番茄基因组研究进展

doi:10.6048/j.issn.1001-4330.2019.02.001

新疆农业科学 ›› 2019, Vol. 56 ›› Issue (2): 197-206.DOI: 10.6048/j.issn.1001-4330.2019.02.001

• • 下一篇

番茄基因组研究进展

唐亚萍¹, 李宁¹, 王娟¹, 王柏柯¹, 杨生保¹, 郭斌², 杨涛¹, 郭春苗¹, 马凯¹, 刘君³, 王欢⁴, 余庆辉¹

1.新疆农业科学院园艺作物研究所,乌鲁木齐 830091;
2.新疆农业大学计算机与信息工程学院,乌鲁木齐830091;
3.中国农业科学院作物科学研究所,北京100081;
4.中国农业科学院生物技术研究所,北京100081

收稿日期:2018-12-06 出版日期:2019-02-20 发布日期:2019-05-22
通信作者: 王欢(1983-),女,北京人,研究员,博士,研究方向为生物信息学,(E-mail)wanghuan@caas.cn
余庆辉(1970-) ,男,广东大浦人,研究员,博士,研究方向为蔬菜遗传育种,(E-mail) yuqinghui98@sina.com
作者简介:唐亚萍(1986-),女,助理研究员,硕士,研究方向为蔬菜遗传育种,(E-mail) tangyaping624@sina.com
基金资助:
农业部产业技术体系(CARS-23-G-25);新疆农科院重点项目前期预研专项(xjzdy-003);自治区创新人才建设专项-天山创新团队(2018D14005);国家重点研发专项(2017YFD0101906)

Advances in Tomato Genome Research

TANG Ya-ping¹, LI Ning¹, WANG Juan¹, WANG Bai-ke¹, YANG Sheng-bao¹, GUO Bin², YANG Tao¹, GUO Chun-miao¹, MA Kai¹, LIU Jun³, WANG Huan⁴, YU Qing-hui¹

1.Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091,China;
2.College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi 830091, China;
3.Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
4.Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Received:2018-12-06 Online:2019-02-20 Published:2019-05-22
Correspondence author: WANG Huan (1983-), female, native place: Beijing, Researcher, Ph. D., research field: Bioinformatics, (E-mail) wanghuan@caas.cn
YU Qing-hui (1970-), male, native place: Dapu, Guangdong,, Researcher, Ph. D., research field: Vegetable genetic breeding, (E-mail) yuqinghui98@sina.com
Supported by:
Industrial Technology System in Ministry of Agriculture(CARS-23-G-25), Pre-research of Key Project in Xinjiang Academy of Agricultural Sciences(xjzdy-003), Tianshan Program for Innovation Team in Xinjang(2018D14005), National Key R&D Program of China (2017YFD0101906)

摘要/Abstract

摘要： 【目的】综述国内外相关高质量番茄基因组研究进展,比较与分析第一、二、三代测序技术的研究成果,为番茄重要性状功能基因的挖掘及新品种选育提供参考。【方法】收集查阅国内外相关官网、文献资料和现有研究前沿技术,整理汇总并进行对比,分析番茄基因组测序技术研究进展。【结果】栽培番茄S. lycopersicum Heinz 1706基因组利用一代和二代测序技术8年完成测序和组装。3个野生番茄基因组采用二代测序技术3年完成,三代测序技术缩短了测序时间,并且在二代测序技术的基础上提高了基因组的质量,提供了完整性高达96.46%的野生番茄品种潘那利的参考基因组。【结论】测序技术推动了番茄基因组研究,三代测序技术与一、二代技术相比,在测序速度、基因序列读长和准确性方面显著提高,也使基因组组装更加精确。

