Skip to content
2000
Volume 21, Issue 1
  • ISSN: 1574-8936
  • E-ISSN: 2212-392X

Abstract

With the development of third-generation sequencing technology, genome assembly has entered a new era. The combination of multiple sequencing methods can combine the strengths of each, resulting in higher-quality assembly results. Telomere-to-Telomere (T2T) genome refers to a zero gap genome that is assembled at the T2T level of one or more chromosomes through the combination of multiple sequencing technologies, such as Pacific Biosciences High-Fidelity (PacBio HiFi), Oxford Nanopore Technologies (ONT) Ultra-long, High-throughput Chromosome Conformation Capture (Hi-C), and others. High-quality reference genomes are the basis for genomics research, and the T2T genome has enabled the exploration of unknown areas of the genome, such as telomeres and centromeres, which has provided a more in-depth direction for research. This review provides a comprehensive overview of the T2T genome, reviewing the development of sequencing technologies and then outlining sequencing strategies, assembly methods, quality assessment processes, and analysis software for the T2T genome with practical examples. Representative T2T genomic species of plants, animals, and microorganisms (., human, Arabidopsis, brewer's yeast, and so on) are presented separately. A summary of the potential and challenges of current T2T genomic applications is provided, along with an outlook for future developments.

© 2026 Bentham Science Publishers
Loading

Article metrics loading...

/content/journals/cbio/10.2174/0115748936338006241023043315
2024-11-04
2026-02-04

  • From This Site

    /content/journals/cbio/10.2174/0115748936338006241023043315
    dcterms_title,dcterms_subject,pub_keyword
    -contentType:Contributor -contentType:Concept -contentType:Institution
    10
    5
Loading full text...

Full text loading...

