1
|
Lichman V, Ozerov M, López ME, Noreikiene K, Kahar S, Pukk L, Burimski O, Gross R, Vasemägi A. Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch. JOURNAL OF FISH BIOLOGY 2024; 105:871-885. [PMID: 38897597 DOI: 10.1111/jfb.15821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole-genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000-100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome-wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data-mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.
Collapse
Affiliation(s)
- Vitalii Lichman
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Mikhail Ozerov
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
- Department of Biology, University of Turku, Turku, Finland
| | - María-Eugenia López
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - Kristina Noreikiene
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Botany and Genetics, Vilnius University, Vilnius, Lithuania
| | - Siim Kahar
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Lilian Pukk
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Oksana Burimski
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Riho Gross
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Anti Vasemägi
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| |
Collapse
|
2
|
Heraghty SD, Jackson JM, Lozier JD. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii. Mol Ecol 2023; 32:5479-5497. [PMID: 37702957 DOI: 10.1111/mec.17125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.
Collapse
Affiliation(s)
- Sam D Heraghty
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jason M Jackson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| |
Collapse
|
3
|
Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023; 32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
Collapse
Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | | | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | | |
Collapse
|
4
|
Chakraborty D, Arefin P, Bhattacharjee SC, Hasan M, Sarkar R, Das S, Rahman S, Habib MS, Islam S, Jahan F, Ray G, Ferdous J, Farhana F, Islam MA, Mostafa M. Biological activity of Mesua ferrea (Nageswar) seed extracts: An in vitro and in silico study. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
5
|
Shelke RG, Rangan L. The whole chloroplast genome of Mesua ferrea: Insight into the dynamic pattern of evolution and its comparison with species from recently diverged families. Gene 2022; 846:146866. [PMID: 36084895 DOI: 10.1016/j.gene.2022.146866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 08/12/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Mesua ferrea is an important source of timber, oil and herbal medicines. In the present investigation, we assembled the whole chloroplast genome of M. ferrea of size 161.4 kb. The genome contained 86 protein-coding genes, 38 tRNAs, 8 rRNA genes and exhibited a characteristic quadripartite structural orientation, with two inverted repeats (27,614 bp) separated by an LSC (88,746 bp) region and an SSC (27,614 bp) (17,470 bp). Interestingly, no gene loss was identified in the M. ferrea genome, contrary to what has been observed in other Clusioid species. We compared the chloroplast genome of M. ferrea with the chloroplast genome of Bonnetia and Garcinia belonging to Bonnetiaceae and Clusiaceae families. Overall, the compared genomes possess a similar synteny of gene order except for a small inversion in Garcinia species. M. ferrea has the largest chloroplast genome size in Clusioid clade owing to the lengthening of the LSC, IR, and non-coding regions. Substantial differences were observed in population of simple sequence repeats (SSRs) and RNA editing sites among the studied genomes. A comparative assessment of chloroplast genomes revealed five highly divergence regions: rpl32, trnS-GCU_trnG-UCC, petN-psbM, psbZ_trnG-GCC and ccsA_ndhD among the analyzed sequences. Phylogenetic analyses and sequence homology search indicate that M. ferrea is closely related to the Garcinia species.
Collapse
Affiliation(s)
- Rahul G Shelke
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781 039, India
| | - Latha Rangan
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781 039, India.
| |
Collapse
|
6
|
The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
Collapse
|
7
|
Chakraborty A, Mahajan S, Bisht MS, Sharma VK. Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity. iScience 2022; 25:105100. [PMID: 36164650 PMCID: PMC9508489 DOI: 10.1016/j.isci.2022.105100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
Ficus benghalensis and Ficus religiosa are large woody trees well known for their long lifespan, ecological and traditional significance, and medicinal properties. To understand the genomic and evolutionary aspects of these characteristics, the whole genomes of these Ficus species were sequenced using 10x Genomics linked reads and Oxford Nanopore long reads. The draft genomes of F. benghalensis and F. religiosa comprised of 392.89 Mbp and 332.97 Mbp, respectively. We established the genome-wide phylogenetic positions of the two Ficus species with respect to 50 other Angiosperm species. Comparative evolutionary analyses with other phylogenetically closer Eudicot species revealed adaptive evolution in genes involved in key cellular mechanisms associated with prolonged survival including phytohormones signaling, senescence, disease resistance, and abiotic stress tolerance, which provide genomic insights into the mechanisms conferring longevity and suggest that longevity is a multifaceted phenomenon. This study also provides clues on the existence of CAM pathway in these Ficus species.
