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Oliveira FCRD, Gallo SSM, Elizeu TKS, Ederli NB. Prevalence and parasite burden of oocysts in captive and free-living saffron finches, Sicalis flaveola. REVISTA BRASILEIRA DE PARASITOLOGIA VETERINARIA = BRAZILIAN JOURNAL OF VETERINARY PARASITOLOGY : ORGAO OFICIAL DO COLEGIO BRASILEIRO DE PARASITOLOGIA VETERINARIA 2024; 33:e000524. [PMID: 38896754 DOI: 10.1590/s1984-29612024029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/16/2024] [Indexed: 06/21/2024]
Abstract
The saffron finch, Sicalis flaveola, a passerine bird, can be found in nearly all Brazilian territory and is also raised in captivity. The objective of this work was to determine the prevalence and load of oocysts in captive saffron finches in the municipality of Campos dos Goytacazes, state of Rio de Janeiro and in free-living saffron finches in the municipality of Eugenopolis, state of Minas Gerais. In this analysis, 30 captive and 30 wild birds were assessed. Feces eliminated in a 24-hour period were collected and weighed to determine the number of oocysts per gram of feces (OoPG). Statistical analyses were performed using Microsoft Excel and GraphPad Prism Software. All birds in the present study were positive for one or more species of coccidia. Captive birds had a mean total oocyst count higher than that of wild birds. No significant differences in OoPG counts were observed when comparing males and females or captive and wild birds. We can conclude that due to the fact that birds both eat and defecate in their cages, it is essential to keep them as clean as possible, since captive birds have a higher prevalence of coccidia.
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Affiliation(s)
| | - Samira Salim Mello Gallo
- Laboratório de Sanidade Animal, Universidade Estadual de Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, RJ, Brasil
| | - Taynara Kerolayne Santos Elizeu
- Laboratório de Sanidade Animal, Universidade Estadual de Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, RJ, Brasil
| | - Nicole Brand Ederli
- Instituto do Noroeste Fluminense de Educação Superior, Universidade Federal Fluminense - UFF, Santo Antônio de Pádua, RJ, Brasil
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2
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Deng X, Seguinot BO, Bradshaw G, Lee JS, Coy S, Kalocsay M, Santagata S, Mitchison T. STMND1 is a phylogenetically ancient stathmin which localizes to motile cilia and exhibits nuclear translocation that is inhibited when soluble tubulin concentration increases. Mol Biol Cell 2024; 35:ar82. [PMID: 38630521 DOI: 10.1091/mbc.e23-12-0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Stathmins are small, unstructured proteins that bind tubulin dimers and are implicated in several human diseases, but whose function remains unknown. We characterized a new stathmin, STMND1 (Stathmin Domain Containing 1) as the human representative of an ancient subfamily. STMND1 features a N-terminal myristoylated and palmitoylated motif which directs it to membranes and a tubulin-binding stathmin-like domain (SLD) that contains an internal nuclear localization signal. Biochemistry and proximity labeling showed that STMND1 binds tubulin, and live imaging showed that tubulin binding inhibits translocation from cellular membranes to the nucleus. STMND1 is highly expressed in multiciliated epithelial cells, where it localizes to motile cilia. Overexpression in a model system increased the length of primary cilia. Our study suggests that the most ancient stathmins have cilium-related functions that involve sensing soluble tubulin.
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Affiliation(s)
- Xiang Deng
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Bryan O Seguinot
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Gary Bradshaw
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Jong Suk Lee
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Shannon Coy
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Marian Kalocsay
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Sandro Santagata
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Timothy Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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3
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Hunter-Barnett S, Viney M. Gut protozoa of wild rodents - a meta-analysis. Parasitology 2024:1-12. [PMID: 38714350 DOI: 10.1017/s0031182024000556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Protozoa are well-known inhabitants of the mammalian gut and so of the gut microbiome. While there has been extensive study of a number of species of gut protozoa in laboratory animals, particularly rodents, the biology of the gut protozoa of wild rodents is much less well-known. Here we have systematically searched the published literature to describe the gut protozoa of wild rodents, in total finding records of 44 genera of protozoa infecting 228 rodent host species. We then undertook meta-analyses that estimated the overall prevalence of gut protozoa in wild rodents to be 24%, with significant variation in prevalence among some host species. We investigated how host traits may affect protozoa prevalence, finding that for some host lifestyles some protozoa differed in their prevalence. This synthesis of existing data on wild rodent gut protozoa provides a better understanding of the biology of these common gut inhabitants and suggests directions for their future study.
