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T2T Genome Sib Dhos | Ultra Long Sequencing

T2T Genome Assembly | Ultra Long Sequencing Featured Image

T2T (Telomere-rau-Telomere) Genome yog tus qauv kub rau kev sib sau ua ke genome zoo, hais txog kev tsim kho genome uas tsis muaj qhov sib txawv lossis tsis muaj qhov sib txawv, uas nthuav dav ntawm ib qho telomere mus rau lwm qhov, thiab rhuav tshem cov kev txwv ntawm kev sib sau ua ke genome ib txwm muaj.

Siv lub zog los ntawm core ONT ultra-long read sequencing thiab kev sib xyaw nrog ntau lub platform deep sequencing thiab cov optimized bioinformatics pipelines, BMKGENE T2T Genome kev daws teeb meem tsom mus rau cov genomic "tsaus ntuj" uas nyuaj tshaj plaws - telomeres (cov nucleoprotein complexes tshwj xeeb ntawm eukaryotic chromosome kawg), cov kab mob siab dua centromeres (cov tandem repeat arrays loj heev), thiab lwm cov complex repeat thiab heterozygous haplotype regions, uas tau ntev tsis daws tau rau cov standard long-read sequencing. Tsis zoo li cov standard long reads uas tsis hla cov regions no thiab ua rau cov sequencing collapse lossis chimeric contigs, ONT ultra-long reads tuaj yeem hla cov unassembleable gaps thiab complex regions. BMKGene cog lus tias yuav xa cov gap-free lossis gap-less, high-quality T2T genomes rau ntau hom tsiaj.

Kev tsim cov T2T genome qhib cov cheeb tsam genomic nyuaj uas yav dhau los tsis tau mus txog, ua kom tiav cov kev tshawb fawb tseem ceeb, thiab muab cov ntaub ntawv ruaj khov, siab raug rau kev tshawb fawb tob tob suav nrog kev hloov pauv ntawm cov tsiaj txhu, kev tshawb nrhiav cov noob caj noob ces, kev yug me nyuam molecular, kev kho mob kom raug thiab lwm yam kev tshawb fawb tshiab.

Tiv Tauj Peb

Cov Lus Qhia Txog Kev Pabcuam

Kev tshawb fawb txog bioinformatics

Cov txiaj ntsig ntawm kev sim

Cov ntawv tshaj tawm tshwj xeeb

Cov yam ntxwv ntawm kev pabcuam

•Xa cov kev sib dhos genome telomere-rau-telomere uas muaj qhov tseeb siab, sib txuas siab, thiab ua tiav siab.

•Kov yeej cov teeb meem sib dhos hauv cov cheeb tsam centromeric thiab cov cheeb tsam rov ua dua ntau heev.

•Tshuaj xyuas cov kev hloov pauv ntawm cov qauv hauv cov cheeb tsam nyuaj xws li centromeres thiab telomeres.

•Tshawb nrhiav keeb kwm ntawm chromosomes thiab kev yug me nyuam, thiab txheeb xyuas cov noob caj noob ces tseem ceeb uas txiav txim siab txog poj niam txiv neej.

Cov Kev Pabcuam Zoo

•Pab neeg ua haujlwm ntev heev uas suav nrog kev rho tawm mus txog rau kev txheeb xyuas cov noob, nrog kev paub dhau los ntawm ntau hom tsiaj.

•Nkag mus rau ob qho tib si PacBio thiab Nanopore cov platform nyeem ntev nrog cov khoom siv siab thiab cov tswv yim sequencing yooj ywm.

•Pab neeg muaj kev paub dhau los hauv kev sib sau ua ke ntawm genome thiab kev tshuaj xyuas bioinformatics raws li tus kheej, txawj ntse hauv T2T genome projects.

•Ntau tshaj 200 qhov project genome ua tiav thiab ntau tshaj 2000 cov yam ntxwv cuam tshuam uas tau sau los.

•Cov kev daws teeb meem kev sim thiab bioinformatic uas tau txais kev txhawb nqa los ntawm cov cai luam tawm thiab cov ntawv pov thawj.

