Indibano yeGenome ye-T2T | Ulandelelwano olude kakhulu
Iimpawu zeNkonzo
•Inika iindibano ze-genome ze-telomere-to-telomere ezichanekileyo kakhulu, ezihambelanayo kakhulu, kunye ne-genome epheleleyo kakhulu.
•Iyawoyisa imingeni yokuhlanganisa kwiindawo eziphakathi nendawo neziphindaphindwayo kakhulu.
•Uhlalutya umahluko kwisakhiwo kwiindawo ezinzima ezifana nee-centromeres kunye nee-telomeres.
•Uhlola imvelaphi ye-chromosome kunye nokwakhiwa kwe-homestode, kwaye uchonga ii-genes eziphambili ezichonga isini.
Iingenelo zeNkonzo
•Iqela leengcali elisebenza ixesha elide kakhulu eligubungela ukuhluza ukuya kulandelelwano, linamava aphumelelayo kwiintlobo ngeentlobo zezilwanyana.
•Ukufikelela kumaqonga e-PacBio kunye ne-Nanopore afundwa ixesha elide ane-output ephezulu kunye namaqhinga okulandelelana aguquguqukayo.
•Iqela elinamava ekuhlanganiseni i-genome kunye nohlalutyo lwe-bioinformatics olulungiselelwe wena, linobuchule kwiiprojekthi ze-genome ze-T2T.
•Iiprojekthi ze-genome eziphumeleleyo ezingaphezu kwama-200 kunye nezinto ezichaphazelayo ezingaphezulu kwama-2000 eziqokelelweyo.
•Izisombululo ezidityanisiweyo zovavanyo kunye ne-bioinformatic ezixhaswa ngamalungelo okushicilela kunye namalungelo okushicilela.
Iinkcukacha zeNkonzo
| Uphando lwe-genome | Ukuhlanganiswa kwejini | Inqanaba le-Chromosome | Ukuzaliswa kwezikhewu | Isaziso seGenome |
| I-50X Illumina NovaSeq PE150 | Ii-30X PacBio CCS HiFi reads | 100X Hi-C | Ukufundwa okude kwe-40-100X ONT Ultra | I-RNA-seq Illumina PE150 10 Gb + (ukhetho) Ubude obupheleleyo be-RNA-seq PacBio 40 Gb okanye iNanopore 12 Gb |
Iimfuno zeNkonzo
Kwisampulu zokulandelelana kweSurvey, iPacBio CCS, iHi-C, kunye ne-transcriptome (ukuze ufumane inkcazelo), nceda ujonge "inqanaba le-chromosomeiimfuno zesampulu yokuhlanganiswa kwe-genome".
Kwi-ONT ultra-long sequencing, kucetyiswa iisampulu zezicubu, ezinemigangatho ephezulu yokuxhasa ukukhutshwa kwe-ultra-HMW DNA.
Ukuze ufumane imiyalelo eneenkcukacha zokulungiselela iisampulu kunye neemfuno, nceda unxibelelane neqela lethu lokuthengisa ukuze ufumane isisombululo esenziwe ngokwezifiso ngokweentlobo.
Ukuhamba komsebenzi wenkonzo
Uyilo lovavanyo
Ukuhanjiswa kwesampulu
Ukukhupha i-DNA
Ukwakhiwa kweThala leeNcwadi
Ukulandelelana
Uhlalutyo lwedatha
Iinkonzo zasemva kokuthengisa
Uhlalutyo oluphambili luquka:
1) Ukuhlanganiswa kweGenome ye-T2T
● I-genome ye-T2T ibhekisa kwi-genome ene-"0 gaps" apho ubuncinane i-chromosome enye ihlanganiswe ngokupheleleyo ukusuka kwi-telomere ukuya kwi-telomere.
● Ukusebenzisa ii-CCS reads ezichanekileyo kakhulu kunye ne-ONT ultra-long reads:
* Yenza i-contig v1 genome nge-hybrid assembly usebenzisa i-hifiasm (v0.25.0).
* Susa iiplastid kunye ne-sequences ezingcolisiweyo yi-BLAST ngokuchasene nedathabheyisi ye-NT.
* I-scaffold idibana ibe yindibano yesikali se-chromosome kusetyenziswa idatha ye-Hi-C kunye ne-3D-DNA.
* Gcwalisa ii-telomeres ezilahlekileyo kwindibano yendawo nge-ONT reads ukuze ufumane i-genome yokugqibela ye-T2T.
