Limits...
Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.

Hao DC, Xiao PG - Evol. Bioinform. Online (2015)

Bottom Line: Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide.The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development.Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, P. R. China.

ABSTRACT
Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

No MeSH data available.


Technology roadmap of RAD-Seq and its utility in population evolution and genetic map.Abbreviations: PE, paired end; QC, quality control; InDel, insertion and deletion; SV, splice variant; PCA, principal component analysis; QTL, quantitative trait loci.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4597484&req=5

f1-ebo-11-2015-197: Technology roadmap of RAD-Seq and its utility in population evolution and genetic map.Abbreviations: PE, paired end; QC, quality control; InDel, insertion and deletion; SV, splice variant; PCA, principal component analysis; QTL, quantitative trait loci.

Mentions: As there is a lack of comprehensive molecular genetic studies on most medicinal plants, it is vital to have some preliminary genome evaluations done before whole-genome sequencing. First, DNA barcoding techniques13 could be used to authenticate the candidate species; second, karyotypes should be determined by observing metaphase chromosomes; last, flow cytometry and pulsed-field gel electrophoresis (PFGE)9,14 could be used to determine the ploidy level and genome size. For example, flow cytometry was used to determine the genome size of four Panax species15 with Oryza sativa as the internal standard. P. notoginseng (San Qi in traditional Chinese medicine) has the largest genome (2454.38 Mb), followed by P. pseudoginseng (2432.72 Mb), P. vietnamensis (2018.02 Mb), and P. stipuleanatus (1947.06 Mb), but their genomes are smaller than the P. ginseng genome (~3.2 Gb). A more reliable approach for species identification without the reference genome is the genome survey via the whole-genome shotgun sequencing.16 Such non-deep sequencing (30√ócoverage), followed by the bioinformatics analysis, is highly valuable in assessing the genome size, heterozygosity, repeat sequence, GC content, etc, facilitating decision making on the whole-genome sequencing approaches. In addition, RAD-Seq (restriction-site associated DNA sequencing; Fig. 1)17 could be chosen to construct a RAD library and perform the low-coverage genome sequencing of reduced representation, which is an effective approach for assessing the heterozygosity of the candidate genome.


Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.

Hao DC, Xiao PG - Evol. Bioinform. Online (2015)

Technology roadmap of RAD-Seq and its utility in population evolution and genetic map.Abbreviations: PE, paired end; QC, quality control; InDel, insertion and deletion; SV, splice variant; PCA, principal component analysis; QTL, quantitative trait loci.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4597484&req=5

f1-ebo-11-2015-197: Technology roadmap of RAD-Seq and its utility in population evolution and genetic map.Abbreviations: PE, paired end; QC, quality control; InDel, insertion and deletion; SV, splice variant; PCA, principal component analysis; QTL, quantitative trait loci.
Mentions: As there is a lack of comprehensive molecular genetic studies on most medicinal plants, it is vital to have some preliminary genome evaluations done before whole-genome sequencing. First, DNA barcoding techniques13 could be used to authenticate the candidate species; second, karyotypes should be determined by observing metaphase chromosomes; last, flow cytometry and pulsed-field gel electrophoresis (PFGE)9,14 could be used to determine the ploidy level and genome size. For example, flow cytometry was used to determine the genome size of four Panax species15 with Oryza sativa as the internal standard. P. notoginseng (San Qi in traditional Chinese medicine) has the largest genome (2454.38 Mb), followed by P. pseudoginseng (2432.72 Mb), P. vietnamensis (2018.02 Mb), and P. stipuleanatus (1947.06 Mb), but their genomes are smaller than the P. ginseng genome (~3.2 Gb). A more reliable approach for species identification without the reference genome is the genome survey via the whole-genome shotgun sequencing.16 Such non-deep sequencing (30√ócoverage), followed by the bioinformatics analysis, is highly valuable in assessing the genome size, heterozygosity, repeat sequence, GC content, etc, facilitating decision making on the whole-genome sequencing approaches. In addition, RAD-Seq (restriction-site associated DNA sequencing; Fig. 1)17 could be chosen to construct a RAD library and perform the low-coverage genome sequencing of reduced representation, which is an effective approach for assessing the heterozygosity of the candidate genome.

Bottom Line: Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide.The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development.Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, P. R. China.

ABSTRACT
Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

No MeSH data available.