References

  1. HeatherJ.M. ChainB. The sequence of sequencers: The history of sequencing DNA.Genomics201610711810.1016/j.ygeno.2015.11.003 26554401
     [Google Scholar]
  2. WrightC.F. FitzPatrickD.R. FirthH.V. Paediatric genomics: Diagnosing rare disease in children.Nat. Rev. Genet.201819525326810.1038/nrg.2017.116 29398702
     [Google Scholar]
  3. BordesC. SargurupremrajM. MishraA. DebetteS. Genetics of common cerebral small vessel disease.Nat. Rev. Neurol.20221828410110.1038/s41582‑021‑00592‑8 34987231
     [Google Scholar]
  4. AndersonS. BankierA.T. BarrellB.G. Sequence and organization of the human mitochondrial genome.Nature1981290580645746510.1038/290457a0 7219534
     [Google Scholar]
  5. EngelS.R. DietrichF.S. FiskD.G. The reference genome sequence of Saccharomyces cerevisiae: Then and now.G3 (Bethesda)20144338939810.1534/g3.113.008995 24374639
     [Google Scholar]
  6. LanderE.S. LintonL.M. BirrenB. Initial sequencing and analysis of the human genome.Nature2001409682286092110.1038/35057062 11237011
     [Google Scholar]
  7. ShendureJ. BalasubramanianS. ChurchG.M. DNA sequencing at 40: Past, present and future.Nature2017550767634535310.1038/nature24286 29019985
     [Google Scholar]
  8. SangerF. NicklenS. CoulsonA.R. DNA sequencing with chain-terminating inhibitors.Proc. Natl. Acad. Sci. USA197774125463546710.1073/pnas.74.12.5463 271968
     [Google Scholar]
  9. ShendureJ. JiH. Next-generation DNA sequencing.Nat. Biotechnol.200826101135114510.1038/nbt1486 18846087
     [Google Scholar]
  10. MetzkerM.L. Sequencing technologies — The next generation.Nat. Rev. Genet.2010111314610.1038/nrg2626 19997069
     [Google Scholar]
  11. SatamH. JoshiK. MangroliaU. Next-generation sequencing technology: Current trends and advancements.Biology (Basel)202312799710.3390/biology12070997 37508427
     [Google Scholar]
  12. EidJ. FehrA. GrayJ. Real-time DNA sequencing from single polymerase molecules.Science2009323591013313810.1126/science.1162986 19023044
     [Google Scholar]
  13. LiuZ. XieZ. LiM. Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data.Genome Biol.202425118810.1186/s13059‑024‑03324‑5 39010145
     [Google Scholar]
  14. YingY.L. HuZ.L. ZhangS. Nanopore-based technologies beyond DNA sequencing.Nat. Nanotechnol.202217111136114610.1038/s41565‑022‑01193‑2 36163504
     [Google Scholar]
  15. LiR. ZhuH. RuanJ. De novo assembly of human genomes with massively parallel short read sequencing.Genome Res.201020226527210.1101/gr.097261.109 20019144
     [Google Scholar]
  16. ChaissonM.J.P. WilsonR.K. EichlerE.E. Genetic variation and the de novo assembly of human genomes.Nat. Rev. Genet.2015161162764010.1038/nrg3933 26442640
     [Google Scholar]
  17. BakerM. De novo genome assembly: What every biologist should know.Nat. Methods20129433333710.1038/nmeth.1935
     [Google Scholar]
  18. ChoiI.Y. KwonE.C. KimN.S. The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy.Genes Genomics202042769971410.1007/s13258‑020‑00941‑9 32445179
     [Google Scholar]
  19. FreelingM. XuJ. WoodhouseM. LischD. A solution to the c-value paradox and the function of junk DNA: The genome balance hypothesis.Mol. Plant20158689991010.1016/j.molp.2015.02.009 25743198
     [Google Scholar]
  20. PellicerJ. LeitchI.J. The application of flow cytometry for estimating genome size and ploidy level in plants.Methods Mol. Biol.2014111527930710.1007/978‑1‑62703‑767‑9_14 24415480
     [Google Scholar]
  21. MgwatyuY. StanderA.A. FerreiraS. WilliamsW. HesseU. Rooibos (Aspalathus linearis) genome size estimation using flow cytometry and k-mer analyses.Plants20209227010.3390/plants9020270 32085566
     [Google Scholar]
  22. HesseU. K-mer-based genome size estimation in theory and practice.Methods Mol. Biol.202326727911310.1007/978‑1‑0716‑3226‑0_4 37335470