2) Uvavanyo lweNdibano
● Uvavanyo lweBUSCO
I-BUSCO v5.2.1 (iBenchmarking Universal Single-Copy Orthologs) yakha iiseti zejini ezinekopi enye kwiimvelaphi eziphambili zendaleko ezisekelwe kwisiseko sedatha se-OrthoDB 10. I-genome ehlanganisiweyo ivavanywa ngokulungelelaniswa ngokuchasene nale seti yejini, ngokusekelwe kumlinganiselo wokuhambelana kunye nokuthembeka.
Inxalenye ephezulu ye-"Complete BUSCOs" ibonisa ukuphelela okuphezulu kwe-genome assembly.
● Ufunda iMephu
Lungelelanisa ufundo olufutshane oluvela kulandelelwano lwesizukulwana esilandelayo (umz., i-Illumina) kwi-genome edibeneyo usebenzisa i-bwa. Lungelelanisa ufundo olude lwesizukulwana sesithathu kwi-genome edibeneyo usebenzisa i-Minimap2.
Ukuphelela kwe-genome edibeneyo kunye nokufana kokugubungela ngokulandelana kuvavanywa ngokusekelwe kwisantya semephu, umlinganiselo wokugubungela i-genome, kunye nokusasazwa kobunzulu.
● Uvavanyo lwe-QC yeGenome
Vavanya indibano usebenzisa iMerqury ngokuthelekisa i-k-mers yokulandelelana okuchanekileyo kunye nendibano ye-genome ukuze ufumane umgangatho we-consensus (QV).
Amaxabiso aphezulu abonisa ukuchaneka okuphezulu kwe-genome edibeneyo.
● Uvavanyo lwe-Genome LAI
I-LAI (i-LTR Assembly Index) ivavanya ukuthembeka kwe-genome assembly njengomlinganiselo we-LTR retrotransposon sequences engaguqukiyo kwi-total LTR sequences. I-Candidate LTR-RT sequences ichongwa kusetyenziswa i-LTR_FINDER (v1.0.7) kunye ne-LTRharvest (v1.5.9), emva koko ihluzwe kwaye idityaniswe kusetyenziswa i-LTR_retriever (v2.8) ukuze kufunyanwe i-LTR retrotransposons ezithembekileyo kwaye kubalwe i-LAI.
Ngokutsho kwempapasho yomphuhlisi we-LAI, amaxabiso e-LAI ahlulwe abe ngamanqanaba amathathu:
I-Draft (0 ≤ LAI <10), iReferensi (10 ≤ LAI <20), kunye neGolide (LAI ≥ 20).
● Ukuchongwa kweeTelomeres kunye neeCentromeres
Chonga iiyunithi eziphindaphindayo zetelomere kwi-genome usebenzisa i-TIDK. Fumana ulandelelwano lwetelomere kwaye ufumane ulwazi lwendawo usebenzisa i-FindTelomeres ngokusekelwe kwiimotifs eziphindaphindayo.
Chonga ukuphindaphinda okunokwenzeka kwe-centromeric usebenzisa i-Centromics ene-long reads yesizukulwana sesithathu, uze ubuyele kwi-genome ukuze ufumane izikhundla ze-centromere kunye nolandelelwano.
1) Imephu yeChromosome yeGenome
2)Izikhundla zeTelomere kwiGenome
| Chr | Ubude beCr(bp) | Uqalo_oluphezulu(bp) | Isiphelo_Esiphezulu(bp) | Ubude_Obuphezulu(bp) | Uqalo_olusezantsi(bp) | Isiphelo_Esisezantsi(bp) | Ubude_obusezantsi(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 |
Ni-ote:
Chr: I-Chromosome ID
Ubude_beChr (bp): Ubude beChromosome
Ukuqala_kwe-Upstream (bp): Indawo yokuqala ye-telomere ephezulu kwi-chromosome
Isiphelo_Esiphezulu (bp): Indawo yokuphela kwetelomere ephezulu kwichromosome
Ubude_Bomphezulu (bp): Ubude be-telomere ephezulu kwi-chromosome
I-Downstream_Start (bp): Indawo yokuqala ye-telomere esezantsi kwi-chromosome
Isiphelo_se-Downstream (bp): Indawo yokuphela kwe-telomere esezantsi kwi-chromosome
Ubude_bezantsi (bp): Ubude be-telomere esezantsi kwi-chromosome
3)Izikhundla zeCentromere kwiGenome
| Chr | Ubude_beChr(bp) | I-Centromics_Start(bp) | Isiphelo_seCentromics(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 |
Phawula:
Chr: I-Chromosome ID
Ubude_beChr (bp): Ubude beChromosome
I-Centromere_Start (bp): Indawo yokuqala ye-centromere kwi-chromosome
I-Centromere_End (bp): Indawo yokuphela kwe-centromere kwi-chromosome
4) Izibalo zeGap kwiZiphumo zokuhlanganisa
| Iqela | Inombolo_Yesithuba | ULen |
| 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 |
| Isimbuku (Umlinganiselo %) | 0 | 347,481,256(100.00) |
Ni-ote:
Iqela: I-Chromosome ID
Inombolo_Yesithuba: Inani lezithuba kwi-chromosome
I-Len (bp): Ubude be-Chromosome
5) Uvavanyo lwe-Genome LAI
| Chr | Ubungakanani obude (bp) | Iqinile | Isimbuku | i-raw_LAI | I-LAI |
| i-genome_epheleleyo | 347,481,256 | 0.046 | 0.36 | 12.94 | 15.18 |
Qaphela: Ngokwempapasho yabaphuhlisi be-LAI, amaxabiso e-LAI ahlulwe abe ngamacandelo amathathu: Uyilo (0 ≤ LAI < 10), Isalathiso (10 ≤ LAI < 20), kunye neGolide (LAI ≥ 20).
