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牛津纳米孔技术(Oxford nanopore technologies, ONT)是新兴的第三代单分子测序技术，以其超长读长、直接测序、实时测序等技术优势在生命科学领域发挥了重要作用，尤其在解决测序读长的技术瓶颈方面有着突破性的进展，并广泛应用于基因组学的研究中。本综述简要介绍了ONT测序的基本原理及优势，并重点阐述了ONT测序在基因组从头组装、基因组结构变异鉴定、三维基因组结构研究及碱基修饰检测领域中的应用及研究进展，同时就ONT测序未来面临的机遇和挑战进行了讨论与展望。
Abstract：Oxford nanopore technologies(ONT) is an emerging third-generation single-molecule sequencing technology, which offers various technical advantages of ultra-long read length, direct sequencing and real-time sequencing. ONT has made significant contributions to the life science field, especially in addressing the technical limitations of short sequencing read length with breakthrough progress and is widely used in genomics research. This review briefly introduced the principles and advantages of ONT sequencing, with a primary focus on the application and research progress of ONT sequencing in the de novo genome assembly, genome structure variation detection, study of three-dimensional genome structures and base modification detection. The future opportunities and challenges of ONT sequencing are also discussed and prospected.
高胜寒，禹海英，吴双阳，等，2018.复杂基因组测序技术研究进展.遗传，40(11):944-963.[GAO S H,YU H Y,WU S Y,et al.,2018.Advances of sequencing and assembling technologies for complex genomes.Hereditas,40(11):944-963.]
唐蝶，周倩，2021.植物基因组组装技术研究进展.生物技术通报，37(6):1-12.[TANG D,ZHOU Q,2021.Research advances in plant genome assembly.Biotechnology Bulletin,37(6):1-12.]
BELSER C,BAURENS F C,NOEL B,et al.,2021.Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.Commun.Biol.,4(1):1047.
BELSER C,ISTACE B,DENIS E,et al.,2018.Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.Nat.Plants,4(11):879-887.
BEWICK A J,JI L X,NIEDERHUTH C E,et al.,2016.On the origin and evolutionary consequences of gene body DNA methylation.Proc.Natl.Acad.Sci.USA,113(32):9111-9116.
BEYTER D,INGIMUNDARDOTTIR H,ODDSSON A,et al.,2021.Long-read sequencing of 3 622 Icelanders provides insight into the role of structural variants in human diseases and other traits.Nat.Genet.,53(6):779-786.
DEKKER J,RIPPE K,DEKKER M,et al.,2002.Capturing chromosome conformation.Science,295(5558):1306-1311.
DENG Y,LIU S C,ZHANG Y L,et al.,2022.A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene disco-very and breeding.Mol.Plant,15(8):1268-1284.
DESCHAMPS S,ZHANG Y,LLACA V,et al.,2018.A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping.Nat.Commun.,9(1):4844.
DESHPANDE A S,ULAHANNAN N,PENDLETON M,et al.,2022.Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing.Nat.Biotechnol.,40(10):1488-1499.
DOSTIE J,RICHMOND T A,ARNAOUT R A,et al.,2006.Chromosome conformation capture carbon copy (5C):a massively parallel solution for mapping interactions between genomic elements.Genome Res.,16(10):1299-1309.
EISENSTEIN M,2012.Oxford Nanopore announcement sets sequencing sector abuzz.Nat.Biotechnol.,30(4):295-296.
FULLER C W,MIDDENDORF L R,BENNER S A,et al.,2009.The challenges of sequencing by synthesis.Nat.Biotechnol.,27(11):1013-1023.
FULLWOOD M J,LIU M H,PAN Y F,et al.,2009.An oestrogen-receptor-alpha-bound human chromatin interactome.Nature,462(7269):58-64.
GONG L A,WONG C H,CHENG W C,et al.,2018.Picky comprehensively detects high-resolution structural variants in nanopore long reads.Nat.Meth.,15(6):455-460.
HUANG X H,TIAN X H,PEI L L,et al.,2022.Multi-omics mapping of chromatin interaction resolves the fine hierarchy of 3D genome in allotetraploid cotton.Plant Biotechnol.J.,20(9):1639-1641.
JAIN M,OLSEN H E,PATEN B,et al.,2016.The Oxford Nanopore MinION:delivery of nanopore sequencing to the genomics community.Genome Biol.,17(1):239.
KERNALEGUEN M,DAVIAUD C,SHEN Y M,et al.,2018.Whole-genome bisulfite sequencing for the analysis of genome-wide DNA methylation and hydroxymethylation patterns at single-nucleotide resolution.Methods Mol.Biol.,1767:311-349.
LEGGETT R M,CLARK M D,2017.A world of opportunities with nanopore sequencing.J.Exp.Bot.,68(20):5419-5429.
LI E,LIU H,HUANG L L,et al.,2019.Long-range interactions between proximal and distal regulatory regions in maize.Nat.Commun.,10(1):2633.
LIEBERMAN-AIDEN E,VAN BERKUM N L,WILLIAMS L,et al.,2009.Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Science,326(5950):289-293.
LIU J N,SEETHARAM A S,CHOUGULE K,et al.,2020.Gapless assembly of maize chromosomes using long-read technologies.Genome Biol.,21(1):121.
LIU Q,FANG L,YU G L,et al.,2019.Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.Nat.Commun.,10(1):2449.