关键词: 番茄; 基因组; 测序技术; 功能基因

Abstract: 【Objective】 As an important vegetable crop, tomato is a model plantform genetic research. The development of sequencing technology will lay a solid foundation for the excavation of important functional genes in tomato.【Method】 High quality of tomato genome information by analyzing and comparing the relative websites、researches and technologies will provide a reliable research strategy for breeders. 【Result】The development of sequencing technology has greatly promoted tomato genome research. It took eight years for sequencing and assembling the genome of cultivated tomato S. lycopersicum Heinz 1706 by first and second generation of sequencing technology. However, three wild tomato species was sequenced by second generation of sequencing technology only within three years. Comparing with the second generation of sequencing technology, the third generation of sequencing technology not only shorten the sequencing time, but also improved the genome quality by providing wild tomato S. pennellii genome sequence with higher integrity of 96.46%.【Conclusion】From the comparison of genome sequencing technology, we gained the conclusion that the third generation of sequencing technology has greatly improved the sequencing speed, the reading length and the accuracy of the genome sequencing. At the same time, it makes the genome assembly more accurate. The decoding of tomato genome information will open a new way for tomato researchers gained new varieties of tomato.

Key words: tomato; genome; sequencing technology; functional genes

中图分类号:

S631.1

唐亚萍, 李宁, 王娟, 王柏柯, 杨生保, 郭斌, 杨涛, 郭春苗, 马凯, 刘君, 王欢, 余庆辉. 番茄基因组研究进展[J]. 新疆农业科学, 2019, 56(2): 197-206.

TANG Ya-ping, LI Ning, WANG Juan, WANG Bai-ke, YANG Sheng-bao, GUO Bin, YANG Tao, GUO Chun-miao, MA Kai, LIU Jun, WANG Huan, YU Qing-hui. Advances in Tomato Genome Research[J]. Xinjiang Agricultural Sciences, 2019, 56(2): 197-206.

