Advances in plant genome construction
-
摘要: 从第一个模式植物拟南芥被测序，植物基因组测序已经有21年的历史。随着科学技术的不断发展进步，测序成本大幅降低，基因组的组装质量显著提升。本文统计了2000 - 2020年间植物参考基因组从头测序的进展，分析了植物基因组测序数量变化与测序技术发展之间的联系，以及测序基因组大小与倍性及重复序列的关系，总结了历年来测序物种的主要分类及其在系统发生树的分布，最后讨论了未来植物基因组潜在的研究方向。Abstract: Since the first model plant, Arabidopsis thaliana(L.)Heynh, was sequenced in 2000, significant advances have been made in the sequencing of plant genomes over the last 21 years. With continuous development of technology, the cost of sequencing has greatly reduced and genome quality has significantly improved. The tremendous information hidden in these sequences should provide valuable resources for biological research. Here, we summarized and discussed the advances in plant reference genome de novo sequencing that have occurred over the last 21 years. We analyzed dynamic changes between the annual amount of sequenced plant genomes and sequencing technology, explored the relationship between sequenced genome size and chromosome ploidy and repetitive sequences, and summarized the main species classifications and distributions of sequenced plant genomes in the species phylogenetic tree. Finally, potential research hotpots of plant genomes were discussed.
-
Keywords:
- Plant genome /
- Sequencing technology /
- Genome size /
- Species distribution /
- Species classification
-
-
[1] Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J]. Nature,2000,408(6814):796-815.
[2] Hamilton JP,Robin C. Advances in plant genome sequencing[J]. Plant J,2012,70(1):177-190.
[3] Neale DB,Martínez PJ,Delatorre AR,Montanari S,Wei XX. Novel insights into tree biology and genome evolution as revealed through genomics[J]. Annu Rev Plant Biol,2017,68:457-483.
[4] Isobe S,Shirasawa K,Hirakawa H. Challenges to genome sequence dissection in sweetpotato[J]. Breed Sci,2017,67(1):35-40.
[5] Thorsten L,Sophien K,Khaoula B. CRISPR crops:plant genome editing toward disease resistance[J]. Annu Rev Phytopatholy,2018,56(1):479-512.
[6] Negrao S,Oliveira MM,Jena KK,Mackill D. Integration of genomic tools to assist breeding in the japonica subspecies of rice[J]. Mol Breed,2008,22:159-168.
[7] Xu X,Pan SK,Cheng SF,Zhang B,Mu DS,et al. Genome sequence and analysis of the tuber crop potato[J].Nature,2011,475(7355):189-195.
[8] Feuillet C,Leach JE,Rogers J,Schnable PS,Eversole K.Crop genome sequencing:lessons and rationales[J].Trends Plant Sci,2011,16(2):77-88.
[9] Albert VA,Barbazuk WB,de Pamphilis CW,Der JP,Leebens-Mack J,et al. The Amborella genome and the evolution of flowering plants[J]. Science, 2013, 342(6165):1241089.
[10] Soundararajan P,Won SY,Kim JS. Insight on rosaceae family with genome sequencing and functional genomics perspective[J]. Biomed Res Int,2019:7519687.
[11] Ahmad R,Anjum MA,Balal RM. From markers to genome based breeding in horticultural crops:an overview[J].Phyton-Int J Exp Bo,2020,89(2):183-204.
[12] Michael TP,Jackson S. The first 50 plant genomes[J].Plant Genome,2013,6(2):1-7.
[13] Shendure J,Balasubramanian S,Church GM,Gilbert W,Rogers J,et al. DNA sequencing at 40:past,present and future[J]. Nature,2017,550(7676):345-535.
[14] Belser C,Istace B,Denis E,Dubarry M,Baurens FC,et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps[J]. Nat Plants,2018,4(11):879-887.
[15] Chen F,Chen JH,Wang ZJ,Zhang JW,Li XJ,et al. Genomics:cracking the mysteries of walnuts[J]. J Genet,2019,98(2):1-3.