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Affiliation(s)
- Simon Hunter-Barnett
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
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4
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Soriano-Vargas E, García-Albarrán MA, Salgado-Miranda C. Eimeria atricillae n. sp. (Apicomplexa: Eimeriidae) from the laughing gull Leucophaeus atricilla (Linnaeus) (Aves: Charadriiformes: Laridae) in Port Isabel, Texas. Syst Parasitol 2024; 101:29. [PMID: 38568282 DOI: 10.1007/s11230-024-10153-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/05/2024] [Indexed: 04/05/2024]
Abstract
A new coccidian species, Eimeria atricillae n. sp. (Apicomplexa: Eimeriidae) collected from the laughing gull Leucophaeus atricilla, is reported from Port Isabel, Texas, USA. Sporulated oöcysts of the new species are spherical to subspherical, 16.0-18.1 × 14.4-16.6 (17.1 × 15.4) μm, with a length/width (L/W) ratio of 1.0-1.1; polar granules are present, but micropyle and oöcyst residuum are absent. Sporocysts are ovoid, 9.1-9.7 × 6.1-7.1 (9.4 × 6.6) μm, with a L/W ratio of 1.3-1.5; Stieda body present, but sub-Stieda and para-Stieda bodies are absent; sporocyst residuum diffuse.
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Affiliation(s)
- Edgardo Soriano-Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco km 15.5, 50295, Toluca, Estado de México, México
| | - Marco Antonio García-Albarrán
- Institute for Biodiversity Research, Development and Sustainability (iBIRDS, A. C.), San Agustín Berros s/n, 50960, Villa Victoria, State of Mexico, Mexico
| | - Celene Salgado-Miranda
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco km 15.5, 50295, Toluca, Estado de México, México.
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5
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Guiry MD. How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing. JOURNAL OF PHYCOLOGY 2024; 60:214-228. [PMID: 38245909 DOI: 10.1111/jpy.13431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
To date (1 November 2023), the online database AlgaeBase has documented 50,589 species of living algae and 10,556 fossil species here referred to four kingdoms (Eubacteria, Chromista, Plantae, and Protozoa), 14 phyla, and 63 classes. The algae are the third most speciose grouping of plant-like organisms after the flowering plants (≈382,000 species) and fungi (≈170,000 species, including lichens) but are the least well defined of all the botanical groupings. Priority is given to phyla and class names that are familiar to phycologists and that are nomenclaturally valid. The most species-rich phylum is the Heterokontophyta to which 18 classes are referred with 21,052 living species and which is dominated by the diatoms in three classes with 18,673 species (16,427 living; 2239 fossil). The next most species-rich phyla are the red algae (7276 living), the green algae (6851 living), the blue-green algae (Cyanobacteria, 5723 living), the charophytes (4950 living, including the Charophyceae, 511 species living, and the Zygnematophyceae, 4335 living species), Dinoflagellata (2956 living, including the Dinophyceae, 2828 extant), and haptophytes (Haptophyta 1722 species, 517 living).
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Affiliation(s)
- Michael D Guiry
- AlgaeBase, Ryan Institute, University of Galway, University Road, Galway, Ireland
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6
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Guzmán-Lara MDC, Soriano-Vargas E. Brief report: Isospora gilvusi n. sp. (Apicomplexa: Eimeriidae) from the warbling vireo Vireo gilvus Vieillot (Passeriformes: Vireonidae) in Morelia, Mexico. Syst Parasitol 2023; 100:611-616. [PMID: 37648904 DOI: 10.1007/s11230-023-10110-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
A new coccidian species, Isospora gilvusi n. sp. (Apicomplexa: Eimeriidae) collected from the warbling vireo Vireo gilvus, is reported from Morelia, Michoacán State, Mexico. Sporulated oöcysts of the new species are spherical to subspherical, 27-31 × 27-29 (30.1 × 28.4) μm, with a length/width (L/W) ratio of 1.1; one or two polar granules are present, but micropyle and oöcyst residuum are absent. Sporocyts are ovoid to drop-shaped, 16-17 × 11-12 (17.0 × 11.5) μm, with a L/W ratio of 1.7; Stieda and sub-Stieda bodies are both present, but para-Stieda body is absent; sporocyst residuum diffuse. At the histological study, endogenous stages were observed in the epithelial cells of the duodenum. This is the second species of Isospora recorded infecting a bird of the family Vireonidae in the New World.