参考文献 59

[1]	Gebhardt, & Christiane. (2016). The historical role of species from the solanaceae plant family in genetic research. Theoretical and Applied Genetics,129(12):2281-2294.
[2]	Martin, G. , Brommonschenkel, S. , Chunwongse, J. , Frary, A. , Ganal, M. , & Spivey, R. , et al. (1993). Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science, 262(5138):1,432-1,436.
[3]	Frary, A., Nesbitt, T.C., Grandillo, S., et al. (2000). Fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science, 289(5476):85-88. .
[4]	Fridman, E. , Pleban, T. , & Zamir, D. . (2000). A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proceedings of the National Academy of Sciences, 97(9):4,718-4,723.
[5]	Maxam, A. M. , & Gilbert, W. . (1977). A new method for sequencing dna. Proceedings of the National Academy of Sciences, 74(2):560-564.
[6]	Sanger, F. , Nicklen, S. , & Coulson, A. R. . (1977). Dna sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences,74(12):5,463-5,467.
[7]	Melamede, R.J. Automatable process for sequencing nucleotide[J]. 1985, US patent.
[8]	Margulies, M.,Egholm, M., Altman, W.E., et al. Genome sequencing in microfabricated high-density picolitre reactors[J]. Nature, 2005, 437(7057): 376-380.
[9]	Fedurco, & M. (2006). BTA, a novel reagent for dna attachment on glass and efficient generation of solid-phase amplified dna colonies. Nucleic Acids Research, 34(3):e22-e22.
[10]	Turcatti, G. , Romieu, A. , Fedurco, M. , & Tairi, A. P. . (2008). A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for dna sequencing by synthesis. Nucleic Acids Research, 36(4):e25.
[11]	Shendure, J., Porreca, G.J., Reppas, N.B., et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science,309(5741), 1,728-1,732.
[12]	Koren, S. , Harhay, G. P. , Smith, T. P. , Bono, J. L. , Harhay, D. M. , & Mcvey, S. D. , et al. (2013). Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology,14(9):R101.
[13]	Koren, S. , & Phillippy, A. M. . (2015). One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Current Opinion in Microbiology,23:110-120.
[14]	Levene, M.J., Kodach, J., Turner, S.W., et a1. (2003). Zero mode wave guides for single-molecule analysis at high concentrations. Science, 299(5607): 682-686.
[15]	Eid, J., Fehr, A., Gray, J., et a1. (2009). Real-time DNA sequencing from single polymerase molecules. Science,323(5910): 133-138.
[16]	Stoddart, D., Heron, A.J., Mikhailova, E., et a1. (2009). Single nucleotide discrimination in immobilized DNA oligo nucleotides with a biological nanopore. Proceeding of the National Academy Sciences of the United States of America,106(19): 7,702-7,707.
[17]	Korlach, J., Turner, S.W. (2012). Going beyond five bases in DNA sequencing. Current Opinion in Structural Biology,22(3): 251-261.
[18]	Phillippy A.M. (2017). New advances in sequence assembly. Genome Research, 27(25): xi-xiii.
[19]	Huddleston, J., Chaisson, M.J.P., Steingerg, K.M., et al. (2017). Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Research, 27(5):677-685.
[20]	Merker, J.D., WengerA.M., Sneddon, T., et al. (2018). Long-read genome sequencing identifies causal structural variation in a Mendelian disease running title: long-read WGS identifies causal SV in mendelian disease. Genet Med,20(1):159-163.
[21]	Sedlazeck, F.J., Rescheneder, P., Smolka, M., et al. (2018).Accurate detection of complex structural variations using single-molecule sequencing. Nature Methods,15: 461-468.
[22]	Pennisi, E. (2017). New technologies boost genome quality. Science,357(6346):10-11.
[23]	Jiao, W.B., Schneeberger, K. (2017). The impact of third generation genomic technologies on plant genome assembly. Current Opinion in Plant Biololgy,36:64-70.
[24]	Jarvis, D.E., Ho, Y.S., Lightfoot, D.J., et al. (2017). The genome of Chenopodium quinoa . Nature,542(7641):307-312.
[25]	Jiao, Y., Peluso, P., Shi, J., et al. (2017). The complex sequence landscape of maize revealed by single molecule technologies. Nature, 546: 524-527.
[26]	Schnable, P.S., Ware, D., Fulton, R.S., et al. (2009). The B73 maize genome: complexity, diversity, and dynamics. Science,326(5956): 1,112-1,115.
[27]	Hirsch, C.N., Hirsch, C.D., Brohammer, A.B., et al. (2016).Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. Plant Cell,28(11): 2,700-2,714.
[28]	Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution [J]. Nature, 2012,485:635-641.
[29]	Aflitos, S., Schijlen, E., De, J. H., De, R. D., Smit, S., & Finkers, R., et al. (2015). Exploring genetic variation in the tomato (solanum section lycopersicon) clade by whole-genome sequencing. Plant Journal for Cell & Molecular Biology,80(1):136-148.
[30]	Bolger, A., Scossa, F., Bolger, M.E., et al. (2014). The genome of the stress-tolerant wild tomato species Solanum pennellii . Nature Genetics, 46(9):1,034-1,038.
