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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2024; 23:579-594. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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Mano H, Boltenkov EV, Marchuk EA, Nakamura K, Yoichi W. The complete chloroplast genome sequence of Hypecoum erectum L. (Papaveraceae). Mitochondrial DNA B Resour 2024; 9:1010-1014. [PMID: 39113749 PMCID: PMC11305052 DOI: 10.1080/23802359.2024.2386410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Hypecoum erectum L., a widespread species in northern Eurasia, is a valuable medicinal plant, but its chloroplast genome has not previously been reported. We determined its complete chloroplast genome using a high-throughput sequencing technique. Its total length was 169,241 bp, consisting of a large single-copy region of 93,301 bp and a small single-copy region of 17,316 bp, separated by a pair of inverted repeat regions of 29,312 bp. A total of 140 genes were annotated, including 91 protein coding genes, 41 tRNA genes, and eight rRNA genes. The phylogenetic analysis shows that H. erectum and H. zhukanum of the subfamily Hypecoideae are monophyletic with the highest support.
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Affiliation(s)
- Haruto Mano
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Eugeny V. Boltenkov
- Botanical Garden-Institute, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Elena A. Marchuk
- Botanical Garden-Institute, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
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Kim SC, Ha YH, Park BK, Jang JE, Kang ES, Kim YS, Kimspe TH, Kim HJ. Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. PLoS One 2023; 18:e0289625. [PMID: 37733832 PMCID: PMC10513226 DOI: 10.1371/journal.pone.0289625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/24/2023] [Indexed: 09/23/2023] Open
Abstract
Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.
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Affiliation(s)
- Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Beom Kyun Park
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ju Eun Jang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Eun Su Kang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Soo Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Tae-Hee Kimspe
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
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Yin X, Huang F, Liu X, Guo J, Cui N, Liang C, Lian Y, Deng J, Wu H, Yin H, Jiang G. Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis. Sci Rep 2022; 12:14241. [PMID: 35987818 PMCID: PMC9392791 DOI: 10.1038/s41598-022-17721-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/29/2022] [Indexed: 11/26/2022] Open
Abstract
Corydalis is one of the few lineages that have been reported to have extensive large-scale chloroplast genome (cp-genome) rearrangements. In this study, novel cp-genome rearrangements of Corydalis pinnata, C. mucronate, and C. sheareri are described. C. pinnata is a narrow endemic species only distributed at Qingcheng Mountain in southwest China. Two independent relocations of the same four genes (trnM-CAU-rbcL) were found relocated from the typically posterior part of the large single-copy region to the front of it. A uniform inversion of an 11-14-kb segment (ndhB-trnR-ACG) was found in the inverted repeat region; and extensive losses of accD, clpP, and trnV-UAC genes were detected in all cp-genomes of all three species of Corydalis. In addition, a phylogenetic tree was reconstructed based on 31 single-copy orthologous proteins in 27 cp-genomes. This study provides insights into the evolution of cp-genomes throughout the genus Corydalis and also provides a reference for further studies on the taxonomy, identification, phylogeny, and genetic transformation of other lineages with extensive rearrangements in cp-genomes.
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Affiliation(s)
- Xianmei Yin
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China
| | - Feng Huang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China
| | - Xiaofen Liu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China
| | - Jiachen Guo
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China
| | - Ning Cui
- Central Laboratory, Shandong Academy of Chinese Medicine, Jinan, 250014, China
| | - Conglian Liang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Yan Lian
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China
| | - Jingjing Deng
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China
| | - Hao Wu
- Central Laboratory, Shandong Academy of Chinese Medicine, Jinan, 250014, China
| | - Hongxiang Yin
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China.
| | - Guihua Jiang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chendu, 611130, China.
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Xu X, Li X, Wang D. New Insights Into the Backbone Phylogeny and Character Evolution of Corydalis (Papaveraceae) Based on Plastome Data. FRONTIERS IN PLANT SCIENCE 2022; 13:926574. [PMID: 35991421 PMCID: PMC9389321 DOI: 10.3389/fpls.2022.926574] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 05/27/2023]
Abstract
A robust backbone phylogeny is fundamental for developing a stable classification and is instructive for further research. However, it was still not available for Corydalis DC., a species-rich (> 500 species), ecologically and medically important, but taxonomically notoriously difficult genus. Here, we constructed backbone phylogeny and estimated the divergence of Corydalis based on the plastome data from 39 Corydalis species (32 newly sequenced), which represent ca. 80% of sections and series across this genus. Our phylogenetic analyses recovered six fully supported main clades (I-VI) and provided full support for the majority of lineages within Corydalis. Section Archaeocapnos was unexpectedly turned out to be sister to the rest of the subg. Corydalis s. l. (clades IV-VI), thus treating as a distinct clade (clade III) to render all the main clades monophyletic. Additionally, some unusual plastome structural rearrangements were constantly detected within Corydalis and were proven to be lineage-specific in this study, which, in turn, provided further support to our phylogeny. A segment containing five genes (trnV-UAC-rbcL) in the plastome's LSC region was either normally located downstream of the ndhC gene in clade I species or translocated downstream of the atpH gene in clade II species or translocated to downstream of the trnK-UUU gene in clade III-VI species. The unique large inversion (ca. 50 kb) in the plastome LSC region of clade III species, representing an intermediate stage of the above translocation in clades IV-VI, firmly supported clade III as a distinct and early diverged clade within this large lineage (clades III-VI). Our phylogeny contradicted substantially with the morphology-based taxonomy, rejected the treatment of tuberous species as an independent evolutionary group, and proved that some commonly used diagnostic characters (e.g., root and rhizome) were results of convergent evolution, suggestive of unreliability in Corydalis. We dated the origin of crown Corydalis to the early Eocene (crown age 49.08 Ma) and revealed possible explosive radiation around 25 Ma, coinciding with the drastic uplift of the Qinghai-Tibetan Plateau in Oligocene and Miocene. This study provided the most reliable and robust backbone phylogeny of Corydalis to date and shed some new insights on the evolution of Corydalis.
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Affiliation(s)
- Xiaodong Xu
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xuexiu Li
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Dong Wang
- School of Life Sciences, Central China Normal University, Wuhan, China
- Bio-Resources key Laboratory of Shaanxi Province, Shaanxi University of Technology, Hanzhong, China
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