LOGSDON G A,VOLLGER M R,HSIEH P,et al.,2021.The structure,function and evolution of a complete human chromosome 8.Nature,593(7857):101-107.
MAXAM A M,GILBERT W,1977.A new method for sequencing DNA.Proc.Natl.Acad.Sci.USA,74(2):560-564.
MCCARTHY A,2010.Third generation DNA sequencing:paci-fic biosciences′ single molecule real time technology.Chem.Biol.,17(7):675-676.
MIGA K H,KOREN S,RHIE A,et al.,2020.Telomere-to-telomere assembly of a complete human X chromosome.Nature,585(7823):79-84.
NAISH M,ALONGE M,WLODZIMIERZ P,et al.,2021.The genetic and epigenetic landscape of the Arabidopsis centromeres.Science,374(6569):7489.
NI P,HUANG N,NIE F,et al.,2021.Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning.Nat.Commun.,12(1):5976.
NI P,HUANG N,ZHANG Z,et al.,2019.DeepSignal:detecting DNA methylation state from Nanopore sequencing reads using deep-learning.Bioinformatics,35(22):4586-4595.
NURK S,KOREN S,RHIE A,et al.,2022.The complete sequence of a human genome.Science,376(6588):44-53.
PAYNE Z L,PENNY G M,TURNER T N,et al.,2023.A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis.Plant Commun.,4(2):100493.
QUAN C,LI Y F,LIU X Y,et al.,2021.Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression.Genome Biol.,22(1):159.
ROSES A D,AKKARI P A,CHIBA-FALEK O,et al.,2016.Structural variants can be more informative for disease diagnostics,prognostics and translation than current SNP mapping and exon sequencing.Expert Opin.Drug Metab.Toxicol.,12(2):135-147.
ROUNDTREE I A,EVANS M E,PAN T,et al.,2017.Dynamic RNA modifications in gene expression regulation.Cell,169(7):1187-1200.
SANGER F,COULSON A R,1975.A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.J.Mol.Biol.,94(3):441-448.
SCHMITT A D,HU M,REN B,2016.Genome-wide mapping and analysis of chromosome architecture.Nat.Rev.Mol.Cell Biol.,17(12):743-755.
SIMONIS M,KLOUS P,SPLINTER E,et al.,2006.Nuclear organization of active and inactive chromatin domains unco-vered by chromosome conformation capture-on-chip (4C).Nat.Genet.,38(11):1348-1354.
SIMPSON J T,WORKMAN R E,ZUZARTE P C,et al.,2017.Detecting DNA cytosine methylation using nanopore sequencing.Nat.Methods,14(4):407-410.
STOIBER M,QUICK J,EGAN R,et al.,2016.De novo identification of DNA modifications enabled by genome-guided nanopore signal processing.Bioinformatics,(2016-12-15) [2023-03-01].DOI:10.1101/094672.
TAO J F,ZHOU J Z,XIE T,et al.,2017.Influence of chromatin 3D organization on structural variations of the Arabidopsis thaliana genome.Mol.Plant,10(2):340-344.
TILAK M K,BOTERO-CASTRO F,GALTIER N,et al.,2018.Illumina library preparation for sequencing the GC-rich fraction of heterogeneous genomic DNA.Genome Biol.Evol.,10(2):616-622.
ULAHANNAN N,PENDLETON M,DESHPANDE A,et al.,2019.Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure.Genomics,(2019-11-07) [2023-03-01].DOI:10.1101/833590.
VAN DIJK E L,JASZCZYSZYN Y,NAQUIN D,et al.,2018.The third revolution in sequencing technology.Trends Genet.,34(9):666-681.
WANG M J,WANG P C,LIN M,et al.,2018.Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.Nat.Plants,4(2):90-97.
WANG P J,CHEN X J,GUO Y C,et al.,2019.Identification of CBF transcription factors in tea plants and a survey of potential CBF target genes under low temperature.Int.J.Mol.Sci.,20(20):5137.
WANG Y H,ZHAO Y,BOLLAS A,et al.,2021.Nanopore sequencing technology,bioinformatics and applications.Nat.Biotechnol.,39(11):1348-1365.
XU T,WU X W,WONG C E,et al.,2022.FIONA1-mediated m6A modification regulates the floral transition in Arabidopsis.Adv.Sci.,9(6):e2103628.
YAN F,XI R M,SHE R X,et al.,2021.Improved de novo chromosome-level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode.Mol.Ecol.Resour.,21(6):2063-2076.
YUEN Z W S,SRIVASTAVA A,DANIEL R,et al.,2021.Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.Nat.Commun.,12(1):3438.
ZHANG H M,LANG Z B,ZHU J K,2018.Dynamics and function of DNA methylation in plants.Nat.Rev.Mol.Cell Biol.,19(8):489-506.
ZHANG Y L,FU J,WANG K,et al.,2022.The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding.Plant Biotechnol.J.,20(9):1642-1644.
ZHAO Z H,TAVOOSIDANA G,SJ?LINDER M,et al.,2006.Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.Nat.Genet.,38(11):1341-1347.
基本信息:
DOI：10.13417/j.gab.042.000233
中图分类号:Q811.4
引用信息:
[1]雷文龙,雷思茹,陈帅,等.纳米孔测序技术在基因组学中的应用研究进展[J].基因组学与应用生物学,2023,42(03):233-241.DOI:10.13417/j.gab.042.000233.
基金信息:
国家自然科学基金项目(32222019)资助
2023-07-07
2023-07-07
2023-07-07