首页 » 文章 » 文章详细信息
International Journal of Genomics Volume 2017 ,2017-08-16
Aquatic Plant Genomics: Advances, Applications, and Prospects
Review Article
Shiqi Hu 1 , 2 Gaojie Li 1 , 2 Jingjing Yang 1 , 2 Hongwei Hou 1 , 2
Show affiliations
Received 2016-12-15, accepted for publication 2017-07-30, Published 2017-07-30

Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.


Copyright © 2017 Shiqi Hu et al. 2017
This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Hongwei Hou.The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China, cas.cn;University of Chinese Academy of Sciences, Beijing 100049, China, ucas.ac.cn.houhw@ihb.ac.cn


Shiqi Hu,Gaojie Li,Jingjing Yang,Hongwei Hou. Aquatic Plant Genomics: Advances, Applications, and Prospects. International Journal of Genomics ,Vol.2017(2017)



[1] Y. G. Kim, J. Cha, S. Chandrasegaran. (1996). Hybrid restriction enzymes: zinc finger fusions to FokI cleavage domain. Proceedings of the National Academy of Sciences.93(3):1156-1160. DOI: 10.1038/35048692.
[2] S. Mishra, G. Wellenreuther, J. Mattusch, H. J. Stärk. et al.(2013). Speciation and distribution of arsenic in the nonhyperaccumulator macrophyte. Plant Physiology.163(3):1396-1408. DOI: 10.1038/35048692.
[3] S. Mishra, S. Srivastava, R. D. Tripathi, P. K. Trivedi. et al.(2008). Thiol metabolism and antioxidant systems complement each other during arsenate detoxification in L. Aquatic Toxicology.86(2):205. DOI: 10.1038/35048692.
[4] T. Li, S. Huang, W. Z. Jiang, D. Wright. et al.(2011). TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Research.39(1):359-372. DOI: 10.1038/35048692.
[5] A. Imanishi, S. Kaneko, Y. Isagi, J. Imanishi. et al.(2011). Development of microsatellite markers for (Nymphaeaceae), an endangered aquatic plant species in Japan. American Journal of Botany.98(8):233-235. DOI: 10.1038/35048692.
[6] J. Silverthorne, C. F. Wimpee, T. Yamada, S. A. Rolfe. et al.(1990). Differential expression of individual genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in. Plant Molecular Biology.15(1):49-58. DOI: 10.1038/35048692.
[7] R. Uesugi, N. Tani, K. Goka, J. Nishihiro. et al.(2005). Isolation and characterization of highly polymorphic microsatellites in the aquatic plant, (Menyanthaceae). Molecular Ecology Notes.5(2):343-345. DOI: 10.1038/35048692.
[8] S. K. Rao, H. Fukayama, J. B. Reiskind, M. Miyao. et al.(2006). Identification of C4 responsive genes in the facultative C4 plant. Photosynthesis Research.88(2):173-183. DOI: 10.1038/35048692.
[9] L. A. Raubeson, R. Peery, T. W. Chumley, C. Dziubek. et al.(2007). Comparative chloroplast genomics: analyses including new sequences from the angiosperms and. BMC Genomics.8:174. DOI: 10.1038/35048692.
[10] W. Wang, Y. Wu, J. Messing. (2012). The mitochondrial genome of an aquatic plant,. PLoS One.7(10):135-139. DOI: 10.1038/35048692.
[11] Y. Y. Liao, X. L. Yue, Y. H. Guo, W. R. Gituru. et al.(2013). Genotypic diversity and genetic structure of populations of the distylous aquatic plant (Menyanthaceae) in China. Journal of Systematics and Evolution.51(5):536-544. DOI: 10.1038/35048692.
[12] A. Montsant, K. Jabbari, U. Maheswari, C. Bowler. et al.(2005). Comparative genomics of the pennate diatom. Plant Physiology.137(2):500-513. DOI: 10.1038/35048692.
[13] A. Cuenca, G. Petersen, O. Seberg. (2013). The complete sequence of the mitochondrial genome of —a member of an early branching lineage of monocotyledons. PLoS One.8(4):542-542. DOI: 10.1038/35048692.
[14] W. Wang, G. Haberer, H. Gundlach, C. Gläßer. et al.(2014). The genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nature Communications.5. DOI: 10.1038/35048692.