     [Google Scholar]
  23. D’HondtL. HöfteM. Van BockstaeleE. LeusL. Applications of flow cytometry in plant pathology for genome size determination, detection and physiological status.Mol. Plant Pathol.201112881582810.1111/j.1364‑3703.2011.00711.x 21726378
     [Google Scholar]
  24. DolezelJ. Plant DNA flow cytometry and estimation of nuclear genome size.Ann. Bot. (Lond.)20059519911010.1093/aob/mci005 15596459
     [Google Scholar]
  25. MarçaisG. KingsfordC. A fast, lock-free approach for efficient parallel counting of occurrences of k -mers.Bioinformatics201127676477010.1093/bioinformatics/btr011 21217122
     [Google Scholar]
  26. Al-QurainyF. GaafarA.R.Z. KhanS. Estimation of genome size in the endemic species Reseda pentagyna and the locally rare species Reseda lutea using comparative analyses of flow cytometry and k-mer approaches.Plants2021107136210.3390/plants10071362 34371565
     [Google Scholar]
  27. MelstedP. HalldórssonB.V. KmerStream: Streaming algorithms for k -mer abundance estimation.Bioinformatics201430243541354710.1093/bioinformatics/btu713 25355787
     [Google Scholar]
  28. Ranallo-BenavidezT.R. JaronK.S. SchatzM.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.Nat. Commun.2020111143210.1038/s41467‑020‑14998‑3 32188846
     [Google Scholar]
  29. LiuB. ShiY. YuanJ. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects.arXiv:130820122013
     [Google Scholar]
  30. ChikhiR. MedvedevP. Informed and automated k -mer size selection for genome assembly.Bioinformatics2014301313710.1093/bioinformatics/btt310 23732276
     [Google Scholar]
  31. ManekarS.C. SatheS.R. Estimating the k-mer coverage frequencies in genomic datasets: A comparative assessment of the state-of-the-art.Curr. Genomics201920121510.2174/1389202919666181026101326 31015787
     [Google Scholar]
  32. ZhouY. XiongJ. ShuZ. The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry.Hortic. Res.2023104uhad02710.1093/hr/uhad027 37090094
     [Google Scholar]
  33. DengY. LiuS. ZhangY. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding.Mol. Plant20221581268128410.1016/j.molp.2022.06.010 35746868
     [Google Scholar]
  34. ChenJ. WangZ. TanK. A complete telomere-to-telomere assembly of the maize genome.Nat. Genet.20235571221123110.1038/s41588‑023‑01419‑6 37322109
     [Google Scholar]
  35. ShangL. HeW. WangT. A complete assembly of the rice Nipponbare reference genome.Mol. Plant20231681232123610.1016/j.molp.2023.08.003 37553831
     [Google Scholar]
  36. BelserC. BaurensF.C. NoelB. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.Commun. Biol.202141104710.1038/s42003‑021‑02559‑3 34493830
     [Google Scholar]
  37. WangB. YangX. JiaY. High-quality Arabidopsis thaliana genome assembly with nanopore and hifi long reads.Genomics Proteomics Bioinformatics202220141310.1016/j.gpb.2021.08.003 34487862
     [Google Scholar]
  38. ZhangL. LiangJ. ChenH. ZhangZ. WuJ. WangX. A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres.Plant Biotechnol. J.20232151022103210.1111/pbi.14015 36688739
     [Google Scholar]
  39. ShiX. CaoS. WangX. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding.Hortic. Res.2023105uhad06110.1093/hr/uhad061 37213686
     [Google Scholar]
  40. BaoY. ZengZ. YaoW. A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance.Hortic. Res.2023104uhad02010.1093/hr/uhad020 37035858
     [Google Scholar]
  41. WangT. WangB. HuaX. A complete gap-free diploid genome in saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus.Nat. Plants20239455457110.1038/s41477‑023‑01378‑0 36997685
     [Google Scholar]
  42. WangY.H. LiuP.Z. LiuH. Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics.Hortic. Res.2023107uhad10310.1093/hr/uhad103 37786729