[16] Singh B,Salaria N,Thakur K,Kukreja S,Gautam S,et al. Functional genomic approaches to improve crop plant heat stress tolerance[J]. F1000Res,2019,8:1721.
[17] Song SH,Tian DM,Zhang Z,Hu SN,Yu J. Rice genomics:over the past two decades and into the future[J].Genom Proteomics Bioinformatics,2018,16(6):397-404.
[18] Isobe S,Shirasawa K,Hirakawa H. Current status in whole genome sequencing and analysis of Ipomoea spp.[J]. Plant Cell Rep,2019,38(11):1365-1371.
[19] Isobe S,Shirasawa K,Hirakawa H. Advances of whole genome sequencing in strawberry with NGS technologies[J]. Hort J,2020,89(2):108-114.
[20] Bolger ME,Weisshaar B,Scholz U,Stein N,Usadel B,et al. Plant genome sequencing-applications for crop improvement[J]. Curr Opin Biotechnol,2014,26:31-37.
[21] Yu J,Hu SN,Wang J,Wong GKS,Li SG,et al. A draft sequence of the rice genome(Oryza sativa L. ssp. indica)[J]. Science,2002,296(5565):79-92.
[22] Derelle E,Ferraz C,Rombauts S,Rouzé P,Worden AZ,et al. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features[J]. Proc Natl Acad Sci USA,2006,103(31):11647-11652.
[23] Sanger F,Nicklen S,Coulson AR. DNA sequencing with chain-terminating inhibitors[J]. Proc Natl Acad Sci USA,1977,74(12):5463-5467.
[24] Ronaghi M,Mathias U,Pål N. A sequencing method based on real-time pyrophosphate[J]. Science,1998,281(5375):363-365.
[25] Avni R,Nave M,Barad O,Baruch K,Twardziok SO,et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication[J]. Science,2017,357(6364):93-97.
[26] Mitros T,Session AM,James BT,Wu GHA,Belaffif MB,et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus[J]. Nat Commun,2020,5442(11):1-11.
[27] Gui S,Peng J,Wang XL,Wu ZH,Cao R,et al. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and Bio Nano genome mapping reveals ancient chromosome rearrangements[J]. Plant J,2018,94(4):721-734.
[28] Eid J,Fehr A,Gray J,Luong K,Lyle J,et al. Real-time DNA sequencing from single polymerase molecules[J].Science,2009,323(5910):133-138.
[29] Hon T,Mars K,Young G,Tsai YC,Karalius JW,et al.Highly accurate long-read Hi Fi sequencing data for five complex genomes[J]. Sci Data,2020,7(1):1-11.
[30] Zhou Q,Tang D,Huang W,Yang ZM,Zhang Y,et al.Haplotype-resolved genome analyses of a heterozygous diploid potato[J]. Nat Genet,2020,52(10):1018-1023.
[31] Chen HT,Zeng Y,Yang YZ,Huang LL,Tang BL,et al.Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa[J]. Nat Commun,2020,11(1):2494.
[32] Sun XP,Jiao C,Schwaninger HD,Chao CT,Ma YM,et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication[J]. Nat Genet,2020,52(12):1423-1432.
[33] Ma DN,Dong SS,Zhang SC,Wei XQ,Xie QJ,et al.Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit(Passiflora edulis)[J]. Mol Ecol Resour,2020,21(3):955-968.
[34] Leggett RM, Clark MD. A world of opportunities with Nanopore sequencing[J]. J Exp Bot,2017,68(20):5419-5429.
[35] Wenger AM,Peluso P,Rowell WJ,Chang PC,Hall RJ,et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome[J]. Nat Biotechnol,2019,37(10):1155-1162.
[36] Dudchenko O,Batra SS,Omer AD,Nyquist SK,Hoeger M,et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds[J]. Science,2017,356(6333):92-95.