Ubude beCh (bp): Ubude beChromosome
Intact: Ubungakanani be-LTR-RTs ezipheleleyo kwi-genome
Isimbuku: Ubungakanani bee-LTRs ezipheleleyo kwi-genome
raw_LAI = Iphelele / Isimbuku × 100
I-LAI: Ixabiso le-LAI elilungisiweyo
Hlola inkqubela phambili eyenziwe ziinkonzo ze-BMKGene's de novo genome assembly ngokusebenzisa ingqokelela yeempapasho ezikhethiweyo:
T2T Gi-enome
ULiu, uShoucheng et al.“Ukuhlanganiswa kwe-telomere-to-telomere genome kunye nedatha ye-multi-omic kunika ulwazi malunga nokuguquka kwengqolowa yesonka se-hexaploid."Imfuza yendalo Umqulu 57,4 (2025): 1008-1020. doi:10.1038/s41588-025-02137-x
Yao, Xue-Feng et al.“Ukuhlanganiswa okupheleleyo kwe-genome yerayisi yaseJapan i-Zhonghua 11."Unxibelelwano lwezityalo Umqulu 6,10 (2025): 101463. doi:10.1016/j.xplc.2025.101463
ULv, Zhiyuan nabanye.“Kufuphi ne-telomere-to-telomere genome assembly yeCamellia pitardii."Idatha yesayensi Umqulu 12,1 1422. 14 Agasti 2025, doi:10.1038/s41597-025-05764-5
UDu, uHaiyuan nabanye.“I-genome assembly ye-Fragaria iinumae ephantse yaphelela."I-BMC genomics Umqulu 26,1 253. 14 Mar. 2025, doi:10.1186/s12864-025-11440-0
Chen, Weikai et al.“Ukuhlanganiswa okupheleleyo kwe-genome kaNicotiana benthamiana kutyhila i-genetic kunye ne-epigenetic landscape ye-centromeres."Izityalo zendalo Umqulu 10,12 (2024): 1928-1943. doi:10.1038/s41477-024-01849-y
I-Genome ye-T2T esonjululwe yi-Haplotype
UKhan, uFalak Sher et al. “Ii-genomes ze-T2T ezingenamisantsa ezisombululwe yi-Haplotype ze-winegrape cultivar iCabernet Sauvignon.”Idatha yesayensi, 10.1038/s41597-026-06910-3. 26 Feb. 2026, doi:10.1038/s41597-026-06910-3
I-T2T Genome + I-Comparative Genome
UHong, uLin et al. "Ukwakhiwa kunye nohlalutyo lwee-genomes ze-telomere-to-telomere kwiiorenji ezimbini ezimnandi: iLonghuihong kunye neNewhall (iCitrus sinensis)."iGigaScienceUmqulu 13 (2024): giae084. doi:10.1093/gigascience/giae084
ULi, uXiao-Jie nabanye. “Uhlalutyo lwe-genome ye-telomere-to-telomere ye-red carrot TXH4 lucacisa indima ye-DcLCYE kunye ne-DcLCYB1 ekuqokeleleni kwe-lycopene kwi-carrot.”Uphando lwezolimoUmqulu 12,11 uhaf192. 29 Jul. 2025, doi:10.1093/hr/uhaf192
I-T2T Genome + i-Pangenome
UWang, uXiaojing nabanye. “I-genome ye-T2T, uhlalutyo lwe-pan-genome, kunye neejini zokuphendula uxinzelelo lobushushu kwiintlobo zeRhododendron.”iMetaUmqulu 4,2 e70010. 5 Mar. 2025, doi:10.1002/imt2.70010