Collapse
Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| | - Manohar S. Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| |
Collapse
|
8
|
Wu S, Malaco Morotti AL, Wang S, Wang Y, Xu X, Chen J, Wang G, Tatsis EC. Convergent gene clusters underpin hyperforin biosynthesis in St John's wort. THE NEW PHYTOLOGIST 2022; 235:646-661. [PMID: 35377483 DOI: 10.1111/nph.18138] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The meroterpenoid hyperforin is responsible for the antidepressant activity of St John's wort extracts, but the genes controlling its biosynthesis are unknown. Using genome mining and biochemical work, we characterize two biosynthetic gene clusters (BGCs) that encode the first three steps in the biosynthesis of hyperforin precursors. The findings of syntenic and phylogenetic analyses reveal the parallel assembly of the two BGCs. The syntenous BGC in Mesua ferrea indicates that the first cluster was assembled before the divergence of the Hypericaceae and Calophyllaceae families. The assembly of the second cluster is the result of a coalescence of genomic fragments after a major duplication event. The differences between the two BGCs - in terms of gene expression, response to methyl jasmonate, substrate specificity and subcellular localization of key enzymes - suggest that the presence of the two clusters could serve to generate separate pools of precursors. The parallel assembly of two BGCs with similar compositions in a single plant species is uncommon, and our work provides insights into how and when these gene clusters form. Our discovery helps to advance our understanding of the evolution of plant specialized metabolism and its genomic organization. Additionally, our results offer a foundation from which hyperforin biosynthesis can be more fully understood, and which can be used in future metabolic engineering applications.
Collapse
Affiliation(s)
- Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
| | - Shanshan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
| | - Ya Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyan Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla County, 666303, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
- CEPAMS - Centre of Excellence for Plant and Microbial Science, Shanghai, 200032, China
| |
Collapse
|
9
|
Antiallergic Properties of Biflavonoids Isolated from the Flowers of Mesua ferrea Linn. SEPARATIONS 2022. [DOI: 10.3390/separations9050127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The methanolic extract from the flowers of Mesua ferrea Linn. (Calophyllaceae) showed significant hyaluronidase inhibitory activity. Following a bioassay-guided separation of the extract, two biflavonoids, viz., mesuaferrone-A (1) and mesuaferrone-B (2), were isolated, along with ten flavonoids (3–12), two xanthones (13 and 14), three triterpenes (15–17), a phenylpropanoid (18), and five aromatics (19–24). Among the isolates, 1 and 2 (IC50 = 51.1 µM and 54.7 µM, respectively) exhibited hyaluronidase inhibitory activity equivalent to that of the commercially available antiallergic agents disodium cromoglycate (64.8 μM) and ketotifen fumarate (76.5 μM). These biflavonoids (1 and 2) are 8-8″ linked dimers that are composed of naringenin (1a) or apigenin (3), with their corresponding monomers lacking inhibitory activity (IC50 > 300 μM). In addition, 1 and 2 (IC50 = 49.4 µM and 49.2 µM, respectively) inhibited the release of β-hexosaminidase, which is a marker of antigen-IgE-mediated degranulation, in rat basophilic leukemia (RBL-2H3) cells. These inhibitory activities were more potent than those of the antiallergic agents tranilast and ketotifen fumarate (IC50 = 282 μM and 158 μM, respectively), as well as one of the corresponding monomers (1a; IC50 > 100 μM). Nonetheless, these effects were weaker than those of the other monomer (3; IC50 = 6.1 μM).
Collapse
|
10
|
Patil AB, Vijay N. Repetitive genomic regions and the inference of demographic history. Heredity (Edinb) 2021; 127:151-166. [PMID: 34002046 PMCID: PMC8322061 DOI: 10.1038/s41437-021-00443-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Inference of demographic histories using whole-genome datasets has provided insights into diversification, adaptation, hybridization, and plant-pathogen interactions, and stimulated debate on the impact of anthropogenic interventions and past climate on species demography. However, the impact of repetitive genomic regions on these inferences has mostly been ignored by masking of repeats. We use the Populus trichocarpa genome (Pop_tri_v3) to show that masking of repeat regions leads to lower estimates of effective population size (Ne) in the distant past in contrast to an increase in Ne estimates in recent times. However, in human datasets, masking of repeats resulted in lower estimates of Ne at all time points. We demonstrate that repeats affect demographic inferences using diverse methods like PSMC, MSMC, SMC++, and the Stairway plot. Our genomic analysis revealed that the biases in Ne estimates were dependent on the repeat class type and its abundance in each atomic interval. Notably, we observed a weak, yet consistently significant negative correlation between the repeat abundance of an atomic interval and the Ne estimates for that interval, which potentially reflects the recombination rate variation within the genome. The rationale for the masking of repeats has been that variants identified within these regions are erroneous. We find that polymorphisms in some repeat classes occur in callable regions and reflect reliable coalescence histories (e.g., LTR Gypsy, LTR Copia). The current demography inference methods do not handle repeats explicitly, and hence the effect of individual repeat classes needs careful consideration in comparative analysis. Deciphering the repeat demographic histories might provide a clear understanding of the processes involved in repeat accumulation.
Collapse
Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
| |
Collapse
|
11
|
Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
Collapse
Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
| |
Collapse
|