     [Google Scholar]
  43. LiF. XuS. XiaoZ. Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa.Hortic. Res.2023103uhad00510.1093/hr/uhad005 36938565
     [Google Scholar]
  44. HanX. ZhangY. ZhangQ. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin c and sucrose metabolism in kiwifruit.Mol. Plant202316245247010.1016/j.molp.2022.12.022 36588343
     [Google Scholar]
  45. SharmaP. MasoulehA.K. ToppB. FurtadoA. HenryR.J. De novo chromosome level assembly of a plant genome from long read sequence data.Plant J.2022109372773610.1111/tpj.15583 34784084
     [Google Scholar]
  46. NavrátilováP. ToegelováH. TulpováZ. Prospects of telomere‐to‐telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.Plant Biotechnol. J.20222071373138610.1111/pbi.13816 35338551
     [Google Scholar]
  47. ShenF. XuS. ShenQ. BiC. LysakM.A. The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits.Nat. Commun.2023141410210.1038/s41467‑023‑39800‑y 37491530
     [Google Scholar]
  48. ZengQ. WeiM. LiS. Complete genome assembly provides insights into the centromere architecture of pumpkin (Cucurbita maxima).Plant Commun.20245910093510.1016/j.xplc.2024.100935 38689498
     [Google Scholar]
  49. FuA. ZhengY. GuoJ. Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics.Hortic. Res.2023101uhac22810.1093/hr/uhac228 36643758
     [Google Scholar]
  50. NieS. ZhaoS.W. ShiT.L. Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color.Hortic. Res.2023101uhac24110.1093/hr/uhac241 36643737
     [Google Scholar]
  51. MaB. WangH. LiuJ. The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes.Hortic. Res.2023107uhad11110.1093/hr/uhad111 37786730
     [Google Scholar]
  52. WangL. ZhangM. LiM. JiangX. JiaoW. SongQ. A telomere-to-telomere gap-free assembly of soybean genome.Mol. Plant202316111711171410.1016/j.molp.2023.08.012 37634078
     [Google Scholar]
  53. YunL. ZhangC. LiangT. Insights into dammarane-type triterpenoid saponin biosynthesis from the telomere-to-telomere genome of Gynostemma pentaphyllum.Plant Commun.20245810093210.1016/j.xplc.2024.100932 38689496
     [Google Scholar]
  54. WeiC. GaoL. XiaoR. Complete telomere‐to‐telomere assemblies of two sorghum genomes to guide biological discovery.iMeta202432e19310.1002/imt2.193 38882488
     [Google Scholar]
  55. LaiY. MaJ. ZhangX. High‐quality chromosome‐level genome assembly and multi‐omics analysis of rosemary (Salvia rosmarinus) reveals new insights into the environmental and genome adaptation.Plant Biotechnol. J.20242271833184710.1111/pbi.14305 38363812
     [Google Scholar]
  56. MoC. WangH. WeiM. Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon.Plant J.202411862249226810.1111/tpj.16705 38430487
     [Google Scholar]
  57. ChenW. WangX. SunJ. Two telomere-to-telomere gapless genomes reveal insights into capsicum evolution and capsaicinoid biosynthesis.Nat. Commun.2024151429510.1038/s41467‑024‑48643‑0 38769327
     [Google Scholar]
  58. BrekkeT.D. PapadopulosA.S.T. JuliàE. A new chromosome-assigned mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome.Mol. Biol. Evol.2023405msad11510.1093/molbev/msad115 37183864
     [Google Scholar]
  59. XueL. GaoY. WuM. Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair.Genome Biol.202122120310.1186/s13059‑021‑02430‑y 34253240
     [Google Scholar]
  60. NurkS. KorenS. RhieA. The complete sequence of a human genome.Science20223766588445310.1126/science.abj6987 35357919
     [Google Scholar]
  61. BlizninaA. MasunagaA. MansfieldM.J. Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from okinawa using nanopore-based sequencing.BMC Genomics202122122210.1186/s12864‑021‑07512‑6 33781200
     [Google Scholar]
