Plant DNA Barcodes, Community Ecology, and Species Interactions

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (30 January 2022) | Viewed by 51587

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Special Issue Editors


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Guest Editor
Department of Botany, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
Interests: biodiversity genomics; DNA barcoding; plant-animal interactions; conservation; The Anthropocene; Zingiberales
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Guest Editor
Fort Worth Botanic Garden, 3220 Botanic Garden Blvd, Fort Worth, TX 76107, USA Botanical Research Institute of Texas, 1700 University Dr, Fort Worth, TX 76107, USA
Interests: biogeography; genomics; phylogenetics; systematics; taxonomy; Compositae; Burseraceae; conservation

Special Issue Information

Dear Colleagues,

The community of biologists has been eager to realize the promise of DNA barcodes since the concept was first proposed in 2003. As we approach twenty years of DNA barcoding, their application continues to increase and methods continue to be developed that utilize this ever-expanding resource for multiple fields of biology. The nearly ten million DNA barcodes available today provide a database that is especially useful for ecology and evolutionary biology. In particular, DNA barcodes provide a rapid resource to identify taxa; quantify and understand species richness; and determine community interactions in primary and secondary habitats. Many ecologists are concerned with the assembly and maintenance of species richness at local and regional scales, which has driven empirical and conceptual advances in the field of community ecology. Evolutionary biologists focus on the description and classification of species diversity, factors controlling the origin and ancestry of biodiversity, and the network of interactions that connect evolutionary units through time and space.  Thanks to these large and well-curated DNA barcoding resources fundamental biological questions can be more rigorously addressed regarding community evolution, assembly, productivity, and species interactions across and among diverse habitats and organisms, including plants, animals, fungi, and microorganisms. DNA barcodes are now routinely used to discover new species, to determine phylogenetic patterns of community diversity, and to uncover the complexities of interactions in almost all domains of life to understand diets, symbioses, pollinator networks, and historically challenging biomes, such as below-ground soil and deep-water marine communities.  This Special Issue will illustrate the wide variety of applications of DNA barcodes, especially in plants, to address questions in ecology and evolutionary biology.

Dr. W. John Kress
Dr. Morgan R. Gostel
Guest Editors

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Keywords

  • DNA barcodes
  • community ecology
  • species interactions
  • evolution
  • species discovery
  • pollination
  • herbivory
  • plants
  • animals
  • fungi
  • microorganisms

Published Papers (12 papers)

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Editorial

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3 pages, 174 KiB  
Editorial
Plant DNA Barcodes, Community Ecology, and Species Interactions
by W. John Kress and Morgan R. Gostel
Diversity 2022, 14(6), 453; https://doi.org/10.3390/d14060453 - 6 Jun 2022
Viewed by 1769
Abstract
The community of biologists has been eager to realize the promise of DNA barcodes since the concept of a rapid method for genetic identification of species was first proposed in 2003 [...] Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)

Research

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20 pages, 2639 KiB  
Article
DNA Barcoding to Enhance Conservation of Sunshine Coast Heathlands
by Hilary Pearl, Tim Ryan, Marion Howard, Yoko Shimizu and Alison Shapcott
Diversity 2022, 14(6), 436; https://doi.org/10.3390/d14060436 - 29 May 2022
Cited by 5 | Viewed by 2795
Abstract
Conservation priorities and decisions can be informed by understanding diversity patterns and the evolutionary history of ecosystems, and phylogenetic metrics can contribute to this. This project used a range of diversity metrics in concert to examine diversity patterns in the Sunshine Coast heathlands, [...] Read more.
Conservation priorities and decisions can be informed by understanding diversity patterns and the evolutionary history of ecosystems, and phylogenetic metrics can contribute to this. This project used a range of diversity metrics in concert to examine diversity patterns in the Sunshine Coast heathlands, an ecosystem under intense pressure. The species richness and composition of 80 heathland sites over nine regional ecosystems of heathland on the Sunshine Coast were enhanced with phylogenetic metrics, determined by barcoding 366 heath species of the region. The resulting data were added to an existing phylogeny of regional rainforest species. The diversity metrics for sites and regional ecosystems were compared using univariate and multivariate statistics. The phylogeny from this study, and the low phylogenetic diversity of the heathlands, is consistent with the theory that heath species evolved on the fringes on a wider Australian rainforest flora. Distinctive heathland communities were highlighted, and the existence of geographically scattered, but compositionally similar, phylogenetically even sites points to a possible “refugial environment”, characterised by moisture and instability. This suggests contrasting conservation implications: the protection of distinctive communities but also the management of the dynamic processes in other wet and alluvial “refugial environments”. The potential for more focused conservation priorities is enhanced. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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33 pages, 7269 KiB  
Article
DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?
by Manuela Dal Forno, James D. Lawrey, Bibiana Moncada, Frank Bungartz, Martin Grube, Eric Schuettpelz and Robert Lücking
Diversity 2022, 14(4), 284; https://doi.org/10.3390/d14040284 - 10 Apr 2022
Cited by 7 | Viewed by 5345
Abstract
Lichens collected worldwide for centuries have resulted in millions of specimens deposited in herbaria that offer the potential to assess species boundaries, phenotypic diversification, ecology, and distribution. The application of molecular approaches to historical collections has been limited due to DNA fragmentation, but [...] Read more.
Lichens collected worldwide for centuries have resulted in millions of specimens deposited in herbaria that offer the potential to assess species boundaries, phenotypic diversification, ecology, and distribution. The application of molecular approaches to historical collections has been limited due to DNA fragmentation, but high-throughput sequencing offers an opportunity to overcome this barrier. Here, we combined a large dataset of ITS sequences from recently collected material and historical collections, obtained through Sanger, 454, or Illumina Sequencing, to test the performance of ITS barcoding in two genera of lichenized Basidiomycota: Cora and Corella. We attempted to generate new sequence data for 62 fresh specimens (from 2016) and 274 historical collections (collected between 1888 and 1998), for a final dataset of 1325 sequences. We compared various quantitative approaches to delimit species (GMYC, bPTP, ASAP, ABGD) and tested the resolution and accuracy of the ITS fungal barcoding marker by comparison with a six-marker dataset. Finally, we quantitatively compared phylogenetic and phenotypic species delimitation for 87 selected Cora species that have been formally described. Our HTS approach successfully generated ITS sequences for 76% of the historical collections, and our results show that an integrative approach is the gold-standard for understanding diversity in this group. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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16 pages, 2467 KiB  
Article
DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates
by Rahul Jamdade, Kareem A. Mosa, Ali El-Keblawy, Khawla Al Shaer, Eman Al Harthi, Mariam Al Sallani, Mariam Al Jasmi, Sanjay Gairola, Hatem Shabana and Tamer Mahmoud
Diversity 2022, 14(4), 262; https://doi.org/10.3390/d14040262 - 30 Mar 2022
Cited by 12 | Viewed by 4603
Abstract
The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital for safe usage, avoiding adulteration, and medicinal plant trading. DNA barcoding has shown to be a valuable molecular identification tool for medicinal plants, ensuring [...] Read more.
The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital for safe usage, avoiding adulteration, and medicinal plant trading. DNA barcoding has shown to be a valuable molecular identification tool for medicinal plants, ensuring the safety and efficacy of plant materials of therapeutic significance. Using morphological characters in genera with closely related species, species delimitation is often difficult. Here, we evaluated the capability of the nuclear barcode ITS2 and plastid DNA barcodes rbcL and matK to identify 20 medicinally important plant species of Caryophyllales. In our analysis, we applied an integrative approach for species discrimination using pairwise distance-based unsupervised operational taxonomic unit “OTU picking” methods, viz., ABGD (Automated Barcode Gap Analysis) and ASAP (Assemble Species by Automatic Partitioning). Along with the unsupervised OTU picking methods, Supervised Machine Learning methods (SML) were also implemented to recognize divergent taxa. Our results indicated that ITS2 was more successful in distinguishing between examined species, implying that it could be used to detect the contamination and adulteration of these medicinally important plants. Moreover, this study suggests that the combination of more than one method could assist in the resolution of morphologically similar or closely related taxa. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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5 pages, 237 KiB  
Article
Data Release: DNA Barcodes of Plant Species Collected for the Global Genome Initiative for Gardens (GGI-Gardens) II
by Morgan R. Gostel, Mónica M. Carlsen, Amanda Devine, Katharine B. Barker, Jonathan A. Coddington and Julia Steier
Diversity 2022, 14(4), 234; https://doi.org/10.3390/d14040234 - 23 Mar 2022
Cited by 2 | Viewed by 2326
Abstract
The Global Genome Initiative for Gardens (GGI-Gardens) is an international partnership of botanic gardens and arboreta that aims to preserve and understand the genomic diversity of plants on Earth. GGI-Gardens has organized a collection program focused on the living collections that partner institutions [...] Read more.
The Global Genome Initiative for Gardens (GGI-Gardens) is an international partnership of botanic gardens and arboreta that aims to preserve and understand the genomic diversity of plants on Earth. GGI-Gardens has organized a collection program focused on the living collections that partner institutions and supports the preservation of herbarium and genomic vouchers. Collections made through GGI-Gardens are deposited in recognized herbaria and Global Genome Biodiversity Network-partnered biorepositories worldwide, meaning that they are made available to the public. With support from its parent organization, the Global Genome Initiative (GGI), plant DNA barcode sequencing is performed using tissues collected through this partnership that represent taxa without barcode sequences in GenBank. This is the second data release published by GGI-Gardens and constitutes 2722 barcode sequences from 174 families and 702 genera of land plants. All DNA barcodes generated in this study are now available through the Barcode of Life Data Systems (BOLD) and GenBank. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
10 pages, 499 KiB  
Article
The Efficiency of DNA Barcoding in the Identification of Afromontane Forest Tree Species
by David Kenfack, Iveren Abiem and Hazel Chapman
Diversity 2022, 14(4), 233; https://doi.org/10.3390/d14040233 - 23 Mar 2022
Cited by 4 | Viewed by 3533
Abstract
The identification of flowering plants using DNA barcoding proposed in last decades has slowly gained ground in Africa, where it has been successfully used to elucidate the systematics and ecology of several plant groups, and to understand their evolutionary history. Existing inferences on [...] Read more.
The identification of flowering plants using DNA barcoding proposed in last decades has slowly gained ground in Africa, where it has been successfully used to elucidate the systematics and ecology of several plant groups, and to understand their evolutionary history. Existing inferences on the effectiveness of DNA barcoding to identify African trees are mostly based on lowland forests, whereas adjacent montane forests significantly differ from the latter floristically and structurally. Here, we tested the efficiency of chloroplast DNA barcodes (rbcLa, matK, and trnH-psbA) to identify Afromontane Forest tree species in a 20.28 ha permanent plot in Ngel Nyaki, Taraba state, Nigeria. We collected, identified, and vouchered 274 individuals with diameter at breast height ≥ 1 cm belonging to 101 morphospecies, 92 genera, and 48 families. rbcLa and matK used alone or in combination performed better than in lowland forests, with the best species discrimination obtained with the two-locus combination of matK + rbcLa. The intragenic spacer trnH-psbA was too variable to align and could not be tested using the genetic distance method employed. Classic DNA barcode can be a powerful tool to identify Afromontane tree species, mainly due to the non-prevalence in these communities of species—rich genera (low species-to-genus ratio) that constitute the biggest challenge of DNA barcoding of flowering plants. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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14 pages, 2272 KiB  
Article
Gradients in the Diversity of Plants and Large Herbivores Revealed with DNA Barcoding in a Semi-Arid African Savanna
by Patrick T. Freeman, Robert O. Ang’ila, Duncan Kimuyu, Paul M. Musili, David Kenfack, Peter Lokeny Etelej, Molly Magid, Brian A. Gill and Tyler R. Kartzinel
Diversity 2022, 14(3), 219; https://doi.org/10.3390/d14030219 - 17 Mar 2022
Cited by 8 | Viewed by 3811
Abstract
Do hotspots of plant biodiversity translate into hotspots in the abundance and diversity of large mammalian herbivores? A common expectation in community ecology is that the diversity of plants and animals should be positively correlated in space, as with the latitudinal diversity gradient [...] Read more.
Do hotspots of plant biodiversity translate into hotspots in the abundance and diversity of large mammalian herbivores? A common expectation in community ecology is that the diversity of plants and animals should be positively correlated in space, as with the latitudinal diversity gradient and the geographic mosaic of biodiversity. Whether this pattern ‘scales down’ to landscape-level linkages between the diversity of plants or the activities of highly mobile megafauna has received less attention. We investigated spatial associations between plants and large herbivores by integrating data from a plant-DNA-barcode phylogeny, camera traps, and a comprehensive map of woody plants across the 1.2-km2 Mpala Forest Global Earth Observatory (ForestGEO) plot, Kenya. Plant and large herbivore communities were strongly associated with an underlying soil gradient, but the richness of large herbivore species was negatively correlated with the richness of woody plants. Results suggest thickets and steep terrain create associational refuges for plants by deterring megaherbivores from browsing on otherwise palatable species. Recent work using dietary DNA metabarcoding has demonstrated that large herbivores often directly control populations of the plant species they prefer to eat, and our results reinforce the important role of megaherbivores in shaping vegetation across landscapes. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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14 pages, 1579 KiB  
Article
Assessment of ITS1, ITS2, 5′-ETS, and trnL-F DNA Barcodes for Metabarcoding of Poaceae Pollen
by Denis O. Omelchenko, Anastasia A. Krinitsina, Artem S. Kasianov, Anna S. Speranskaya, Olga V. Chesnokova, Svetlana V. Polevova and Elena E. Severova
Diversity 2022, 14(3), 191; https://doi.org/10.3390/d14030191 - 5 Mar 2022
Cited by 9 | Viewed by 4327
Abstract
Grass pollen is one of the major causes of allergy. Aerobiological monitoring is a necessary element of the complex of anti-allergic measures, but the similar pollen morphology of Poaceae species makes it challenging to discriminate species in airborne pollen mixes, which impairs the [...] Read more.
Grass pollen is one of the major causes of allergy. Aerobiological monitoring is a necessary element of the complex of anti-allergic measures, but the similar pollen morphology of Poaceae species makes it challenging to discriminate species in airborne pollen mixes, which impairs the quality of aerobiological monitoring. One of the solutions to this problem is the metabarcoding approach employing DNA barcodes for taxonomical identification of species in a mix by high-throughput sequencing of the pollen DNA. A diverse set of 14 grass species of different genera were selected to create a local reference database of nuclear ITS1, ITS2, 5′-ETS, and plastome trnL-F DNA barcodes. Sequences for the database were Sanger sequenced from live field and herbarium specimens and collected from GenBank. New Poaceae-specific primers for 5′-ETS were designed and tested to obtain a 5′-ETS region less than 600 bp long, suitable for high-throughput sequencing. The DNA extraction method for single-species pollen samples and mixes was optimized to increase the yield for amplification and sequencing of pollen DNA. Barcode sequences were analyzed and compared by the barcoding gap and intra- and interspecific distances. Their capability to correctly identify grass pollen was tested on artificial pollen mixes of various complexity. Metabarcoding analysis of the artificial pollen mixes showed that nuclear DNA barcodes ITS1, ITS2, and 5′-ETS proved to be more efficient than the plastome barcode in both amplification from pollen DNA and identification of grass species. Although the metabarcoding results were qualitatively congruent with the actual composition of the pollen mixes in most cases, the quantitative results based on read-counts did not match the actual ratio of pollen grains in the mixes. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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12 pages, 1818 KiB  
Article
Patterns of Herbivory in Neotropical Forest Katydids as Revealed by DNA Barcoding of Digestive Tract Contents
by Christine M. Palmer, Nicole L. Wershoven, Sharon J. Martinson, Hannah M. ter Hofstede, W. John Kress and Laurel B. Symes
Diversity 2022, 14(2), 152; https://doi.org/10.3390/d14020152 - 21 Feb 2022
Cited by 5 | Viewed by 3422
Abstract
Many well-studied animal species use conspicuous, repetitive signals that attract both mates and predators. Orthopterans (crickets, katydids, and grasshoppers) are renowned for their acoustic signals. In Neotropical forests, however, many katydid species produce extremely short signals, totaling only a few seconds of sound [...] Read more.
Many well-studied animal species use conspicuous, repetitive signals that attract both mates and predators. Orthopterans (crickets, katydids, and grasshoppers) are renowned for their acoustic signals. In Neotropical forests, however, many katydid species produce extremely short signals, totaling only a few seconds of sound per night, likely in response to predation by acoustically orienting predators. The rare signals of these katydid species raises the question of how they find conspecific mates in a structurally complex rainforest. While acoustic mechanisms, such as duetting, likely facilitate mate finding, we test the hypothesis that mate finding is further facilitated by colocalization on particular host plant species. DNA barcoding allows us to identify recently consumed plants from katydid stomach contents. We use DNA barcoding to test the prediction that katydids of the same species will have closely related plant species in their stomach. We do not find evidence for dietary specialization. Instead, katydids consumed a wide mix of plants within and across the flowering plants (27 species in 22 genera, 16 families, and 12 orders) with particular representation in the orders Fabales and Laurales. Some evidence indicates that katydids may gather on plants during a narrow window of rapid leaf out, but additional investigations are required to determine whether katydid mate finding is facilitated by gathering at transient food resources. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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11 pages, 1041 KiB  
Article
Are Introduced Alien Species More Predisposed to Invasion in Recipient Environments If They Provide a Wider Range of Services to Humans?
by Kowiyou Yessoufou and Annie Estelle Ambani
Diversity 2021, 13(11), 553; https://doi.org/10.3390/d13110553 - 30 Oct 2021
Cited by 3 | Viewed by 2274
Abstract
The drivers of invasion success of alien species remain, to some extent, a matter of debate. Here, we suggest that the services (the benefits humans obtain from a species) provided by alien plants could predict their invasion status, such that alien species providing [...] Read more.
The drivers of invasion success of alien species remain, to some extent, a matter of debate. Here, we suggest that the services (the benefits humans obtain from a species) provided by alien plants could predict their invasion status, such that alien species providing more services would be more likely to be invasive than not. The rationale for this expectation is that alien species providing multiple services stand a better chance of being introduced in various numbers and multiple times outside their native range (propagule pressure theory). We investigated this hypothesis on alien woody species in South Africa. First, we defined 12 services provided by all the 210 known naturalized alien woody plants in South Africa. Then, we tested for a phylogenetic signal in these services using a DNA barcode-based phylogeny. Finally, we tested for potential links between the services and invasion status by fitting GLM models with appropriate error families. We found a phylogenetic signal in most services, suggesting that closely related species tend to provide similar services. Counter-intuitively, we consistently found that alien non-invasive species tend to provide more services, or even unique services, in comparison to alien invasive species. Although alternative scenarios are plausible to explain this unexpected finding, we speculate that harvesting alien plants for human benefits may limit their invasion ability. This warrants further investigation. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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Review

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17 pages, 375 KiB  
Review
Using DNA Metabarcoding to Identify Floral Visitation by Pollinators
by Abigail Lowe, Laura Jones, Lucy Witter, Simon Creer and Natasha de Vere
Diversity 2022, 14(4), 236; https://doi.org/10.3390/d14040236 - 24 Mar 2022
Cited by 14 | Viewed by 5229
Abstract
The identification of floral visitation by pollinators provides an opportunity to improve our understanding of the fine-scale ecological interactions between plants and pollinators, contributing to biodiversity conservation and promoting ecosystem health. In this review, we outline the various methods which can be used [...] Read more.
The identification of floral visitation by pollinators provides an opportunity to improve our understanding of the fine-scale ecological interactions between plants and pollinators, contributing to biodiversity conservation and promoting ecosystem health. In this review, we outline the various methods which can be used to identify floral visitation, including plant-focused and insect-focused methods. We reviewed the literature covering the ways in which DNA metabarcoding has been used to answer ecological questions relating to plant use by pollinators and discuss the findings of this research. We present detailed methodological considerations for each step of the metabarcoding workflow, from sampling through to amplification, and finally bioinformatic analysis. Detailed guidance is provided to researchers for utilisation of these techniques, emphasising the importance of standardisation of methods and improving the reliability of results. Future opportunities and directions of using molecular methods to analyse plant–pollinator interactions are then discussed. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
23 pages, 1052 KiB  
Review
The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation
by Morgan R. Gostel and W. John Kress
Diversity 2022, 14(3), 213; https://doi.org/10.3390/d14030213 - 13 Mar 2022
Cited by 44 | Viewed by 10636
Abstract
DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput [...] Read more.
DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role. Full article
(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)
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