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Roestel JA, Wiersema JH, Jansen RK, Borsch T, Gruenstaeudl M. On the importance of sequence alignment inspections in plastid phylogenomics - an example from revisiting the relationships of the water-lilies. Cladistics 2024. [PMID: 38761095 DOI: 10.1111/cla.12584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/20/2024] Open
Abstract
The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.
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Affiliation(s)
- Jessica A Roestel
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| | - John H Wiersema
- Department of Botany, National Museum of Natural History - Smithsonian Institution, Washington, DC, 37012, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas Borsch
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Department of Biological Sciences, Fort Hays State University, Hays, KS, 67601, USA
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2
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Panklai T, Suphrom N, Temkitthawon P, Totoson P, Chootip K, Yang XL, Ge HM, Yao ZJ, Chaichamnong N, Ingkaninan K, Girard C. Phosphodiesterase 5 and Arginase Inhibitory Activities of the Extracts from Some Members of Nelumbonaceae and Nymphaeaceae Families. Molecules 2023; 28:5821. [PMID: 37570790 PMCID: PMC10420992 DOI: 10.3390/molecules28155821] [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: 05/27/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
The objectives of this study were (1) to investigate the effect of extracts from some plants in the families Nelumbonaceae and Nymphaeaceae on phosphodiesterase 5 (PDE5) and arginase, which have been used in erectile dysfunction treatment, and (2) to isolate and identify the compounds responsible for such activities. The characterization and quantitative analysis of flavonoid constituents in the active extracts were performed by HPLC. Thirty-seven ethanolic extracts from different parts of plants in the genus Nymphaea and Victoria of Nymphaeaceae and genus Nelumbo of Nelumbonaceae were screened for PDE5 and arginase inhibitory activities. The ethanolic extracts of the receptacles and pollens of Nelumbo nucifera Gaertn., petals of Nymphaea cyanea Roxb. ex G.Don, Nymphaea stellata Willd., and Victoria amazonica (Poepp.) Sowerby and the petals and receptacles of Nymphaea pubescens Willd. showed IC50 values on PDE5 of less than 25 μg/mL while none of the extracts showed effects on arginase. The most active extract, N. pubescens petal extract, was fractionated to isolate and identify the PDE5 inhibitors. The results showed that six flavonoid constituents including quercetin 3'-O-β-xylopyranoside (1), quercetin 3-methyl ether 3'-O-β-xylopyranoside (2), quercetin (3), 3-O-methylquercetin (4), kaempferol (5) and 3-O-methylkaempferol (6) inhibited PDE5 with IC50 values at the micromolar level.
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Affiliation(s)
- Teerapap Panklai
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand; (T.P.); (P.T.)
- Université de Franche-Comté, PEPITE, 25000 Besançon, France; (P.T.); (C.G.)
| | - Nungruthai Suphrom
- Department of Chemistry, Faculty of Science and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand;
| | - Prapapan Temkitthawon
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand; (T.P.); (P.T.)
| | - Perle Totoson
- Université de Franche-Comté, PEPITE, 25000 Besançon, France; (P.T.); (C.G.)
| | - Krongkarn Chootip
- Department of Physiology, Faculty of Medical Science and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand;
| | - Xiao-Liang Yang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advance Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; (X.-L.Y.); (Z.-J.Y.)
| | - Hui-Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China;
| | - Zhu-Jun Yao
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advance Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; (X.-L.Y.); (Z.-J.Y.)
| | - Nattiya Chaichamnong
- Division of Applied Thai Traditional Medicine, Faculty of Public Health, Naresuan University, Phitsanulok 65000, Thailand;
| | - Kornkanok Ingkaninan
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand; (T.P.); (P.T.)
| | - Corine Girard
- Université de Franche-Comté, PEPITE, 25000 Besançon, France; (P.T.); (C.G.)
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Henning T, Acuña-Castillo R, Cornejo X, Gonzáles P, Segovia E, Wong Sato AA, Weigend M. When the absence of evidence is not the evidence of absence: Nasa (Loasaceae) rediscoveries from Peru and Ecuador, and the contribution of community science networks. PHYTOKEYS 2023; 229:1-19. [PMID: 38313362 PMCID: PMC10838191 DOI: 10.3897/phytokeys.229.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/08/2023] [Indexed: 02/06/2024]
Abstract
Documentation of plant taxa has long been subject to the temporal and spatial selectivity of professional research expeditions, especially in tropical regions. Therefore, rare and/or narrowly endemic species are sometimes known only from very few and very old herbarium specimens. However, these taxa are very important from a conservation perspective. The lack of observations of living plants and confirmation of the actual occurrence of taxa hinders the planning and implementation of effective conservation measures. Community science networks have recently made tremendous contributions to documenting biodiversity in many regions across the globe. The rediscovery of six species of Nasa (Loasaceae) from Peru and Ecuador primarily via the platform iNaturalist, is reported.
