PE150 10 GB

(yeem)

Tag nrho ntev rna-seq pacbio 40 gb lossis

Nanopore 12 GB

Kev pabcuam yuav tsum tau ua

Rau cov lus nug gen, genome sib dhos thiab hi-c los ua ke:

Cov ntaub so ntswg lossis rho tawm nucleic acids	Ntsuam Xyuas	Genome sib dhos nrog pacbio	Hi-c los ua ke
Tsiaj Viscera	0.5-1 g	≥ 3.5 g	≥2 g
Cov leeg tsiaj	0.5-1 g	≥ 5 g	≥2 g
Cov ntshav Mammalian	1.5 ml	≥ 5 ml	≥2 ml
Nqaij qaib / Ntses Ntshav	1.5 ml	≥ 0.5 ml	≥2 ml
Tsob ntoo- nplooj ntawv tshiab	1-2 g	≥ 5 g	≥ 4 g
Cov cells		≥ 1x10⁸	≥ 1x10⁷
Tus kab	0.5-1 g	≥ 3 g	≥ 2 g
Rho DNA	Kev siab: ≥1 ng / μl Npaum li cas ≥ 30 ng Txwv tsis pub lossis tsis muaj kev nyuaj siab lossis paug	Concentration: ≥ 50 ng / μl Tus nqi: 10 μg / ntws ntawm tes / qauv OD260 / 280 = 1.7-2.2 OD260 / 230 = 1.8-2.5 Txwv tsis pub lossis tsis muaj kev nyuaj siab lossis paug	-

Rau Genome Annotation nrog Transcriptomics:

Cov ntaub so ntswg lossis rho tawm nucleic acids	ICACE Transcriptome	Pacbio transcriptome	Nanopore Transcriptome
Nroj tsuag- hauv paus / kav / petal	450 mg	600 Mg
Tsob nroj - Nplooj / noob	300 mg	300 mg
Cog - Txiv Hmab Txiv Ntoo	1.2 g	1.2 g
Tsiaj Lub Plawv / Txoj hnyuv	300 mg	300 mg
Tsiaj Viscera / Hlwb	240 mg	240 mg
Cov leeg tsiaj	450 mg	450 mg
Tsiaj pob txha / plaub hau / tawv nqaij	1 g	1 g
Arthropod - Kab	6	6
Arthropod -crustacea	300 mg	300 mg
Tag nrho cov ntshav	1 raj	1 raj
Rho tawm RNA	Concentration: ≥ 20 ng / μl Nqi ≥ 0.3 μg OD260 / 280 = 1.7-2.5 OD260 / 230 = 0.5-25-2.5 Rov nrho≥ 6 5-8s / 18S≥1	Concentration: ≥ 100 ng / μl Tus nqi ≥ 0.75 μg OD260 / 280 = 1.7-2.5 OD260 / 230 = 0.5-25-2.5 Rov nrho≥ 8 5-8s / 18S≥1	Concentration: ≥ 100 ng / μl Tus nqi ≥ 0.75 μg OD260 / 280 = 1.7-2.5 OD260 / 230 = 0.5-25-2.5 Rov nrho≥ 7.5 5-8s / 18S≥1

Pom zoo tus qauv xa mus

Thawv: 2 Ml Centrifuge Tube (Tin Ntawv Nyiaj tsis pom zoo)

(Rau feem ntau ntawm cov qauv, peb pom zoo kom tsis txhob khaws cia hauv EJANOL.)

Qauv kos cim npe: Cov qauv yuav tsum yog sau kom pom tseeb thiab zoo ib yam rau cov qauv xa cov qauv cov ntaub ntawv.

Cov zaub mov xa tuaj: qhuav-dej khov: Kuaj yuav tsum tau ntim rau hauv cov hnab ua ntej thiab faus rau hauv cov dej khov qhuav.

Kev ua hauj lwm

Kev Pabcuam Khiav

Kev Tshawb Fawb Kev Tshawb Fawb

Qauv Xa

DNA extraction

Kev Siv Hauv Tsev Qiv Ntawv

Ze

Cov Ntaub Ntawv Kev Ntsuam Xyuas

Cov Kev Pab Tom Qab Muag

Yav dhau los: Tib neeg tag nrho ceev sib npaug

Tom ntej: Hi-c raws li genome sib dhos

Ua tiav Bioinformatic tsom xam, sib cais hauv 4 kauj ruam:

1) Kev Ntsuam Xyuas Genome, raws li K-Fer Kev Ntsuam Xyuas nrog NGS nyeem:

Kev kwv yees ntawm genome loj

Kev kwv yees ntawm heterozygosity

Kwv yees kev rov ua dua thaj chaw

2) Genome sib dhos nrog Pacbio HiFi:

De novorooj sib sau

Kev ntsuas kev sib dhos: suav nrog Kev Tshawb Xyuas Kev Ua Lag Luam rau Genome thiab qhia rov qab ntawm NGS thiab Pacbio HiFi nyeem

3) Hi-C Asfullly:

Hi-C Liv Liv QC: Kev kwv yees ntawm siv tau Hi-C Kev Sib Tham

Hi-C Assbly: pawg ntawm cov sib txuas ua pab pawg, tom qab kev txiav txim sib cais nyob hauv txhua pab pawg thiab muab cov kev paub sib txuas

Hi-C Kev Ntsuam Xyuas

4) Genome Annotation:

Tsis-coding RNA twv ua ntej

Rov ua dua cov cim qhia ua ntu zus (transposons thiab tandem rov qab)

Tus caj ces

§De novo: ab pib algorithms

Ua raws li homology

Raws li cov transcriptome, nrog ntev thiab nyeem luv: nyeem yogde novosib sau los yog mapped rau cov cua ntsawj ntshab genome

§ Notionation of kev kwv yees cov noob nrog ntau yam databases

1) Kev Tshawb Fawb Genu-K-Mer Ntsuam Xyuas

2) Genome sib dhos

2) Gacbio HiFi nyeem cov ntawv qhia rau cua ntsawj ua ke

2) Hi-c Assbly - Kev kwv yees ntawm Hi-C raug kev cuam tshuam nrog khub

3) Hi-c post-sib dhos kev tshuaj ntsuam

4) Genome Annotation - kev sib xyaw ua ke ntawm kev kwv yees noob

4) Genome Annotation - Kwv Tij Cov Noob Annotation

Tshawb cov kev nce qib uas yooj yim los ntawm BMKGene's de novo gorge genome cov kev pabcuam los ntawm kev sau cov ntawv tshaj tawm:

Li, C. li al. (2021) GENOME SeATES QHIA TXOG KEV LEM YAM TXUJ CI THIAB QHIA TXOG KEV TXHAWB THIAB QHIA TXOG KEV TXHAWB HAUV QAB ZIB AVO, 1). DOI: 10.18 / s41467-021-21399-x.

Li, Y. li al. (2023) 'Cov kev hloov pauv loj tshaj plaws ua rau Genome qib kev hloov pauv mus rau Gayal (BOS frontal (bolecular biology thiab evecution, 40 (1). DOI: 10.1093 / Molbev / MSad006.

TIAN, T. LI AL. (2023) 'Genetic sib dhos thiab kev ua kom muaj caj ces ntawm cov chaw nkaum uas txaus ntshai tiv thaiv kev kub ntxhov-tiv thaiv bateplasm', xwm genetics 2023 55: 3), pp. 496-506. DOI: 10.18 / s41588-023-01297-y.

Zhang, F. li al. (2023) 'qhia kev hloov pauv ntawm tropane alkaloid bihoynthes los ntawm kev tshuaj xyuas ob lub siab rau hauv Solanaceae tsev neeg', kev sib txuas lus 2023 14: 1, 4 (1). DOI: 10.18 / s41467-023-37133-4.

Kev Tshawb Fawb Teeb Meem Cov Lus Qhia:

Telomere-rau-telomere Assembly:Fu, A. li al. (2023) 'telomere-rau-telomere genome sib dhos ntawm iab meldo (Momordica Charantia L. Vais thiab Ripening cov cwj pwm caj ces', Horticulture kev tshawb fawb, 10 (1). DOI: 10.1093 / hr / uhac228.

Haplotyple Assembly:Hu, W. li al. (2021) 'Allele-txhais cov Genome qhia tau sib txawv biallelic thaum lub sij hawm coassa evolution', cov nroj tsuag molecular, 14 (6), pp. 851-854. DOI: 10.1016 / J.Molp.202.04.04.009.

Giant Genome Assembly:Yuan, J. li al. (2022) 'Chiga-Chromosomes thiab Giga-Giga-Giga-Giga-Giga-Giga-Giga-Giga-ostii', Xwm sib txuas lus 2022 13 (1, pp. 1-16. DOI: 10.18 / s41467-022-35063-1.

Gorgno Granitemle:Zhang, Q. li al. (2022) '' genomic kev pom rau hauv cov chromosome txo cov autopolypidid BACACTARAT ', Xwm Genetics 2022: 6, 54 (pp. 885-896. DOI: 10.18 / s41588-022-01084-1.