[37] Bocklandt S,Hastie A,Cao H. Bionano genome mapping:high-throughput,ultra-long molecule genome analysis system for precision genome assembly and haploidresolved structural variation discovery[J]. Adv Exp Med Biol,2019,1129:97-118.
[38] Van de PY,Mizrachi E,Marchal K. The evolutionary significance of polyploidy[J]. Nat Rev,2017,18:411-424.
[39] Sun X,Zhu S,Li N,Cheng Y,Zhao J,et al. A chromosome-level genome assembly of garlic(Allium sativum)provides insights into genome evolution and Allicin biosynthesis[J]. Mol Plant,2020,13(9):1328-1339.
[40] Dodsworth S,Chase MW,Kelly LJ,Leich IJ,Macas J,et al. Genomic repeat abundances contain phylogenetic signal[J]. Syst Biol,2015,64(1):112-126.
[41] Qiu H,Price DC,Weber APM,Reeb V,Yang EC,et al.Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea[J]. Curr Biol,2013,23(19):865-866.
[42] Gao XY,Zhang X,Chen W,Li J,Yang WJ,et al. Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves[J]. Phytochemistry,2020,178(7):112460.
[43] The International Wheat Genome Sequencing Consortium(IWGSC). A chromosome-based draft sequence of the hexaploid bread wheat(Triticum aestivum)genome[J].Science,2014,345(6194):1251788.
[44] Zimin AV,Puiu D,Hall R,Kingan S,Clavijo BJ,Salzberg SL. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum[J]. GigaScience,2017,6(11):gix097.
[45] Stevens KA,Wegrzyn JL,Zimin A,Puiu D,Crepeau M,et al. Sequence of the sugar pine megagenome[J].Genet,2016,204(4):1613-1626.
[46] Warren RL,Keeling CL,Yuen MMS,Raymond A,Taylor GA,et al. Improved white spruce(Picea glauca)genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism[J]. Plant J,2015,83(2):189-212.
[47] Nystedt B,Street NR,Wetterbom A,Zuccolo A,Lin YC,et al. The Norway spruce genome sequence and conifer genome evolution[J]. Nature,2013,497(7451):579-584.
[48] Schnable PS,Ware D,Fulton RS,Stein JC,Wei FS,et al. The B73 maize genome:complexity,diversity,and dynamics[J]. Science,2009,326(5956):1112-1115.
[49] Leisner CP,Hamilton JP,Crisovan E,Manrique-Carpintero NC,Marand AP,et al. Genome sequence of M6,a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense,reveals residual heterozygosity[J]. Plant J,2018,94(3):562-570.
[50] Chen ZJ,Sreedasyam A,Ando A,Song QX,de Santiago LM,et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement[J]. Nature Genet,2020,52(5):525-533.
[51] Sun FM,Fan GY,Hu Q,Zhou YM,Guan M,et al. The high-quality genome of Brassica napus cultivar‘ZS11’reveals the introgression history in semi-winter morphotype[J]. Plant J,2017,92(3):452-468.
[52] Bayer PE,Hurgobin B,Golicz AA,Chan CKK,Yuan YX,et al. Assembly and comparison of two closely related Brassica napus genomes[J]. Plant Biotechnol J,2017,15(2):1602-1610.
[53] Sierro N,Battey JND,Ouadi S,Bakaher N,Bovet L,et al. The tobacco genome sequence and its comparison with those of tomato and potato[J]. Nat Commun,2014,5:3833.
[54] Guo LB,Qiu J,Ye CY,Jin GL,Mao LF,et al. Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed[J]. Nat Commun,2017,8(1):1031.
[55] Hu Y,Chen JD,Fang L,Zhang ZY,Ma W,et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature Genet,2019,51(4):739-748.
[56] Matsuzaki M,Misumi O,Shin T,Maruyama S,Takahara M,et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D[J]. Nature,2004,428(6983):653-657.
[57] Tuskan GA,Di Fazio S,Jansson S,Bohlmann J,Grigoriev I,et al. The genome of black cottonwood,Populus trichocarpa(Torr.&Gray)[J]. Science,2006,313(5793):1596-1604.