[31]	Strickler, S. R. , Bombarely, A. , Munkvold, J. D. , York, T. , & Mueller, L. A. . (2015). Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PeerJ, 3(2):e793.
[32]	Schmidt, M.H., Vogel, A., Denton, A.K., et al. (2017). De Novo Assembly of a New Solanum pennellii Accession UsingNanopore Sequencing. Plant Cell,29(10): 2,336-2,348.
[33]	Rothan, C., Diouf, I., Causse, M. (2019). Trait discovery and editing in tomato [J]. The Plant Journal., doi: 10.1111/tpj.14152.
[34]	Sauvage, C., Segura, V., Bauchet, G., et al. (2014). Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits. Plant Physiology,165: 1,120-1,132.
[35]	Causse, M., Desplat, N., Pascual, L., et al. (2013). Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics,14:719.
[36]	Lin, T., Zhu, G., Zhang, J., et al. (2014). Genomic analyses provide insights into the history of tomato breeding. Nature Genetics,46:1,220-1,226.
[37]	Tieman, D., Zhu, G., Resende, M.F.J., et al. (2017). A chemical genetic roadmap to improved tomato flavor. Science,355(6323):391-394
[38]	Bauchet, G., Grenier, S., Samson, N., et al. (2017). Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytologist,215: 624-641.
[39]	Zhu, G. Wang, S., Huang, Z., et al. (2018). Rewiring of the fruit metabolome in tomato breeding. Cell, 172(1-2):249-261.
[40]	Blanca, J., Montero-Pau, J., Sauvage, C., at al. (2015). Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics, 16: 257.
[41]	Sahu, K.K., Chattopadhyay, D. (2017). Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping. BMC Genomics,18: 430.
[42]	Alseekh, S., Tong, H., Scossa, F., et al. (2017). Canalization of Tomato Fruit Metabolism. The Plant Cell, 29: 2753-2765.
[43]	Bauchet, G., Grenier, S., Samson, N., et al. (2017). Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytologist,215: 624-641.
[44]	Gaiero, P., Vaio, M., Peters, S.A., et al. (2018). Comparative analysis of repetitive sequences among species from the potato and the tomato clades. Annals of Botany, doi: 10.1093/aob/ mcy186.
[45]	Li, R. , Li, Y. , Zheng, H. , Luo, R. , Zhu, H. , & Li, Q. , et al. (2009). Building the sequence map of the human pan-genome. NATURE BIOTECHNOLOGY, 28(1):57-63.
[46]	Sherman, R.M., Forman, J., Antonescu, V., et al. (2019). Author correction: assembly of a pan-genome from deep sequencing of 910 humans of african descent. Nature genetics, 51(2), 364. doi.org/10.1038/s41588-018-0273-y.
[47]	Li, Y.H., Zhou, G., Ma, J., et al. (2014). De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology, 32(10):1,045-1,052.
[48]	Golicz, A. A. , Bayer, P. E. , Barker, G. C. , Edger, P. P. , Kim, H. R. , & Martinez, P. A. , et al. (2016). The pangenome of an agronomically important crop plant brassica oleracea. Nature Communications,7, 13390.
[49]	Gordon, S. P. , Contreras-Moreira, B. , Woods, D. P. , Des Marais, D. L. , Burgess, D. , & Shu, S. , et al. (2017). Extensive gene content variation in the brachypodium distachyon pan-genome correlates with population structure. Nature Communications,8(1):2184.
[50]	Zhao, Q. , Feng, Q. , Lu, H. , Li, Y. , Wang, A. , & Tian, Q. , et al. (2018). Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nature Genetics,50(2):278-284.
[51]	Stein, J. C. , Yu, Y. , Copetti, D. , Zwickl, D. J. , & Wing, R. A. . (2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus oryza. Nature Genetics, 50(W1):285-296.
[52]	Causse, M., Giovannoni, J., Bouzayen, M., et al. The tomato genome[M]. Germany, Springer, 2016.
[53]	Yu, Q. H. , Wang, B. , Li, N. , Tang, Y. , Yang, S. , & Yang, T. , et al. (2017). Crispr/cas9-induced targeted mutagenesis and gene replacement to generate long-shelf life tomato lines. Scientific Reports,7(1):11874.
[54]	Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002). Capturing chromosome conformation. Science,295(5558):1,306-1,311.
[55]	Simonis M., Klous P., Splinter E., et al. (2006). Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genetics,38(11):1,348-1,354.
[56]	Dostie, J., Richmond, T. A., Arnaout, R. A., Selzer, R. R., Lee, W. L., & Honan, T. A., et al. (2006). Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Research,16: 1,299-1,309.
[57]	Wang, M. , Wang, P. , Lin, M. , Ye, Z. , Li, G. , & Tu, L. , et al. (2018). Evolutionary dynamics of 3d genome architecture following polyploidization in cotton. Nature Plants, 4(2):90-97
[58]	Dong, Q. , Li, N. , Li, X. , Yuan, Z. , Xie, D. , & Wang, X. , et al. (2018). Genome-wide hi-c analysis reveals extensive hierarchical chromatin interactions in rice. The Plant Journal. DOI:10.1111/tpj.13,925
[59]	Feng, S., Cokus, S. J., Schubert, V., Zhai, J., Pellegrini, M., & Jacobsen, S. E. (2014). Genome-wide hi-c analyses in wild-type and mutants reveal high-resolution chromatin interactions in arabidopsis. Molecular Cell,55(5):694-707.