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Affiliation(s)
- María Dolores Claudia Guzmán-Lara
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco km 15.5, 50200, Toluca, Mexico
| | - Edgardo Soriano-Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco km 15.5, 50200, Toluca, Mexico.
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7
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Nicolas E, Simion P, Guérineau M, Terwagne M, Colinet M, Virgo J, Lingurski M, Boutsen A, Dieu M, Hallet B, Van Doninck K. Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes. Nat Commun 2023; 14:7638. [PMID: 37993452 PMCID: PMC10665377 DOI: 10.1038/s41467-023-43075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
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Affiliation(s)
- Emilien Nicolas
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
| | - Paul Simion
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
- Université de Rennes, Ecosystèmes, biodiversité, évolution (ECOBIO UMR 6553), CNRS, Rennes, France
| | - Marc Guérineau
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Matthieu Terwagne
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Mathilde Colinet
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Julie Virgo
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Maxime Lingurski
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Anaïs Boutsen
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Marc Dieu
- Université de Namur, MaSUN-mass spectrometry facility, Namur, 5000, Belgium
| | - Bernard Hallet
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, 1348, Belgium.
| | - Karine Van Doninck
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium.
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8
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Buchinger TJ, Li W. Chemical communication and its role in sexual selection across Animalia. Commun Biol 2023; 6:1178. [PMID: 37985853 PMCID: PMC10662023 DOI: 10.1038/s42003-023-05572-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
Sexual selection has been studied as a major evolutionary driver of animal diversity for roughly 50 years. Much evidence indicates that competition for mates favors elaborate signaling traits. However, this evidence comes primarily from a few taxa, leaving sexual selection as a salient evolutionary force across Animalia largely untested. Here, we reviewed the evidence for sexual selection on communication across all animal phyla, classes, and orders with emphasis on chemoreception, the only sense shared across lifeforms. An exhaustive literature review documented evidence for sexual selection on chemosensory traits in 10 of 34 animal phyla and indications of sexual selection on chemosensory traits in an additional 13 phyla. Potential targets of sexual selection include structures and processes involved in production, delivery, and detection of chemical signals. Our review suggests sexual selection plays a widespread role in the evolution of communication and highlights the need for research that better reflects animal diversity.
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Affiliation(s)
- Tyler J Buchinger
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.
- Biology Department, Albion College, Albion, MI, USA.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
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9
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Schulz G, Camenzind T, Sánchez-Galindo LM, Schneider D, Scheu S, Krashevska V. Response of protists to nitrogen addition, arbuscular mycorrhizal fungi manipulation, and mesofauna reduction in a tropical montane rainforest in southern Ecuador. J Eukaryot Microbiol 2023; 70:e12996. [PMID: 37577763 DOI: 10.1111/jeu.12996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
The tropical Andes are a species-rich and nitrogen-limited system, susceptible to increased nitrogen (N) inputs from the atmosphere. However, our understanding of the impacts of increased N input on belowground systems, in particular on protists and their role in nutrient cycling, remains limited. We explored how increased N affects protists in tropical montane rainforests in Ecuador using high-throughput sequencing (HTS) of environmental DNA from two litter layers. In addition, we manipulated the amount of arbuscular mycorrhizal fungi (AMF) and mesofauna, both playing a significant role in N cycling and interacting in complex ways with protist communities. We found that N strongly affected protist community composition in both layers, while mesofauna reduction had a stronger effect on the lower layer. Changes in concentration of the AMF marker lipid had little effect on protists. In both layers, the addition of N increased phagotrophs and animal parasites and decreased plant parasites, while mixotrophs decreased in the upper layer but increased in the lower layer. In the upper layer with higher AMF concentration, mixotrophs decreased, while in the lower layer, photoautotrophs increased and plant parasites decreased. With reduced mesofauna, phagotrophs increased and animal parasites decreased in both layers, while plant parasites increased only in the upper layer. The findings indicate that to understand the intricate response of protist communities to environmental changes, it is critical to thoroughly analyze these communities across litter and soil layers, and to include HTS.