[15] E. L. Peredo, U. M. King, D. H. Les. (2013). The plastid genome of : adaptation to submersed environments is accompanied by the complete loss of the NDH complex in an aquatic angiosperm. PLoS One.8(7):88-91. DOI: 10.1038/35048692.
[16] S. R. Silva, D. G. Pinheiro, E. J. Meer, T. P. Michael. et al.(2016). The complete chloroplast genome sequence of the leafy bladderwort, L. (Lentibulariaceae). Conservation Genetics Resources.9(2):213-216. DOI: 10.1038/35048692.
[17] T. Huotari, H. Korpelainen. (2012). Complete chloroplast genome sequence of and comparative analyses with other monocot plastid genomes. Gene.508(1):96-105. DOI: 10.1038/35048692.
[18] S. Mishra, M. Alfeld, R. Sobotka, E. Andresen. et al.(2016). Analysis of sublethal arsenic toxicity to : subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis. Journal of Experimental Botany.67(15):4639-4646. DOI: 10.1038/35048692.
[19] M. M. Mahfouz, L. Li, M. Shamimuzzaman, A. Wibowo. et al.(2011). De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proceedings of the National Academy of Sciences.108(6):2623-2628. DOI: 10.1038/35048692.
[20] J. C. Miller, S. Tan, G. Qiao, K. A. Barlow. et al.(2011). A TALE nuclease architecture for efficient genome editing. Nature Biotechnology.29(2):143-148. DOI: 10.1038/35048692.
[21] U. N. Rai, R. D. Tripathi, N. K. Singh, A. K. Upadhyay. et al.(2013). Constructed wetland as an ecotechnological tool for pollution treatment for conservation of Ganga river. Bioresource Technology.148(11):535-541. DOI: 10.1038/35048692.
[22] R. D. Tripathi, R. Singh, P. Tripathi, S. Dwivedi. et al.(2014). Arsenic accumulation and tolerance in rootless macrophyte are mediated through antioxidants, amino acids and phytochelatins. Aquatic Toxicology.157:70-80. DOI: 10.1038/35048692.
[23] M. Jinek, K. Chylinski, I. Fonfara, M. Hauer. et al.(2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science.337(6096):816-821. DOI: 10.1038/35048692.
[24] S. S. Merchant, S. E. Prochnik, O. Vallon, E. H. Harris. et al.(2007). The genome reveals the evolution of key animal and plant functions. Science.318(5848):245-250. DOI: 10.1038/35048692.
[25] E. V. Armbrust, J. A. Berges, C. Bowler, B. R. Green. et al.(2004). The genome of the diatom : ecology, evolution, and metabolism. Science.306(5693):79-86. DOI: 10.1038/35048692.
[26] R. Ming, R. Vanburen, Y. Liu, M. Yang. et al.(2013). Genome of the long-living sacred lotus (.). Genome Biology.14(5):241-251. DOI: 10.1038/35048692.
[27] M. Matsuzaki, O. Misumi, T. Shin-I, S. Maruyama. et al.(2004). Genome sequence of the ultrasmall unicellular red alga 10D. Nature.428(6983):653-657. DOI: 10.1038/35048692.
[28] B. J. Pollux, M. D. Jong, A. Steegh, E. Verbruggen. et al.(2007). Reproductive strategy, clonal structure and genetic diversity in populations of the aquatic macrophyte in river systems. Molecular Ecology.16(2):313-325. DOI: 10.1038/35048692.
[29] X. W. Zou. (2005). Development of aquatic plants at home and abroad (in Chinese). China Flowers & Horticulture.15:10-12. DOI: 10.1038/35048692.
[30] A. V. Hoeck, N. Horemans, P. Monsieurs, H. X. Cao. et al.(2015). The first draft genome of the aquatic model plant , opens the route for future stress physiology research and biotechnological applications. Biotechnology for Biofuels.8(1):1-13. DOI: 10.1038/35048692.
[31] J. Martinez-Garrido, M. Gonzalez-Wanguemert, E. A. Serrao. (2014). New highly polymorphic microsatellite markers for the aquatic angiosperm reveal population diversity and differentiation. Genome.57(1):57-59. DOI: 10.1038/35048692.
[32] A. V. Mardanov, N. V. Ravin, B. B. Kuznetsov, T. H. Samigullin. et al.(2008). Complete sequence of the duckweed () chloroplast genome: structural organization and phylogenetic relationships to other angiosperms. Journal of Molecular Evolution.66(6):555-564. DOI: 10.1038/35048692.
[33] W. Wang, J. Messing. (2011). High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS One.6(9). DOI: 10.1038/35048692.
[34] J. Barta, J. D. Stone, J. Pech, D. Sirova. et al.(2015). The transcriptome of , a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with. BMC Plant Biology.15(1):1-14. DOI: 10.1038/35048692.
[35] T. Li, B. Liu, M. H. Spalding, D. P. Weeks. et al.(2012). High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature Biotechnology.30(5):390-392. DOI: 10.1038/35048692.
[36] M. Eisenstein. (2012). The battle for sequencing supremacy. Nature Biotechnology.30(11):1023-1026. DOI: 10.1038/35048692.
[37] S. Mishra, R. D. Tripathi, S. Srivastava, S. Dwivedi. et al.(2009). Thiol metabolism play significant role during cadmium detoxification by , L. Bioresource Technology.100(7):2155-2161. DOI: 10.1038/35048692.
[38] E. Ibarra-Laclette, V. A. Albert, C. A. Péreztorres, F. Zamudiohernández. et al.(2011). Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome. BMC Plant Biology.11(1):1-16. DOI: 10.1038/35048692.
[39] Q. Sun, W. B. Liu, C. Wang. (2011). Different response of phytochelatins in two aquatic macrophytes exposed to cadmium at environmentally relevant concentrations. African Journal of Biotechnology.10(33):6292-6299. DOI: 10.1038/35048692.
[40] M. Gurushidze, G. Hensel, S. Hiekel, S. Schedel. et al.(2014). True-breeding targeted gene knock-out in barley using designer TALE-nuclease in haploid cells. PLoS One.9(3, article e92046). DOI: 10.1038/35048692.
[41] T. A. Akhtar, M. A. Lampi, B. M. Greenberg. (2005). Identification of six differentially expressed genes in response to copper exposure in the aquatic plant (duckweed). Environmental Toxicology & Chemistry.24(7):1705-1715. DOI: 10.1038/35048692.
[42] Z. Feng, B. Zhang, W. Ding, X. Liu. et al.(2013). Efficient genome editing in plants using a CRISPR/Cas system. Cell Research.23(10):1229-1232. DOI: 10.1038/35048692.
[43] W. Wang, J. Messing. (2015). Status of duckweed genomics and transcriptomics. Plant Biology (Stuttgart, Germany).17:10-15. DOI: 10.1038/35048692.
[44] D. E. Salt, R. D. Smith, I. Raskin. (1998). Phytoremediation. Annual Review of Plant Biology.49(49):643-668. DOI: 10.1038/35048692.
[45] L. Xiao, C. Xi, D. J. Oliver, C. B. Xiang. et al.(2009). Isolation of a low-sulfur tolerance gene from , using a functional gene-mining approach. Planta.231(1):211-219. DOI: 10.1038/35048692.
[46] O. Keskinkan, M. Z. L. Goksu, M. Basibuyuk, C. F. Forster. et al.(2004). Heavy metal adsorption properties of a submerged aquatic plant (). Bioresource Technology.92(2):197-200. DOI: 10.1038/35048692.
[47] T. Wendt, P. B. Holm, C. G. Starker, M. Christian. et al.(2013). TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants. Plant Molecular Biology.83(3):279-285. DOI: 10.1038/35048692.
[48] O. Hidalgo, S. Garcia, T. Garnatje, M. Mumbrú. et al.(2015). Genome size in aquatic and wetland plants: fitting with the large genome constraint hypothesis with a few relevant exceptions. Plant Systematics and Evolution.301(7):1927-1936. DOI: 10.1038/35048692.
[49] E. Ibarra-Laclette, E. Lyons, G. Hernández-Guzmán, C. A. Pérez-Torres. et al.(2013). Architecture and evolution of a minute plant genome. Nature.498(7452):94-98. DOI: 10.1038/35048692.
[50] T. D. Barbosa, R. J. Trad, M. M. Bajay, M. C. Amaral. et al.(2015). Microsatellite markers isolated from s.L. (Cabombaceae) from an enriched genomic library. Applications in Plant Sciences.3(11). DOI: 10.1038/35048692.
[51] P. Schnable, D. Ware, R. Fulton, J. Stein. et al.(2009). The b73 maize genome: complexity, diversity, and dynamics. Science.326(5956):1112-1115. DOI: 10.1038/35048692.
[52] J. B. Whittall, S. A. Hodges. (2004). Cryptic species in an endangered pondweed community (, potamogetonaceae) revealed by AFLP markers. American Journal of Botany.91(12):2022-2029. DOI: 10.1038/35048692.
[53] J. Hu, L. Pan, H. Liu, S. Wang. et al.(2011). Comparative analysis of genetic diversity in sacred lotus ( Gaertn.) using AFLP and SSR markers. Molecular Biology Reports.39(4):3637-3647. DOI: 10.1038/35048692.
[54] L. Carretero-Paulet, T. H. Chang, P. Librado, E. Ibarra-Laclette. et al.(2015). Genome-wide analysis of adaptive molecular evolution in the carnivorous plant. Genome Biology & Evolution.7(2):444. DOI: 10.1038/35048692.
[55] H. Kumar, P. Priya, N. Singh, M. Kumar. et al.(2016). RAPD and ISSR marker-based comparative evaluation of genetic diversity among Indian germplasms of : an aquatic food plant. Applied Biochemistry and Biotechnology.180(7):1345-1360. DOI: 10.1038/35048692.
[56] C. Qin, C. Yu, Y. Shen, X. Fang. et al.(2014). Whole-genome sequencing of cultivated and wild peppers provides insights into capsicum domestication and specialization. Proceedings of the National Academy of Sciences of the United States of America.111(14):5135-5140. DOI: 10.1038/35048692.
[57] K. F. Mayer, J. Rogers, J. Doležel, C. Pozniak. et al.(2014). A chromsome-based draft sequence of the hexaploid bread wheat () genome. Science.345(6194). DOI: 10.1038/35048692.
[58] Q. Jiang, F. Wang, H. W. Tan, M. Y. Li. et al.(2015). De novo transcriptome assembly, gene annotation, marker development, and miRNA potential target genes validation under abiotic stresses in. Molecular Genetics and Genomics.290(2):671-683. DOI: 10.1038/35048692.
[59] L. Y. Chen, S. Y. Zhao, Q. F. Wang, M. L. Moody. et al.(2015). Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats. Scientific Reports.5. DOI: 10.1038/35048692.
[60] Tomato Genome Consortium. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature.485(7400):635-641. DOI: 10.1038/35048692.
[61] J. Jeon, S. J. Bong, J. S. Park, Y. K. Park. et al.(2017). De novo transcriptome analysis and glucosinolate profiling in watercress ( R. Br.). BMC Genomics.18(1):401. DOI: 10.1038/35048692.
[62] J. F. Li, J. E. Norville, J. Aach, M. Mccormack. et al.(2013). Multiplex and homologous recombination-mediated genome editing in Arabidopsis and using guide RNA and Cas9. Nature Biotechnology.31(8):688-691. DOI: 10.1038/35048692.
[63] M. Amano, S. Iida, K. Kosuge. (2012). Comparative studies of thermotolerance: different modes of heat acclimation between tolerant and intolerant aquatic plants of the genus Potamogeton. Annals of Botany.109(2):443-452. DOI: 10.1038/35048692.
[64] D. Wang, S. Z. Xie, J. Yang, Q. F. Wang. et al.(2014). Molecular characteristics and expression patterns of Rubisco activase, novel alternative splicing variants in a heterophyllous aquatic plant,. Photosynthetica.52(1):83-95. DOI: 10.1038/35048692.
[65] Q. Shan, Y. Wang, J. Li, Y. Zhang. et al.(2013). Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology.31(8):686-688. DOI: 10.1038/35048692.
[66] J. Zalewska-Gałosz, M. Ronikier. (2011). : a new hybrid between linear-leaved pondweeds from central Europe. Preslia -Praha.83(3):259-273. DOI: 10.1038/35048692.
[67] D. Shukla, R. Kesari, S. Mishra, S. Dwivedi. et al.(2012). Expression of phytochelatin synthase from aquatic macrophyte L. enhances cadmium and arsenic accumulation in tobacco. Plant Cell Reports.31(9):1687-1699. DOI: 10.1038/35048692.
[68] J. Miao, D. Guo, J. Zhang, Q. Huang. et al.(2013). Targeted mutagenesis in rice using CRISPR-Cas system. Cell Research.23(10):1233-1236. DOI: 10.1038/35048692.
[69] S. K. Baniwal, K. Bharti, K. Y. Chan, M. Fauth. et al.(2005). Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. Journal of Biosciences.29(4):471-487. DOI: 10.1038/35048692.
[70] M. Shri, R. Dave, S. Diwedi, D. Shukla. et al.(2014). Heterologous expression of phytochelatin synthase, , in rice leads to lower arsenic accumulation in grain. Scientific Reports.4(8):5784-5784. DOI: 10.1038/35048692.
[71] E. Vierling. (1991). The roles of heat shock proteins in plants. Annual Review of Plant Physiology and Plant Molecular Biology.42:579-620. DOI: 10.1038/35048692.
[72] V. Nekrasov, B. Staskawicz, D. Weigel. (2013). Targeted mutagenesis in the model plant using Cas9 RNA-guided endonuclease. Nature Biotechnology.31(8):691-693. DOI: 10.1038/35048692.
[73] Y. Y. Yuan, Q. F. Wang, J. M. Chen. (2013). Development of SSR markers in aquatic plant (Menyanthaceae) based on information from transcriptome sequencing (in Chinese). Plant Sclence Journal.31(5):485-492. DOI: 10.1038/35048692.
[74] Y. Zheng, G. Jagadeeswaran, K. Gowdu, N. Wang. et al.(2013). Genome-wide analysis of microRNAs in sacred lotus, (Gaertn). Tropical Plant Biology.6(2-3):117-130. DOI: 10.1038/35048692.
[75] L. Y. Chen, J. M. Chen, R. W. Gituru, Q. F. Wang. et al.(2012). Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae. BMC Evolutionary Biology.12(1):1-12. DOI: 10.1038/35048692.
[76] F. Y. Ellmouni, M. A. Karam, R. M. Ali, D. C. Albach. et al.(2017). Molecular and morphometric analysis of L. section (Hill) Dumort. Aquatic Botany.136:95-111. DOI: 10.1038/35048692.
[77] A. G. Initiative. (2000). Analysis of the genome sequence of the flowering plant. Nature.408(6814):796-815. DOI: 10.1038/35048692.
[78] K. Koga, Y. Kadono, H. Setoguchi. (2007). The genetic structure of populations of the vulnerable aquatic macrophyte (Ranunculaceae). Journal of Plant Research.120(2):167-174. DOI: 10.1038/35048692.
[79] Y. Kameyama, M. Ohara. (2006). Predominance of clonal reproduction, but recombinant origins of new genotypes in the free-floating aquatic bladderwort f. tenuicaulis (Lentibulariaceae). Journal of Plant Research.119(4):357-362. DOI: 10.1038/35048692.
[80] S. A. Goff, D. Ricke, T. H. Lan, G. Presting. et al.(2002). A draft sequence of the rice genome (L. ssp. ). Science.296(5565):92-100. DOI: 10.1038/35048692.
[81] M. Thudi, Y. Li, S. A. Jackson, G. D. May. et al.(2012). Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics.11(1):3-11. DOI: 10.1038/35048692.
[82] B. Wang, W. Li, J. Wang. (2005). Genetic diversity of in China. Aquatic Botany.81(3):277-283. DOI: 10.1038/35048692.
[83] L. Pan, X. Wang, J. Jin, X. Yu. et al.(2015). Bioinformatic identification and expression analysis of microRNA and their targets. Applications in Plant Sciences.3(9, article 1500046). DOI: 10.1038/35048692.
[84] B. Halliwell, J. M. C. Gutteridge. (1999). Free Radicals in Biology and Medicine. DOI: 10.1038/35048692.
[85] J. Silverthorne, E. M. Tobin. (1990). Post-transcriptional regulation of organ-specific expression of individual rbcs mRNAs in. Plant Cell.2(12):1181-1190. DOI: 10.1038/35048692.
[86] S. K. Upadhyay, J. Kumar, A. Alok, R. Tuli. et al.(2013). RNA-guided genome editing for target gene mutations in wheat. G3-Genes Genomes Genetics.3(12):2233-2238. DOI: 10.1038/35048692.
浏览 73次
下载全文 7次
评分次数 0次
用户评分 0.0分
分享 14次