Cov Lus Qhia Txog Kev Pabcuam

Kev tshawb nrhiav txog genome	Kev sib sau ua ke ntawm genome	Qib Chromosome	Kev txhaws qhov sib txawv	Cov Lus Cim Genome
50X Illumina NovaSeq PE150	30X PacBio CCS HiFi nyeem	100X Hi-C	40-100X ONT Nyeem ntev heev	RNA-seq Illumina PE150 10 Gb + (yeem xaiv tau) RNA-seq PacBio 40 Gb lossis Nanopore 12 Gb

Cov Kev Cai rau Kev Pabcuam

Yog xav paub ntxiv txog kev soj ntsuam, PacBio CCS, Hi-C, thiab transcriptome (rau kev sau ntawv) cov qauv sequencing, thov mus saib "theem chromosomeCov kev cai rau kev sib sau ua ke ntawm cov qauv genome".

Rau ONT ultra-long sequencing, cov qauv ntaub so ntswg raug pom zoo, nrog rau cov qauv zoo dua los txhawb kev rho tawm cov DNA ultra-HMW.

Yog xav paub ntxiv txog kev npaj cov qauv thiab cov kev cai, thov hu rau peb pab neeg muag khoom kom tau txais kev daws teeb meem raws li hom.

Kev Ua Haujlwm Pabcuam

Tsim qauv kev sim

Kev xa khoom qauv

Kev rho tawm DNA

Kev tsim kho tsev qiv ntawv

Kev txheeb xyuas kab ke

Kev tshuaj xyuas cov ntaub ntawv

Cov kev pab cuam tom qab muag

Yav dhau los: Kev kawm txog Proteomics

Tom ntej no:

Cov kev tshuaj xyuas tseem ceeb suav nrog:

1) Kev Sib Dhos Genome T2T

● T2T genome txhais tau hais tias yog ib lub genome uas muaj "0 qhov sib txawv" uas tsawg kawg yog ib lub chromosome tau sib sau ua ke tag nrho los ntawm telomere mus rau telomere.

● Siv cov kev nyeem CCS uas raug siab thiab ONT nyeem ntev heev:

* Tsim cov contig v1 genome los ntawm kev sib dhos hybrid siv hifiasm (v0.25.0).

* Tshem tawm cov plastid thiab cov kab mob uas muaj kuab paug los ntawm BLAST tawm tsam NT database.

* Cov scaffold txuas rau hauv cov chromosome-scale sib dhos siv cov ntaub ntawv Hi-C nrog 3D-DNA.

* Sau cov telomeres uas ploj lawm los ntawm kev sib sau ua ke hauv zos nrog ONT nyeem kom tau txais cov genome T2T kawg.

2) Kev Ntsuam Xyuas Kev Sib Dhos

● Kev Ntsuam Xyuas BUSCO

BUSCO v5.2.1 (Benchmarking Universal Single-Copy Orthologs) tsim cov txheej txheem ib-copy rau cov kab mob tseem ceeb raws li OrthoDB 10 database. Cov genome sib sau ua ke raug soj ntsuam los ntawm kev sib phim nrog cov txheej txheem gene no, raws li qhov sib piv thiab kev ncaj ncees.

Qhov feem pua ntau dua ntawm "Tiav BUSCOs" qhia txog kev sib sau ua ke ntawm genome siab dua.

● Nyeem Daim Ntawv Qhia

Siv bwa los kho cov kev nyeem luv luv los ntawm tiam tom ntej sequencing (piv txwv li, Illumina) rau cov genome uas tau sib sau ua ke. Siv Minimap2 kho cov kev nyeem ntev ntawm tiam thib peb rau cov genome uas tau sib sau ua ke.

Qhov ua tiav ntawm cov genome sib sau ua ke thiab kev sib xws ntawm kev npog sequencing raug soj ntsuam raws li qhov nrawm ntawm kev kos duab, qhov piv ntawm kev npog genome, thiab kev faib tawm tob.

● Kev Ntsuam Xyuas QC ntawm Genome

Siv Merqury los ntsuas qhov kev sib dhos los ntawm kev sib piv cov kev nyeem sequencing uas raug siab k-mers nrog cov genome sib dhos kom tau txais qhov zoo sib xws (QV).

Cov nqi zoo dua qhia tau tias muaj qhov tseeb dua ntawm cov genome uas tau sib sau ua ke.

● Kev Ntsuam Xyuas Genome LAI

LAI (LTR Assembly Index) ntsuas qhov kev sib dhos ntawm cov noob caj noob ces raws li qhov sib piv ntawm cov kab ke LTR retrotransposon uas tsis hloov pauv rau tag nrho cov kab ke LTR. Cov kab ke LTR-RT uas tau xaiv tau raug txheeb xyuas siv LTR_FINDER (v1.0.7) thiab LTRharvest (v1.5.9), tom qab ntawd lim thiab koom ua ke siv LTR_retriever (v2.8) kom tau txais LTR retrotransposons uas muaj kev ntseeg siab thiab xam LAI.