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Affiliation(s)
- Garvin Schulz
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Laura M Sánchez-Galindo
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Goettingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Valentyna Krashevska
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
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10
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Li S, Qi B, Peng X, Wang W, Wang W, Liu P, Liu B, Peng Z, Wang Q, Li Y. Genome size and GC content of myxomycetes. Eur J Protistol 2023; 90:125991. [PMID: 37331249 DOI: 10.1016/j.ejop.2023.125991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/20/2023]
Abstract
More than 1272 myxomycetes species have been described, accounting for more than half of all Amoebozoa species. However, the genome size of only three myxomycetes species has been reported. Therefore, we used flow cytometry to present an extensive survey and a phylogeny-based analysis of genome size and GC content evolution in 144 myxomycetes species. The genome size of myxomycetes ranged from 18.7 Mb to 470.3 Mb, and the GC content ranged from 38.7% to 70.1%. Bright-spored clade showed larger genome sizes and more intra-order genome size variations than the dark-spored clade. GC content and genome size were positively correlated in both bright-spored and dark-spored clades, and spore size was positively correlated with genome size and GC content in the bright-spored clade. We provided the first genome size data set in Myxomycetes, and our results will provide helpful information for future Myxomycetes studies, such as genome sequencing.
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Affiliation(s)
- Shu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Xueyan Peng
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wan Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Pu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China.
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
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11
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Panstruga R, Antonin W, Lichius A. Looking outside the box: a comparative cross-kingdom view on the cell biology of the three major lineages of eukaryotic multicellular life. Cell Mol Life Sci 2023; 80:198. [PMID: 37418047 PMCID: PMC10329083 DOI: 10.1007/s00018-023-04843-3] [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: 02/22/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/08/2023]
Abstract
Many cell biological facts that can be found in dedicated scientific textbooks are based on findings originally made in humans and/or other mammals, including respective tissue culture systems. They are often presented as if they were universally valid, neglecting that many aspects differ-in part considerably-between the three major kingdoms of multicellular eukaryotic life, comprising animals, plants and fungi. Here, we provide a comparative cross-kingdom view on the basic cell biology across these lineages, highlighting in particular essential differences in cellular structures and processes between phyla. We focus on key dissimilarities in cellular organization, e.g. regarding cell size and shape, the composition of the extracellular matrix, the types of cell-cell junctions, the presence of specific membrane-bound organelles and the organization of the cytoskeleton. We further highlight essential disparities in important cellular processes such as signal transduction, intracellular transport, cell cycle regulation, apoptosis and cytokinesis. Our comprehensive cross-kingdom comparison emphasizes overlaps but also marked differences between the major lineages of the three kingdoms and, thus, adds to a more holistic view of multicellular eukaryotic cell biology.