[58] Huang S,Li RQ,Zhang ZH,Li L,Gu XF,et al. The genome of the cucumber,Cucumis sativus L.[J]. Nature Genet,2009,41(12):1275-1281.
[59] Ming R,Van Buren R,Liu YL,Yang M,Han YP,et al. Genome of the long-living sacred lotus(Nelumbo nucifera Gaertn.)[J]. Genome Biol,2013,14(5):R41.
[60] One Thousand Plant Transcriptomes Initiative. One thousand plant transcriptomes and the phylogenomics of green plants[J]. Nature,2019,574(7780):679-685.
[61] Lang DD,Zhang SL,Ren PP,Liang F,Sun ZY,et al.Comparison of the two up-to-date sequencing technologies for genome assembly:Hi Fi reads of Pacbio SequelⅡsystem and ultralong reads of Oxford Nanopore[J]. GigaScience,2020,9(12):123.
[62] Zhou CX,Olukolu B,Gemenet DC,Wu S,Gruneberg W,et al. Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations[J]. Nature Genet,2020,52(11):1256-1264.
[63] Jiao YP,Peluso P,Shi JH,Liang T,Stitzer MC,et al. Improved maize reference genome with single-molecule technologies[J]. Nature,2017,546(7659):524-527.
[64] Belton JM,McCord RP,Gibcus JH,Naumova N,Zhan Y,Dekker J. Hi-C:a comprehensive technique to capture the conformation of genomes[J]. Methods,2012,58(3):268-276.
[65] Phillippy AM. New advances in sequence assembly[J].Genome Res,2017,27(5):xi-xiii.
[66] Wei QZ,Wang JL,Wang WH,Hu TH,Hu HJ,Bao CG. A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant[J]. Hortic Res,2020,7(1):153.
[67] Xie T,Zheng JF,Liu S,Peng C,Zhou YM,et al. De novo plant genome assembly based on chromatin interactions:a case study of Arabidopsis thaliana[J]. Mol Plant,2015,8(3):489-492.
[68] Zhang XT,Zhang SC,Zhao Q,Ming R,Tang HB. Assembly of allele-aware,chromosomal-scale autopolyploid genomes based on Hi-C data[J]. Nat Plants,2019,5(8):833-845.
[69] Vanburen R,Wai CM,Wang XW,Pardo J,Yocca AE,et al. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff[J]. Nat Commun,2020,11(1):884.
[70] Zhang JS,Zhang XT,Tang HB,Zhang Q,Hua XT,et al.Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.[J]. Nature Genet,2018,50(11):1565-1573.
[71] Bertioli DJ,Jenkins J,Clevenger J,Dudchenko O,Gao DY,et al. The genome sequence of segmental allotetraploid peanut Arachis hypogaea[J]. Nature Genet,2019,51(5):877-884.
[72] Hulsekemp AM,Maheshwari S,Stoffel K,Hill TA,Jaffe D,et al. Reference quality assembly of the 3. 5-Gb genome of Capsicum annuum from a single linked-read library[J]. Hortic Res,2018,5:4.
[73] Gao CX,Zhang MN,Chen L. The Comparison of two single-cell sequencing platforms:BD Rhapsody and 10x genomics chromium[J]. Curr Genomics,2020,21(8):602-609.
[74] Ming R,Hou SB,Feng Y,Yu QY,Dionne-Laporte A,et al. The draft genome of the transgenic tropical fruit tree papaya(Carica papaya Linnaeus)[J]. Nature,2008,452(7190):991-996.
[75] Sahu SK,Liu M,Yssel A,Kariba R,Muthemba S,et al.Draft genomes of two artocarpus plants,Jackfruit(A. heterophyllus)and Breadfruit(A. altilis)[J]. Genes,2020,11(1):27.
[76] Dhont A,Denoeud F,Aury JM,Baurens FC,Carreel F,et al. The banana(Musa acuminata)genome and the evolution of monocotyledonous plants[J]. Nature,2012,488(7410):213-217.