Raws li LAI tus tsim tawm cov ntawv tshaj tawm, LAI tus nqi raug muab faib ua peb theem:

Draft (0 ≤ LAI < 10), Reference (10 ≤ LAI < 20), thiab kub (LAI ≥ 20).

● Kev txheeb xyuas Telomeres thiab Centromeres

Siv TIDK los nrhiav cov chav telomere rov ua dua hauv cov genome. Nrhiav cov kab ke telomere thiab tau txais cov ntaub ntawv qhov chaw siv FindTelomeres raws li cov qauv rov ua dua.

Txheeb xyuas cov kev rov ua dua ntawm centromeric siv Centromics nrog kev nyeem ntev ntawm tiam thib peb, tom qab ntawd rov xa mus rau lub genome kom tau txais cov chaw thiab cov kab ke ntawm centromere.

1) Daim Ntawv Qhia Txog Chromosome Genome

2)Cov Haujlwm Telomere hauv Genome

Chr	Chr Ntev (bp)	Pib Sab Sauv(bp)	Qhov kawg ntawm tus dej ntws (bp)	Qhov Ntev Sab Sauv (bp)	Pib Hauv Qab (bp)	Qhov kawg ntawm txoj kev nqes dej (bp)	Qhov Ntev Ntawm Tus Dej (bp)
Chr01	55,340,768	53	2,036	1,984	55,338,794	55,340,768	1,975
Chr02	56,588,289	1	2,760	2,760	56,584,191	56,588,289	4,099
Chr03	46,886,733	20	3,001	2,982	46,881,994	46,886,733	4,740
Chr04	49,401,798	1	2,143	2,143	49,399,160	49,401,798	2,639
Chr05	45,855,317	10	3,043	3,034	45,852,809	45,855,317	2,509
Chr06	45,285,625	1	3,268	3,268	45,283,427	45,285,625	2,199
Chr07	48,122,726	1	2,317	2,317	48,120,519	48,122,726	2,208

Nsau tseg:

Chr: Tus lej Chromosome

Chr_Length (bp): Qhov ntev ntawm Chromosome

Upstream_Start (bp): Qhov chaw pib ntawm lub telomere sab saud ntawm lub chromosome

Upstream_End (bp): Qhov kawg ntawm telomere sab saud ntawm lub chromosome

Upstream_Length (bp): Qhov ntev ntawm lub telomere sab saud ntawm lub chromosome

Downstream_Start (bp): Qhov chaw pib ntawm telomere downstream ntawm lub chromosome

Downstream_End (bp): Qhov kawg ntawm telomere downstream ntawm chromosome

Downstream_Length (bp): Qhov ntev ntawm telomere downstream ntawm lub chromosome

3)Cov Centromere Positions hauv Genome

Chr	Chr_Length(bp)	Centromics_Start(bp)	Centromics_End(bp)
Chr01	55,340,768	18,943,204	23,005,555
Chr02	56,588,289	28,114,720	30,677,916
Chr03	46,886,733	24,487,558	24,929,326
Chr04	49,401,798	20,976,875	22,563,388
Chr05	45,855,317	18,578,095	19,715,924
Chr06	45,285,625	19,398,436	19,950,173
Chr07	48,122,726	26,390,720	27,913,284

Lus Cim:

Chr: Tus lej Chromosome

Chr_Length (bp): Qhov ntev ntawm Chromosome

Centromere_Start (bp): Qhov chaw pib ntawm centromere ntawm lub chromosome

Centromere_End (bp): Qhov kawg ntawm lub centromere ntawm lub chromosome

4) Cov Txheeb Xyuas Qhov Sib Txawv ntawm Cov Txiaj Ntsig Sib Dhos

Pawg	Tus lej sib txawv	Len
Chr01	0	55,340,768
Chr02	0	56,588,289
Chr03	0	46,886,733
Chr04	0	49,401,798
Chr05	0	45,855,317
Chr06	0	45,285,625
Chr07	0	48,122,726
Tag Nrho (Ratio%)	0	347,481,256 (100.00)

Nsau tseg:

Pawg: Chromosome ID

Gap_Number: Tus naj npawb ntawm cov qhov sib txawv ntawm cov chromosome

Len (bp): Qhov ntev ntawm Chromosome

5) Kev Ntsuam Xyuas Genome LAI

Chr	Chr Ntev (bp)	Tsis muaj dab tsi ntxiv lawm	Tag Nrho	raw_LAI	LAI
tag nrho_genome	347,481,256	0.046	0.36	12.94	15.18

Lus Cim: Raws li cov neeg tsim khoom LAI tau tshaj tawm, cov nqi LAI raug muab faib ua peb pawg: Qauv (0 ≤ LAI < 10), Siv (10 ≤ LAI < 20), thiab Kub (LAI ≥ 20).