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Affiliation(s)
- Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074, Aachen, Germany
| | - Alexander Lichius
- inncellys GmbH, Dorfstrasse 20/3, 6082, Patsch, Austria
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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12
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Gonçalves‐Souza T, Chaves LS, Boldorini GX, Ferreira N, Gusmão RAF, Perônico PB, Sanders NJ, Teresa FB. Bringing light onto the Raunkiæran shortfall: A comprehensive review of traits used in functional animal ecology. Ecol Evol 2023; 13:e10016. [PMID: 37091571 PMCID: PMC10115901 DOI: 10.1002/ece3.10016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
Trait-based approaches elucidate the mechanisms underlying biodiversity response to, or effects on, the environment. Nevertheless, the Raunkiæran shortfall-the dearth of knowledge on species traits and their functionality-presents a challenge in the application of these approaches. We conducted a systematic review to investigate the trends and gaps in trait-based animal ecology in terms of taxonomic resolution, trait selection, ecosystem type, and geographical region. In addition, we suggest a set of crucial steps to guide trait selection and aid future research to conduct within and cross-taxon comparisons. We identified 1655 articles using virtually all animal groups published from 1999 to 2020. Studies were concentrated in vertebrates, terrestrial habitats, the Palearctic realm, and mostly investigated trophic and habitat dimensions. Additionally, they focused on response traits (79.4%) and largely ignored intraspecific variation (94.6%). Almost 36% of the data sets did not provide the rationale behind the selection of morphological traits. The main limitations of trait-based animal ecology were the use of trait averages and a rare inclusion of intraspecific variability. Nearly one-fifth of the studies based only on response traits conclude that trait diversity impacts ecosystem processes or services without justifying the connection between them or measuring them. We propose a guide for standardizing trait collection that includes the following: (i) determining the type of trait and the mechanism linking the trait to the environment, ecosystem, or the correlation between the environment, trait, and ecosystem, (ii) using a "periodic table of niches" to select the appropriate niche dimension to support a mechanistic trait selection, and (iii) selecting the relevant traits for each retained niche dimension. By addressing these gaps, trait-based animal ecology can become more predictive. This implies that future research will likely focus on collaborating to understand how environmental changes impact animals and their capacity to provide ecosystem services and goods.
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Affiliation(s)
- Thiago Gonçalves‐Souza
- Department of Biology, Ecological Synthesis and Biodiversity Conservation LabFederal Rural University of PernambucoRecifeBrazil
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
- School for Environment and Sustainability, Institute for Global Change BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Leonardo S. Chaves
- Graduate Program in Ethnobiology and Nature Conservation, Department of BiologyFederal Rural University of PernambucoRecifeBrazil
- Escola de Educação e HumanidadesUniversidade Católica de PernambucoRecifeBrazil
| | - Gabriel X. Boldorini
- Department of Biology, Ecological Synthesis and Biodiversity Conservation LabFederal Rural University of PernambucoRecifeBrazil
- Graduate Program in Ethnobiology and Nature Conservation, Department of BiologyFederal Rural University of PernambucoRecifeBrazil
| | - Natália Ferreira
- Graduate Program in Biodiversity, Department of BiologyFederal Rural University of PernambucoRecifeBrazil
| | - Reginaldo A. F. Gusmão
- Department of Biology, Ecological Synthesis and Biodiversity Conservation LabFederal Rural University of PernambucoRecifeBrazil
- Graduate Program in Ethnobiology and Nature Conservation, Department of BiologyFederal Rural University of PernambucoRecifeBrazil
| | - Phamela Bernardes Perônico
- Graduate Program in Natural Resources of CerradoState University of GoiásAnápolisBrazil
- Biogeography and Aquatic Ecology LabState University of GoiásAnápolisBrazil
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Fabrício B. Teresa
- Graduate Program in Natural Resources of CerradoState University of GoiásAnápolisBrazil
- Biogeography and Aquatic Ecology LabState University of GoiásAnápolisBrazil
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Göker M, Oren A. Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749690 DOI: 10.1099/ijsem.0.005650] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Observations made after introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP) indicate that the addition of a category should usually be conducted before informal names at that rank become widely used. It is thus investigated whether it would be beneficial to add further categories. An extrapolation from the number of names validly published under the ICNP at the distinct principal categories was conducted. This extrapolation indicated that two principal ranks above phylum rank would also harbour validly published names if the according categories were covered by the ICNP. The appropriate categories would be kingdom and domain, regarded as separate principal ranks. The benefit from introducing these ranks is confirmed by analysing the previous taxonomic activity above phylum level and the nomenclatural problems associated with this activity. An etymological examination of the way names of taxa above genus level are formed under distinct codes of nomenclature provides hints for implementing additional categories. According emendations of the ICNP are proposed to include kingdom and domain as a means of further stabilizing prokaryotic nomenclature.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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14
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Gomis-Rüth FX, Stöcker W. Structural and evolutionary insights into astacin metallopeptidases. Front Mol Biosci 2023; 9:1080836. [PMID: 36685277 PMCID: PMC9848320 DOI: 10.3389/fmolb.2022.1080836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.
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Affiliation(s)
- F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC), Barcelona, Catalonia, Spain,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
| | - Walter Stöcker
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz (JGU), Mainz, Germany,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
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Juravel K, Porras L, Höhna S, Pisani D, Wörheide G. Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLoS One 2023; 18:e0282444. [PMID: 36952565 PMCID: PMC10035847 DOI: 10.1371/journal.pone.0282444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
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Affiliation(s)
- Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Luis Porras
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Höhna
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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Measuring the Impact of Conservation: The Growing Importance of Monitoring Fauna, Flora and Funga. DIVERSITY 2022. [DOI: 10.3390/d14100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Many stakeholders, from governments to civil society to businesses, lack the data they need to make informed decisions on biodiversity, jeopardising efforts to conserve, restore and sustainably manage nature. Here we review the importance of enhancing biodiversity monitoring, assess the challenges involved and identify potential solutions. Capacity for biodiversity monitoring needs to be enhanced urgently, especially in poorer, high-biodiversity countries where data gaps are disproportionately high. Modern tools and technologies, including remote sensing, bioacoustics and environmental DNA, should be used at larger scales to fill taxonomic and geographic data gaps, especially in the tropics, in marine and freshwater biomes, and for plants, fungi and invertebrates. Stakeholders need to follow best monitoring practices, adopting appropriate indicators and using counterfactual approaches to measure and attribute outcomes and impacts. Data should be made openly and freely available. Companies need to invest in collecting the data required to enhance sustainability in their operations and supply chains. With governments soon to commit to the post-2020 global biodiversity framework, the time is right to make a concerted push on monitoring. However, action at scale is needed now if we are to enhance results-based management adequately to conserve the biodiversity and ecosystem services we all depend on.
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Tyler SEB, Tyler LDK. Therapeutic roles of plants for 15 hypothesised causal bases of Alzheimer's disease. NATURAL PRODUCTS AND BIOPROSPECTING 2022; 12:34. [PMID: 35996065 PMCID: PMC9395556 DOI: 10.1007/s13659-022-00354-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/15/2022] [Indexed: 05/26/2023]
Abstract
Alzheimer's disease (AD) is progressive and ultimately fatal, with current drugs failing to reverse and cure it. This study aimed to find plant species which may provide therapeutic bioactivities targeted to causal agents proposed to be driving AD. A novel toolkit methodology was employed, whereby clinical symptoms were translated into categories recognized in ethnomedicine. These categories were applied to find plant species with therapeutic effects, mined from ethnomedical surveys. Survey locations were mapped to assess how this data is at risk. Bioactivities were found of therapeutic relevance to 15 hypothesised causal bases for AD. 107 species with an ethnological report of memory improvement demonstrated therapeutic activity for all these 15 causal bases. The majority of the surveys were found to reside within biodiversity hotspots (centres of high biodiversity under threat), with loss of traditional knowledge the most common threat. Our findings suggest that the documented plants provide a large resource of AD therapeutic potential. In demonstrating bioactivities targeted to these causal bases, such plants may have the capacity to reduce or reverse AD, with promise as drug leads to target multiple AD hallmarks. However, there is a need to preserve ethnomedical knowledge, and the habitats on which this knowledge depends.
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Affiliation(s)
| | - Luke D K Tyler
- School of Natural Sciences, Bangor University, Gwynedd, UK
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Worldwide Dispersion of Coccidia from Migratory Birds: First Report of Eimeria bazi Chauhan et Bhatia, 1970 (Eimeriidae) Outside Asia from Buff-Necked Ibises Theristicus caudatus (Boddaert, 1783) (Threskiornithidae) in South America. Acta Parasitol 2022; 67:1343-1353. [PMID: 35836092 DOI: 10.1007/s11686-022-00585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Eimeria spp. are coccidian protozoan parasites of domestic and wild animals. Pelecaniform birds are hosts of some Eimeria spp., however, from the family Threskiornithidae only one eimerian species is recorded, Eimeria bazi Chauhan et Bhatia, 1970 which was described from red-naped ibises Pseudibis papillosa (Temminck, 1824) in India. In this study, in turn, this species is morphologically and molecularly identified from buff-necked ibises Theristicus caudatus (Boddaert, 1783) in Brazil. PURPOSE This study aimed to report E. bazi from buff-necked ibises T. caudatus in southeastern Brazil, revealing the worldwide distribution of this coccidian species, in addition to providing preliminary genotypic identification via sequencing of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. METHODS A total of 73 fecal samples were collected from a flock of buff-necked ibises, which remained on the campus of the Federal Rural University of Rio de Janeiro (Universidade Federal Rural do Rio de Janeiro-UFRRJ) from March 2019 to August 2020. Fecal samples were processed by the Sheather's method to recover oocysts. The morphological and morphometrical studies of the oocysts were performed using an optical microscope and graphic editing software. Molecular analysis was performed by sequencing of the COI gene, and the phylogenetic analysis was based in the neighbor-joining and maximum likelihood estimates. RESULTS Forty-five fecal samples were positive for oocysts identified as E. bazi. This oocysts are ovoidal, 26.2 × 18.9 μm, with smooth to slightly rough wall, c.1.7 μm thick. Micropyle robust and protruding, sometimes with a polar body attached. Oocyst residuum absent, but one or two small polar granules are present. Sporocysts ovoidal to lemon-shaped, 14.2 × 8.7 μm. The Stieda body is knob-like to rounded and sub-Stieda body is absent or vestigial. Sporocyst residuum is composed of granules often membrane-bound. Sporozoites are vermiform, with refractile bodies. This morphology was consistent with the original description of E. bazi from P. papillosa in India. Molecular analysis at the COI gene exhibited low similarity with coccidians sequenced for the same genic region deposited in GenBank, sitting E. bazi separately on the cladogram. CONCLUSIONS The morphological and molecular studies support the identification of E. bazi from T. caudatus in South America, thus revealing the wide distribution of this eimerian species in the world provided by migratory birds and/or with intercontinental distribution.
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Invasive alien species records are exponentially rising across the Earth. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Abstract
Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means of recovering morphological, molecular, and phylogenetic traits for species identification. Traditional identification still relies on external diagnostic characters, which are limited and usually exhibit large phenotypic plasticity within the species, rendering them useless for species delimitation and identification. We decided to increase the number of sequences of the Acari mitochondrial COI (Cytochrome C oxidase I) marker and ITS nuclear ribosomal DNA region for species identification in Tetranychidae and Phytoseiidae. The molecular data allow us to establish species boundaries and phylogenetic relationships among several clades of Acari, mainly Tetranychidae and Phytoseiidae. Sequence comparisons between complete COI and the Acari mitochondrial COI, ITS1-5,8S-ITS2, and ITS2 among all Acari sequences have demonstrated that the selected regions, even small, gave enough informative positions for both species’ identification and phylogenetic studies. Analyses of both DNA regions have unveiled their use as species identification characters, with special emphasis on Acari mitochondrial COI for Tetranychidae and Phytoseiidae species in comparison with the Folmer fragment, which has been universally used as a barcode marker. We demonstrated that the Acari mitochondrial COI region is also a suitable marker to establish a barcode dataset for Acari identification. Our phylogenetic analyses are congruent with other recent works, showing that Acari is a monophyletic group, of which Astigmata, Ixodida, Mesostigmata, Oribatida, and Prostigmata are also monophyletic.
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21
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Cavalier-Smith T. Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi. PROTOPLASMA 2022; 259:487-593. [PMID: 34940909 PMCID: PMC9010356 DOI: 10.1007/s00709-021-01665-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/03/2021] [Indexed: 05/19/2023]
Abstract
I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.
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22
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HODDA M. Phylum Nematoda: a classification, catalogue and index of valid genera, with a census of valid species. Zootaxa 2022; 5114:1-289. [DOI: 10.11646/zootaxa.5114.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
A classification of the entire Phylum Nematoda is presented, based on current molecular, developmental and morphological evidence. The classification reflects the evolutionary relationships within the phylum, as well as significant areas of uncertainty, particularly related to the early evolution of nematodes. It includes 3 classes, 8 subclasses, 12 superorders, 32 orders, 53 suborders, 101 superfamilies, 276 families, 511 subfamilies, 3030 genera, and 28537 species. All valid species named from the time of publication of the previous classification and census (2010) to the end of 2019 are listed, along with the number of valid species in each genus. Taxonomic authorities are provided for taxon names of all ranks. The habitats where the species in each genus are found are listed, and an alphabetic index of genus names is provided. The systematics of nematodes is reviewed, along with a history of nematode classification; evolutionary affinities and origins of nematodes; and the current diagnosis of the group. Short overviews of the general biology, ecology, scientific and economic importance of the group are presented.
