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Liu LJ, Liu CK, Cai J, Deng JJ, He XJ, Zhou SD. The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis. BMC PLANT BIOLOGY 2024; 24:106. [PMID: 38342898 PMCID: PMC10860227 DOI: 10.1186/s12870-024-04784-4] [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: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND The genus Libanotis Haller ex Zinn, nom. cons., a contentious member of Apiaceae, encompasses numerous economically and medicinally significant plants, comprising approximately 30 species distributed across Eurasia. Despite many previous taxonomic insights into it, phylogenetic studies of the genus are still lacking. And the establishment of a robust phylogenetic framework remains elusive, impeding advancements and revisions in the taxonomic system for this genus. Plastomes with greater variability in their genetic characteristics hold promise for building a more robust Libanotis phylogeny. RESULTS During our research, we sequenced, assembled, and annotated complete plastomes for twelve Libanotis species belong to three sections and two closely related taxa. We conducted a comprehensive comparative analysis through totally thirteen Libanotis plastomes for the genus, including an additional plastome that had been published. Our results suggested that Libanotis plastome was highly conserved between different subclades, while the coding regions were more conserved than the non-coding regions, and the IR regions were more conserved than the single copy regions. Nevertheless, eight mutation hotspot regions were identified among plastomes, which can be considered as candidate DNA barcodes for accurate species identification in Libanotis. The phylogenetic analyses generated a robustly framework for Libanotis and revealed that Libanotis was not a monophyletic group and their all three sections were polygenetic. Libanotis schrenkiana was sister to L. sibirica, type species of this genus, but the remainders scattered within Selineae. CONCLUSION The plastomes of Libanotis exhibited a high degree of conservation and was effective in enhancing the support and resolution of phylogenetic analyses within this genus. Based on evidence from both phylogeny and morphology, we propose the recognition of "Libanotis sensu stricto" and provide taxonomic recommendations for other taxa that previously belonged to Libanotis. In conclusion, our study not only revealed the phylogenetic position and plastid evolution of Libanotis, but also provided new insights into the phylogeny of the family Apiaceae and phylogenetic relationships within the tribe Selineae.
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Affiliation(s)
- Li-Jia Liu
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- College of Resources Environment and Chemistry, Chuxiong Normal University, Chuxiong, 675000, China
| | - Jing Cai
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jiao-Jiao Deng
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Song-Dong Zhou
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Mazumdar P, Jalaluddin NSM, Nair I, Tian Tian T, Rejab NAB, Harikrishna JA. A review of Hydrocotyle bonariensis, a promising functional food and source of health-related phytochemicals. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:2503-2516. [PMID: 37599849 PMCID: PMC10439074 DOI: 10.1007/s13197-022-05516-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/02/2022] [Accepted: 05/26/2022] [Indexed: 08/22/2023]
Abstract
Hydrocotyle bonariensis is an edible herb, that is also used for traditional medical purposes. It is high in antioxidants, phenols, and flavonoids. However, there is limited information on the nutritional composition and the mechanisms by which nutritional and functional constituents of H. bonariensis affect human metabolism. With an aim to identify gaps in evidence to support the mainstream use of H. bonariensis for health and as a functional food, this review summarises current knowledge of the taxonomy, habitat characteristics, nutritional value and health-related benefits of H. bonariensis and its extracts. Ethno-medical practices for the plant are supported by pharmacological studies, yet animal model studies, clinical trials and food safety assessments are needed to support the promotion of H. bonariensis and its derivatives as superfoods and for use in the modern pharmaceutical industry.
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Affiliation(s)
- Purabi Mazumdar
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Indiran Nair
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Tan Tian Tian
- Green World Genetics Sdn. Bhd, 52200 Kuala Lumpur, Malaysia
| | - Nur Ardiyana Binti Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Cai H, Ren Y, Du J, Liu L, Long L, Yang M. Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species. Int J Mol Sci 2023; 24:12954. [PMID: 37629135 PMCID: PMC10454583 DOI: 10.3390/ijms241612954] [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: 02/13/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860-157,025 bp in length, with 37.58-37.6% GC content. Repeat analysis showed that the Deutzia species had 41-45 scattered repeats and 199-201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29-31 RNA editing events and 163-194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp.
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Affiliation(s)
- Hongyu Cai
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Yachao Ren
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Juan Du
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Shijiazhuang Botanical Garden, Shijiazhuang 050299, China
| | - Lingyun Liu
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Lianxiang Long
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Minsheng Yang
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
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Zheng HY, Guo XL, Price M, He XJ, Zhou SD. Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:673200. [PMID: 34108984 PMCID: PMC8183463 DOI: 10.3389/fpls.2021.673200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/07/2021] [Indexed: 05/13/2023]
Abstract
Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.
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Affiliation(s)
- Hong-Yi Zheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Cuevas Guzmán R, Nuñez-López NM, Canales-Piña S, Morales-Arias JG. Prionosciadium tamayoi (Apiaceae), una especie nueva del occidente de México. REV MEX BIODIVERS 2020. [DOI: 10.22201/ib.20078706e.2020.91.3338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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