  62. HuangZ. XuZ. BaiH. Evolutionary analysis of a complete chicken genome.Proc. Natl. Acad. Sci. USA20231208e221664112010.1073/pnas.2216641120 36780517
     [Google Scholar]
  63. ZhangT. XingW. WangA. Comparison of long-read methods for sequencing and assembly of lepidopteran pest genomes.Int. J. Mol. Sci.202224164910.3390/ijms24010649 36614092
     [Google Scholar]
  64. O’DonnellS. YueJ.X. SaadaO.A. Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.Nat. Genet.20235581390139910.1038/s41588‑023‑01459‑y 37524789
     [Google Scholar]
  65. LiH. DurbinR. Genome assembly in the telomere-to-telomere era.Nat. Rev. Genet.202425965867010.1038/s41576‑024‑00718‑w 38649458
     [Google Scholar]
  66. CoombeL. LiJ.X. LoT. LongStitch: High-quality genome assembly correction and scaffolding using long reads.BMC Bioinformatics202122153410.1186/s12859‑021‑04451‑7 34717540
     [Google Scholar]
  67. JauhalA.A. NewcombR.D. Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO.Mol. Ecol. Resour.20212151416142110.1111/1755‑0998.13364 33629477
     [Google Scholar]
  68. RiceE.S. GreenR.E. New approaches for genome assembly and scaffolding.Annu. Rev. Anim. Biosci.201971174010.1146/annurev‑animal‑020518‑115344 30485757
     [Google Scholar]
  69. HuJ. WangZ. SunZ. NextDenovo: An efficient error correction and accurate assembly tool for noisy long reads.Genome Biol.202425110710.1186/s13059‑024‑03252‑4 38671502
     [Google Scholar]
  70. KolmogorovM. YuanJ. LinY. PevznerP.A. Assembly of long, error-prone reads using repeat graphs.Nat. Biotechnol.201937554054610.1038/s41587‑019‑0072‑8 30936562
     [Google Scholar]
  71. ChengH. ConcepcionG.T. FengX. ZhangH. LiH. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.Nat. Methods202118217017510.1038/s41592‑020‑01056‑5 33526886
     [Google Scholar]
  72. AlongeM. SoykS. RamakrishnanS. RaGOO: Fast and accurate reference-guided scaffolding of draft genomes.Genome Biol.201920122410.1186/s13059‑019‑1829‑6 31661016
     [Google Scholar]
  73. ChenY. YeW. ZhangY. XuY. High speed BLASTN: An accelerated MegaBLAST search tool.Nucleic Acids Res.201543167762776810.1093/nar/gkv784 26250111
     [Google Scholar]
  74. SahlinK. BaudeauT. CazauxB. MarchetC. A survey of mapping algorithms in the long-reads era.Genome Biol.202324113310.1186/s13059‑023‑02972‑3 37264447
     [Google Scholar]
  75. AlongeM. LebeigleL. KirscheM. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.Genome Biol.202223125810.1186/s13059‑022‑02823‑7 36522651
     [Google Scholar]
  76. XuM. GuoL. GuS. TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads.Gigascience202099giaa09410.1093/gigascience/giaa094 32893860
     [Google Scholar]
  77. CappellettiE. PirasF.M. SolaL. The localization of centromere protein A is conserved among tissues.Commun. Biol.20236196310.1038/s42003‑023‑05335‑7 37735603
     [Google Scholar]
  78. HanM. YangY. ZhangM. WangK. Considerations regarding centromere assembly in plant whole-genome sequencing.Methods2021187545610.1016/j.ymeth.2020.09.006 32920129
     [Google Scholar]
  79. ZhangM. LiuR. WangF. Telomere and g-quadruplex colocalization analysis by immunofluorescence fluorescence in situ hybridization (IF-FISH).Methods Mol. Biol.2019199932733310.1007/978‑1‑4939‑9500‑4_23 31127589
     [Google Scholar]
  80. PriceC.M. Fluorescence in situ hybridization.Blood Rev.19937212713410.1016/S0268‑960X(05)80023‑2 8369661
     [Google Scholar]
  81. ChrzanowskaN.M. KowalewskiJ. LewandowskaM.A. Use of fluorescence in situ hybridization (FISH) in diagnosis and tailored therapies in solid tumors.Molecules2020258186410.3390/molecules25081864 32316657
     [Google Scholar]
  82. HallingK.C. KippB.R. Fluorescence in situ hybridization in diagnostic cytology.Hum. Pathol.20073881137114410.1016/j.humpath.2007.04.015 17640552
     [Google Scholar]