[77] Monat C,Pera B,Ndjiondjop MN,Sow M,Tranchant-Dubreuil C,et al. De novo assemblies of three Oryza glaberrima accessions provide first insights about pan-genome of African rices[J]. Genome Biol Evol,2017,9(1):1-6.
[78] Qin P,Lu HW,Du HL,Wang H,Chen WL,et al. Pangenome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations[J]. Cell,2021,184(13):3542-3558.
[79] Zhao Q,Feng Q,Lu HY,Li Y,Wang AH,et al. Pangenome analysis highlights the extent of genomic variation in cultivated and wild rice[J]. Nat Genet,2018,50(2):278-284.
[80] Wang WS,Mauleon R,Hu ZQ,Chebotarov D,Tai SS,et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice[J]. Nature,2018,557(7703):43-49.
[81] Liu YC,Du HL,Li PC,Shen YT,Peng H,et al. Pangenome of wild and cultivated soybeans[J]. Cell,2020,182(1):162-176.
[82] Gao L,Gonda I,Sun HH,Ma QY,Bao K,et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor[J]. Nat Genet,2019,51(6):1044-1051.
[83] Hübner S,Bercovich,Todesco M,Mandel JR,Odenheimer J,et al. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance[J]. Nat Plants,2019,5(1):54-62.
[84] Montenegro JD,Golicz AA,Bayer PE,Hurgobin B,Lee HT,et al. The pangenome of hexaploid bread wheat[J].Plant J,2017,90(5):1007-1013.
[85] Walkowiak S,Gao LL,Monat,C,Haberer G,Kassa MT,et al. Multiple wheat genomes reveal global variation in modern breeding[J]. Nature,2020,588(7837):277-283.
[86] Zhang X,Wang G,Zhang S,Chen S,Wang Y,et al. Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution[J]. Cell,2020,183(4):875-889.
-
期刊类型引用(9)
1. 王英豪，余嘉鑫，唐海宝，张兴坦. 植物复杂基因组与泛基因组研究现状与展望. 中国科学:生命科学. 2024(02): 233-246 . 
百度学术
2. 杨智，杨永. 重要林木樟科植物全基因组测序研究进展. 植物学报. 2024(02): 302-318 . 百度学术
3. 周强，郭栋财，蔡永生，陈全家，曲延英，郑凯. 棉花独脚金内酯D27基因表达与功能分析. 核农学报. 2024(07): 1234-1248 . 百度学术
4. 杜明阳，马健芝，多杰措，罗天蓉，熊辉岩，陈亦婷，段瑞君. 蒿叶猪毛菜GPAT基因家族成员鉴定及其在干旱胁迫下的表达模式分析. 植物遗传资源学报. 2024(10): 1781-1792 . 百度学术
5. 钟远遵，朱昔娇，刘丽，范剑明，谢金兰. 基于叶绿体基因组psbA-trnH序列的桫椤物种鉴定研究初探. 绿色科技. 2024(23): 84-90 . 百度学术
6. 沈涛，虞泓，王元忠. 滇龙胆居群遗传多样性和遗传结构分析. 中草药. 2023(03): 926-938 . 百度学术
7. 张开京，何帅帅，贾利，胡玉超，杨德坤，陆晓民，张其安，严从生. 黄瓜DIR家族基因的全基因组鉴定及其表达分析. 中国农业科学. 2023(04): 711-728 . 百度学术
8. 卜璇，肖桂青. 单分子测序技术在农林相关植物中的应用. 生命的化学. 2023(06): 881-887 . 百度学术
9. 刘哲源，康宇立，唐巧玲，李蕾，王友华. 基于全球蔬菜分子育种专利的信息分析及技术展望. 中国蔬菜. 2022(09): 1-7 . 百度学术
其他类型引用(25)
计量
- 文章访问数: 926
- HTML全文浏览量: 41
- PDF下载量: 534
- 被引次数: 34
下载:
