Whole-genome sequencing in medicinal plants: current progress and prospect

被引:13
作者
Pei, Yifei [1 ]
Leng, Liang [2 ,3 ]
Sun, Wei [1 ]
Liu, Baocai [4 ]
Feng, Xue [1 ]
Li, Xiwen [1 ]
Chen, Shilin [2 ,3 ]
机构
[1] China Acad Chinese Med Sci, Inst Chinese Mat Med, Beijing 100700, Peoples R China
[2] Chengdu Univ Tradit Chinese Med, Inst Herbgen, Chengdu 611137, Peoples R China
[3] Chengdu Univ Tradit Chinese Med, Innovat Inst Chinese Med & Pharm, Chengdu 611137, Peoples R China
[4] Fujian Acad Agr Sci, Inst Agr Bioresource, Fuzhou 350003, Peoples R China
关键词
herbgenomics; whole genome; high throughput sequencing; research strategy; model species; application; LEVEL REFERENCE GENOME; PROVIDES INSIGHTS; DRAFT GENOME; DENDROBIUM-OFFICINALE; GENETIC DIVERSITY; BIOSYNTHESIS; EVOLUTION; REVEALS; DNA; DOMESTICATION;
D O I
10.1007/s11427-022-2375-y
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
引用
收藏
页码:258 / 273
页数:16
相关论文
共 176 条
[1]   Herbal medicine for treatment of children diagnosed with COVID-19: A review of guidelines [J].
Ang, Lin ;
Lee, Hye Won ;
Kim, Anna ;
Lee, Ju Ah ;
Zhang, Junhua ;
Lee, Myeong Soo .
COMPLEMENTARY THERAPIES IN CLINICAL PRACTICE, 2020, 39
[2]   Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].
Kaul, S ;
Koo, HL ;
Jenkins, J ;
Rizzo, M ;
Rooney, T ;
Tallon, LJ ;
Feldblyum, T ;
Nierman, W ;
Benito, MI ;
Lin, XY ;
Town, CD ;
Venter, JC ;
Fraser, CM ;
Tabata, S ;
Nakamura, Y ;
Kaneko, T ;
Sato, S ;
Asamizu, E ;
Kato, T ;
Kotani, H ;
Sasamoto, S ;
Ecker, JR ;
Theologis, A ;
Federspiel, NA ;
Palm, CJ ;
Osborne, BI ;
Shinn, P ;
Conway, AB ;
Vysotskaia, VS ;
Dewar, K ;
Conn, L ;
Lenz, CA ;
Kim, CJ ;
Hansen, NF ;
Liu, SX ;
Buehler, E ;
Altafi, H ;
Sakano, H ;
Dunn, P ;
Lam, B ;
Pham, PK ;
Chao, Q ;
Nguyen, M ;
Yu, GX ;
Chen, HM ;
Southwick, A ;
Lee, JM ;
Miranda, M ;
Toriumi, MJ ;
Davis, RW .
NATURE, 2000, 408 (6814) :796-815
[3]   The genome of Theobroma cacao [J].
Argout, Xavier ;
Salse, Jerome ;
Aury, Jean-Marc ;
Guiltinan, Mark J. ;
Droc, Gaetan ;
Gouzy, Jerome ;
Allegre, Mathilde ;
Chaparro, Cristian ;
Legavre, Thierry ;
Maximova, Siela N. ;
Abrouk, Michael ;
Murat, Florent ;
Fouet, Olivier ;
Poulain, Julie ;
Ruiz, Manuel ;
Roguet, Yolande ;
Rodier-Goud, Maguy ;
Barbosa-Neto, Jose Fernandes ;
Sabot, Francois ;
Kudrna, Dave ;
Ammiraju, Jetty Siva S. ;
Schuster, Stephan C. ;
Carlson, John E. ;
Sallet, Erika ;
Schiex, Thomas ;
Dievart, Anne ;
Kramer, Melissa ;
Gelley, Laura ;
Shi, Zi ;
Berard, Aurelie ;
Viot, Christopher ;
Boccara, Michel ;
Risterucci, Ange Marie ;
Guignon, Valentin ;
Sabau, Xavier ;
Axtell, Michael J. ;
Ma, Zhaorong ;
Zhang, Yufan ;
Brown, Spencer ;
Bourge, Mickael ;
Golser, Wolfgang ;
Song, Xiang ;
Clement, Didier ;
Rivallan, Ronan ;
Tahi, Mathias ;
Akaza, Joseph Moroh ;
Pitollat, Bertrand ;
Gramacho, Karina ;
D'Hont, Angelique ;
Brunel, Dominique .
NATURE GENETICS, 2011, 43 (02) :101-108
[4]  
Bemer M., 2018, Plant chromatin dynamics: methods and protocols
[5]   Antiviral effect of phytochemicals from medicinal plants: Applications and drug delivery strategies [J].
Ben-Shabat, Shimon ;
Yarmolinsky, Ludmila ;
Porat, Daniel ;
Dahan, Arik .
DRUG DELIVERY AND TRANSLATIONAL RESEARCH, 2020, 10 (02) :354-367
[6]   Reference genome sequence of the model plant Setaria [J].
Bennetzen, Jeffrey L. ;
Schmutz, Jeremy ;
Wang, Hao ;
Percifield, Ryan ;
Hawkins, Jennifer ;
Pontaroli, Ana C. ;
Estep, Matt ;
Feng, Liang ;
Vaughn, Justin N. ;
Grimwood, Jane ;
Jenkins, Jerry ;
Barry, Kerrie ;
Lindquist, Erika ;
Hellsten, Uffe ;
Deshpande, Shweta ;
Wang, Xuewen ;
Wu, Xiaomei ;
Mitros, Therese ;
Triplett, Jimmy ;
Yang, Xiaohan ;
Ye, Chu-Yu ;
Mauro-Herrera, Margarita ;
Wang, Lin ;
Li, Pinghua ;
Sharma, Manoj ;
Sharma, Rita ;
Ronald, Pamela C. ;
Panaud, Olivier ;
Kellogg, Elizabeth A. ;
Brutnell, Thomas P. ;
Doust, Andrew N. ;
Tuskan, Gerald A. ;
Rokhsar, Daniel ;
Devos, Katrien M. .
NATURE BIOTECHNOLOGY, 2012, 30 (06) :555-+
[7]   Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions [J].
Burton, Joshua N. ;
Adey, Andrew ;
Patwardhan, Rupali P. ;
Qiu, Ruolan ;
Kitzman, Jacob O. ;
Shendure, Jay .
NATURE BIOTECHNOLOGY, 2013, 31 (12) :1119-+
[8]   Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes [J].
Campoy, Jose A. ;
Sun, Hequan ;
Goel, Manish ;
Jiao, Wen-Biao ;
Folz-Donahue, Kat ;
Wang, Nan ;
Rubio, Manuel ;
Liu, Chang ;
Kukat, Christian ;
Ruiz, David ;
Huettel, Bruno ;
Schneeberger, Korbinian .
GENOME BIOLOGY, 2020, 21 (01)
[9]   An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes [J].
Castanera, Raul ;
Ruggieri, Valentino ;
Pujol, Marta ;
Garcia-Mas, Jordi ;
Casacuberta, Josep M. .
FRONTIERS IN PLANT SCIENCE, 2020, 10
[10]   Draft genome sequence of the oilseed species Ricinus communis [J].
Chan, Agnes P. ;
Crabtree, Jonathan ;
Zhao, Qi ;
Lorenzi, Hernan ;
Orvis, Joshua ;
Puiu, Daniela ;
Melake-Berhan, Admasu ;
Jones, Kristine M. ;
Redman, Julia ;
Chen, Grace ;
Cahoon, Edgar B. ;
Gedil, Melaku ;
Stanke, Mario ;
Haas, Brian J. ;
Wortman, Jennifer R. ;
Fraser-Liggett, Claire M. ;
Ravel, Jacques ;
Rabinowicz, Pablo D. .
NATURE BIOTECHNOLOGY, 2010, 28 (09) :951-U3