Chr Ntev (bp): Ntev ntawm Chromosome

Tsis muaj qhov puas tsuaj: Feem pua ntawm cov LTR-RTs tsis muaj qhov puas tsuaj hauv lub genome

Tag Nrho: Feem pua ntawm tag nrho cov LTRs hauv lub genome

raw_LAI = Intact / Tag Nrho × 100

LAI: Tus nqi LAI kho lawm

Tshawb nrhiav kev nce qib uas tau pab txhawb los ntawm BMKGene's de novo genome assembly services los ntawm kev sau cov ntawv tshaj tawm uas tau xaiv los ntawm:

T2T Genome

Liu, Shoucheng et al."Ib qho kev sib dhos ntawm telomere-rau-telomere genome ua ke nrog cov ntaub ntawv ntau-omic muab kev nkag siab rau hauv kev hloov pauv ntawm cov nplej qhob cij hexaploid."Kev tshawb fawb txog noob caj noob ces ntawm xwm vol. 57,4 (2025): 1008-1020. doi: 10.1038/s41588-025-02137-x

Yao, Xue-Feng et al."Kev sib sau ua ke ntawm cov noob caj noob ces ntawm cov nplej japonica Zhonghua 11."Kev sib txuas lus ntawm cov nroj tsuag vol. 6,10 (2025): 101463. doi:10.1016/j.xplc.2025.101463

Lv, Zhiyuan et al."Nyob ze ntawm telomere-rau-telomere genome sib dhos ntawm Camellia pitardii."Cov ntaub ntawv tshawb fawb vol. 12,1 1422. 14 Aug. 2025, doi:10.1038/s41597-025-05764-5

Du, Haiyuan thiab lwm tus."Ib qho kev sib sau ua ke ntawm genome ntawm Fragaria iinumae yuav luag tiav."BMC genomics vol. 26,1 253. 14 Peb. 2025, doi:10.1186/s12864-025-11440-0

Chen, Weikai et al."Kev sib sau ua ke ntawm genome ntawm Nicotiana benthamiana qhia txog cov qauv caj ces thiab epigenetic ntawm centromeres."Cov nroj tsuag ntuj vol. 10,12 (2024): 1928-1943. doi: 10.1038/s41477-024-01849-y

Haplotype-daws T2T Genome

Khan, Falak Sher et al. "Cov noob caj noob ces T2T uas tsis muaj qhov sib txawv ntawm Haplotype ntawm cov txiv hmab Cabernet Sauvignon."Cov ntaub ntawv tshawb fawb, 10.1038/s41597-026-06910-3. 26 Lub Ob Hlis 2026, doi: 10.1038/s41597-026-06910-3

T2T Genome + Comparative Genome

Hong, Lin et al. "Kev tsim thiab kev tshuaj xyuas ntawm cov noob caj noob ces telomere-rau-telomere rau 2 lub txiv kab ntxwv qab zib: Longhuihong thiab Newhall (Citrus sinensis)."GigaSciencevol. 13 (2024): giae084. doi:10.1093/gigascience/giae084

Li, Xiao-Jie et al. "Kev tshuaj xyuas ntawm telomere-rau-telomere genome ntawm cov zaub qhwv liab TXH4 piav qhia txog lub luag haujlwm ntawm DcLCYE thiab DcLCYB1 hauv kev sib sau ua ke ntawm lycopene hauv cov zaub qhwv."Kev tshawb fawb txog kev cog qoob loovol. 12.11 Nws 192. 29 Lub Xya hli ntuj 2025 10: 1093/hr/uhaf192

T2T Genome + Pangenome

Wang, Xiaojing et al. "T2T genome, kev tshuaj xyuas pan-genome, thiab cov noob teb rau kev ntxhov siab kub hauv Rhododendron hom."iMetavol. 4, 2e70010. 5 Mar. 2025, doi: 10.1002/imt2.70010