  83. LinY. YeC. LiX. quarTeT: A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.Hortic. Res.2023108uhad12710.1093/hr/uhad127 37560017
     [Google Scholar]
  84. RhodesD. FairallL. SimonssonT. CourtR. ChapmanL. Telomere architecture.EMBO Rep.20023121139114510.1093/embo‑reports/kvf246 12475927
     [Google Scholar]
  85. QuinlanA.R. HallI.M. BEDTools: A flexible suite of utilities for comparing genomic features.Bioinformatics201026684184210.1093/bioinformatics/btq033 20110278
     [Google Scholar]
  86. LangmeadB. SalzbergS.L. Fast gapped-read alignment with Bowtie 2.Nat. Methods20129435735910.1038/nmeth.1923 22388286
     [Google Scholar]
  87. RhodesD. GiraldoR. Telomere structure and function.Curr. Opin. Struct. Biol.19955331132210.1016/0959‑440X(95)80092‑1 7583629
     [Google Scholar]
  88. WangP. WangF. A proposed metric set for evaluation of genome assembly quality.Trends Genet.202339317518610.1016/j.tig.2022.10.005 36402623
     [Google Scholar]
  89. SimãoF.A. WaterhouseR.M. IoannidisP. KriventsevaE.V. ZdobnovE.M. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs.Bioinformatics201531193210321210.1093/bioinformatics/btv351 26059717
     [Google Scholar]
  90. RhieA. WalenzB.P. KorenS. PhillippyA.M. Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies.Genome Biol.202021124510.1186/s13059‑020‑02134‑9 32928274
     [Google Scholar]
  91. NeversY. Warwick VesztrocyA. RossierV. Quality assessment of gene repertoire annotations with OMArk.Nat. Biotechnol.202410.1038/s41587‑024‑02147‑w 38383603
     [Google Scholar]
  92. YuW. LuoH. YangJ. Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.Genome Res.202434232634010.1101/gr.278232.123 38428994
     [Google Scholar]
  93. MurigneuxV. RaiS.K. FurtadoA. Comparison of long-read methods for sequencing and assembly of a plant genome.Gigascience2020912giaa14610.1093/gigascience/giaa146 33347571
     [Google Scholar]
  94. OuS. ChenJ. JiangN. Assessing genome assembly quality using the LTR Assembly Index (LAI).Nucleic Acids Res.20184621e12610.1093/nar/gky730 30107434
     [Google Scholar]
  95. VenterJ.C. AdamsM.D. MyersE.W. The sequence of the human genome.Science200129155071304135110.1126/science.1058040 11181995
     [Google Scholar]
  96. HoytS.J. StorerJ.M. HartleyG.A. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.Science20223766588eabk311210.1126/science.abk3112 35357925
     [Google Scholar]
  97. AganezovS. YanS.M. SotoD.C. A complete reference genome improves analysis of human genetic variation.Science20223766588eabl353310.1126/science.abl3533 35357935
     [Google Scholar]
  98. VollgerM.R. GuitartX. DishuckP.C. Segmental duplications and their variation in a complete human genome.Science20223766588eabj696510.1126/science.abj6965 35357917
     [Google Scholar]
  99. AltemoseN. LogsdonG.A. BzikadzeA.V. Complete genomic and epigenetic maps of human centromeres.Science20223766588eabl417810.1126/science.abl4178 35357911
     [Google Scholar]
  100. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.Nature2004432701869571610.1038/nature03154 15592404
     [Google Scholar]
  101. CelnikerS.E. RubinG.M. The drosophila melanogaster genome.Annu. Rev. Genomics Hum. Genet.2003418911710.1146/annurev.genom.4.070802.110323 14527298
     [Google Scholar]
  102. M Kellis Identification of functional elements and regulatory circuits by Drosophila modENCODE.Science33060121787179710.1126/science.1198374 21177974
     [Google Scholar]
  103. KimB.Y. GellertH.R. ChurchS.H. Single-fly genome assemblies fill major phylogenomic gaps across the drosophilidae tree of life.PLoS Biol.2024227e300269710.1371/journal.pbio.3002697 39024225
     [Google Scholar]
  104. Analysis of the genome sequence of the flowering plant arabidopsis thaliana.Nature2000408681479681510.1038/35048692 11130711