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Affiliation(s)
- Tilo Henning
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Rafael Acuña-Castillo
- Escuela de Biología, Universidad de Costa Rica, Apdo. Postal 11501-2060, San Pedro de Montes de Oca, San José, Costa Rica
| | - Xavier Cornejo
- Herbario Luis A. Fournier Origgi, Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), Universidad de Costa Rica, Apdo. Postal 11501-2060, San Pedro de Montes de Oca, San José, Costa Rica
| | - Paúl Gonzáles
- Herbario GUAY, Departamento de Botánica, Facultad de Ciencias Naturales, Universidad de Guayaquil, P.O. Box 09-01-10634, Guayaquil, Ecuador
| | - Edgar Segovia
- Laboratorio de Florística, Departamento de Dicotiledóneas, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Jesús María, Peru
| | | | - Maximilian Weigend
- Plant Ecology Division, CORBIDI, Calle Santa Rita 105 Of. 2, Urb. Huertos de San Antonio Monterrico, Lima, Surco, Peru
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Zhang H, Ding J, Holstein N, Wang N. Betula mcallisteri sp. nov. (sect. Acuminatae, Betulaceae), a new diploid species overlooked in the wild and in cultivation, and its relation to the widespread B. luminifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1113274. [PMID: 37324661 PMCID: PMC10268003 DOI: 10.3389/fpls.2023.1113274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/19/2023] [Indexed: 06/17/2023]
Abstract
Taxa are traditionally identified using morphological proxies for groups of evolutionarily isolated populations. These proxies are common characters deemed by taxonomists as significant. However, there is no general rule on which character or sets of characters are appropriate to circumscribe taxa, leading to discussions and uncertainty. Birch species are notoriously hard to identify due to strong morphological variability and factors such as hybridization and the existence of several ploidy levels. Here, we present evidence for an evolutionarily isolated line of birches from China that are not distinguishable by traditionally assumed taxon recognition proxies, such as fruit or leaf characters. We have discovered that some wild material in China and some cultivated in the Royal Botanic Gardens Edinburgh, formerly recognized as Betula luminifera, differ from other individuals by having a peeling bark and a lack of cambial fragrance. We use restriction site-associated DNA sequencing and flow cytometry to study the evolutionary status of the unidentified Betula samples to assess the extent of hybridization between the unidentified Betula samples and typical B. luminifera in natural populations. Molecular analyses show the unidentified Betula samples as a distinct lineage and reveal very little genetic admixture between the unidentified samples and B. luminifera. This may also be facilitated by the finding that B. luminifera is tetraploid, while the unidentified samples turned out to be diploid. We therefore conclude that the samples represent a yet unrecognized species, which is here described as Betula mcallisteri.
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Affiliation(s)
- Huayu Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of The Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Junyi Ding
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of The Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Norbert Holstein
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Nian Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of The Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
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5
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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6
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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de Mestier A, Lücking R, Gutierrez J, Brokamp G, Celis M, Borsch T. Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae). Ecol Evol 2023; 13:e9736. [PMID: 36694555 PMCID: PMC9843533 DOI: 10.1002/ece3.9736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well-distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy.
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Affiliation(s)
- Astrid de Mestier
- Botanischer GartenFreie Universität BerlinBerlinGermany,Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
| | | | - Jorge Gutierrez
- Jardín Botánico Nacional CalabazarUniversidad de La HabanaBoyerosCuba
| | - Grischa Brokamp
- Botanischer GartenFreie Universität BerlinBerlinGermany,Fachbereich Wald und UmweltHochschule für Nachhaltige Entwicklung EberswaldeEberswaldeGermany
| | - Marcela Celis
- Departamento de Química y BiologíaUniversidad del NorteBarranquillaColombia
| | - Thomas Borsch
- Botanischer GartenFreie Universität BerlinBerlinGermany,Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
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