番茄基因组研究进展

Advances in Tomato Genome Research

PDF下载

可视化

摘要/Abstract

引用本文

使用本文

参考文献 59

相关文章 15

编辑推荐

Metrics

[1]	王丹丹, 李燕, 张庆银, 李世东, 庞永超, 马琨芝, 马龙, 牛瑞生, 钟增明, 齐连芬, 师建华. 不同微生物菌处理对番茄土壤微生物多样性的影响[J]. 新疆农业科学, 2023, 60(9): 2248-2257.
[2]	蒲敏, 阮向阳, 肖乐乐, 索常凯, 陈国永, 冶军, 高波. 枸溶性钙镁肥对加工番茄钙、镁吸收及品质的影响[J]. 新疆农业科学, 2023, 60(8): 1987-1995.
[3]	肖林刚, 马艳, 宋兵伟, 焦锐斌, 邢剑飞. 温室膜下微喷灌溉技术研究进展[J]. 新疆农业科学, 2023, 60(7): 1731-1740.
[4]	刘江娜, 张西英, 李荣霞, 张小伟, 白云凤, 张爱萍. 番茄SlLCY-B2及其启动子的分子特征和sgRNA分析[J]. 新疆农业科学, 2023, 60(6): 1460-1465.
[5]	陈开旭, 郭翠洁, 杨帆, 任斐儿, 李晓斌, 刘武军. 基于全基因组重测序分析新疆细毛羊遗传多样性[J]. 新疆农业科学, 2023, 60(5): 1292-1300.
[6]	陈果, 郝晓燕, 高升旗, 胡文冉, 赵准, 黄全生. 玉米钙依赖蛋白激酶全基因组鉴定及抗旱表达分析[J]. 新疆农业科学, 2023, 60(4): 857-864.
[7]	杜红艳, 庞胜群, 马海翔, 吉雪花. 加工番茄早熟突变体农艺性状相关性及通径分析[J]. 新疆农业科学, 2023, 60(4): 943-950.
[8]	朱普生, 刘慧英, 曹泽, 刘凯歌, 李雪珍. 外源GSNO对NaCl胁迫下番茄幼苗生长及光合特性的影响[J]. 新疆农业科学, 2023, 60(2): 351-358.
[9]	曾军, 武磊, 高雁, 张卓, 林青, 刘建伟, 杨红梅, 霍向东, 史应武. 光合细菌叶面肥喷施对设施有机番茄产量和品质的影响[J]. 新疆农业科学, 2023, 60(12): 3018-3024.
[10]	刘升学, 李思琪, 王晓东, 杨德松. 番茄早疫病菌dsRNA多样性分析[J]. 新疆农业科学, 2023, 60(12): 3057-3064.
[11]	张萍, 罗晓霞, 万传星, 张利莉. 链霉菌TRM SA0054 Tubercidin合成基因簇挖掘[J]. 新疆农业科学, 2023, 60(11): 2806-2815.
[12]	芦大伟, 哈丽哈什·依巴提, 李青军. 磷肥用量对滴灌加工番茄产量、品质及磷肥利用率的影响[J]. 新疆农业科学, 2023, 60(1): 185-191.
[13]	李岳雁, 李玉姗, 王帆, 郭雅文, 王飞燕, 高杰, 宋羽. 不同品种番茄果实性状遗传多样性及聚类分析[J]. 新疆农业科学, 2022, 59(9): 2147-2157.
[14]	李春雨, 谭占明, 程云霞, 束胜, 何涛, 靳钰婕, 马新超, 杜佳庚, 张婧. 水肥耦合对沙培番茄生长发育及品质的影响[J]. 新疆农业科学, 2022, 59(9): 2158-2169.
[15]	马雪红, 刘婷, 李传天, 朱金芳. HPLC法测定番茄红素胶束中番茄红素Z/E异构体含量[J]. 新疆农业科学, 2022, 59(9): 2209-2216.