     [Google Scholar]
  105. NaishM. AlongeM. WlodzimierzP. The genetic and epigenetic landscape of the Arabidopsis centromeres.Science20213746569eabi748910.1126/science.abi7489 34762468
     [Google Scholar]
  106. HouX. WangD. ChengZ. WangY. JiaoY. A near-complete assembly of an Arabidopsis thaliana genome.Mol. Plant20221581247125010.1016/j.molp.2022.05.014 35655433
     [Google Scholar]
  107. SchnableP.S. WareD. FultonR.S. The B73 maize genome: Complexity, diversity, and dynamics.Science200932659561112111510.1126/science.1178534 19965430
     [Google Scholar]
  108. YangN. XuX.W. WangR.R. Contributions of Zea mays subspecies mexicana haplotypes to modern maize.Nat. Commun.201781187410.1038/s41467‑017‑02063‑5 29187731
     [Google Scholar]
  109. SunS. ZhouY. ChenJ. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.Nat. Genet.20185091289129510.1038/s41588‑018‑0182‑0 30061735
     [Google Scholar]
  110. SongJ.M. XieW.Z. WangS. Two gap-free reference genomes and a global view of the centromere architecture in rice.Mol. Plant202114101757176710.1016/j.molp.2021.06.018 34171480
     [Google Scholar]
  111. LiK. JiangW. HuiY. Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution.Mol. Plant202114101745175610.1016/j.molp.2021.06.017 34171481
     [Google Scholar]
  112. ZhangY. FuJ. WangK. The telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding.Plant Biotechnol. J.20222091642164410.1111/pbi.13880 35748695
     [Google Scholar]
  113. JayakodiM. PadmarasuS. HabererG. The barley pan-genome reveals the hidden legacy of mutation breeding.Nature2020588783728428910.1038/s41586‑020‑2947‑8 33239781
     [Google Scholar]
  114. MascherM. WickerT. JenkinsJ. Long-read sequence assembly: A technical evaluation in barley.Plant Cell20213361888190610.1093/plcell/koab077 33710295
     [Google Scholar]
  115. ShenY. WangY. ChenT. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.Science20173556329eaaf479110.1126/science.aaf4791 28280153
     [Google Scholar]
  116. ZhaoY. CoelhoC. HughesA.L. Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.Cell20231862452205236.e1610.1016/j.cell.2023.09.025 37944511
     [Google Scholar]
  117. ZhouR. JenkinsJ.W. ZengY. Haplotype‐resolved genome assembly of Populus tremula × P. alba reveals aspen‐specific megabase satellite DNA.Plant J.202311641003101710.1111/tpj.16454 37675609
     [Google Scholar]
  118. LiuX. ArshadR. WangX. The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars.Sci. Data202310163110.1038/s41597‑023‑02546‑9 37716992
     [Google Scholar]
  119. SunX. JiaoC. SchwaningerH. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication.Nat. Genet.202052121423143210.1038/s41588‑020‑00723‑9 33139952
     [Google Scholar]
  120. ZhangC. XieL. YuH. WangJ. ChenQ. WangH. The T2T genome assembly of soybean cultivar ZH13 and its epigenetic landscapes.Mol. Plant202316111715171810.1016/j.molp.2023.10.003 37803825
     [Google Scholar]
  121. HuG. FengJ. XiangX. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars.Nat. Genet.2022541738310.1038/s41588‑021‑00971‑3 34980919
     [Google Scholar]
/content/journals/cbio/10.2174/0115748936338006241023043315
Loading
Decoding the Genetic Code: Scientific Exploration of the Telomere-to-Telomere (T2T) Genome
Curr Bioinform 21, 1 (2026); https://doi.org/10.2174/0115748936338006241023043315
/content/journals/cbio/10.2174/0115748936338006241023043315
/content/journals/cbio/10.2174/0115748936338006241023043315
Loading

Data & Media loading...


  • Article Type:     Review Article
Keyword(s): bioinformatics; genome assembly; genomics; high-quality genomes; sequencing; Telomere-to-Telomere (T2T)

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test