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Sibraa L, Barton D, Shamsi S. Occurrence of Temnocephalidae flatworms in Australia. J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2033869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lachlan Sibraa
- School of Agriculture, Environment and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Diane Barton
- School of Agriculture, Environment and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Shokoofeh Shamsi
- School of Agriculture, Environment and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
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Adeola AO, Ore OT, Fapohunda O, Adewole AH, Akerele DD, Akingboye AS, Oloye FF. Psychotropic Drugs of Emerging Concerns in Aquatic Systems: Ecotoxicology and Remediation Approaches. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00334-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Biomolecules from Microalgae and Cyanobacteria: Applications and Market Survey. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12041924] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nowadays, microalgae and cyanobacteria have become a promising and sustainable source of useful products, thanks to their richness in bioactive metabolites of high value (antibiotics, toxins, pharmaceutically active compounds, plant growth regulators, and others). These photoautotroph microorganisms generate biomass using photosynthesis. This review, which distinguishes microalgae and Cyanobacteria, often called blue-green microalgae, aims to present their classification and taxonomic diversity as the ecological niches occupied by them. In addition, the usages of open ponds and photobioreactors to produce various microalgae and Cyanobacteria strains and the high-value bioactive compounds from these microorganisms are summarized. Finally, the numerous commercial applications of these phytoplanktons in different fields, such as food, dietary supplements, feed, cosmetic, and biofuel applications, are reviewed.
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Abstract
Junctophilins (JPHs) comprise a family of structural proteins that connect the plasma membrane to intracellular organelles such as the endo/sarcoplasmic reticulum. Tethering of these membrane structures results in the formation of highly organized subcellular junctions that play important signaling roles in all excitable cell types. There are four JPH isoforms, expressed primarily in muscle and neuronal cell types. Each JPH protein consists of 6 'membrane occupation and recognition nexus' (MORN) motifs, a joining region connecting these to another set of 2 MORN motifs, a putative alpha-helical region, a divergent region exhibiting low homology between JPH isoforms, and a carboxy-terminal transmembrane region anchoring into the ER/SR membrane. JPH isoforms play essential roles in developing and maintaining subcellular membrane junctions. Conversely, inherited mutations in JPH2 cause hypertrophic or dilated cardiomyopathy, while trinucleotide expansions in the JPH3 gene cause Huntington Disease-Like 2. Loss of JPH1 protein levels can cause skeletal myopathy, while loss of cardiac JPH2 levels causes heart failure and atrial fibrillation, among other disease. This review will provide a comprehensive overview of the JPH gene family, phylogeny, and evolutionary analysis of JPH genes and other MORN domain proteins. JPH biogenesis, membrane tethering, and binding partners will be discussed, as well as functional roles of JPH isoforms in excitable cells. Finally, potential roles of JPH isoform deficits in human disease pathogenesis will be reviewed.
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Affiliation(s)
- Stephan E Lehnart
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Department of Cardiology and Pneumology, Georg-August University Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Germany
| | - Xander H T Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States; Departments of Molecular Physiology and Biophysics, Medicine (Cardiology), Pediatrics (Cardiology), Neuroscience, and Center for Space Medicine, Baylor College of Medicine, Houston, Texas, United States
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Sunthudlakhar P, Sithisarn P, Rojsanga P, Jarikasem S. HPLC quantitative analysis of protocatechuic acid contents in 11 Phellinus mushroom species collected in Thailand. BRAZ J PHARM SCI 2022. [DOI: 10.1590/s2175-97902022e20656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | | | | | - Siripen Jarikasem
- Thailand Institute of Scientific and Technological Research, Thailand
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Prospective on the application of abiotic stresses to enhance the industrial production of exopolysaccharides from microalgae. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Verma S, Toppo K, Nayaka S. Comprehensive checklist of algal class Chlorophyceae (sensu Fritsch, 1935) for Uttar Pradesh, India, with updated taxonomic status. JOURNAL OF THREATENED TAXA 2021. [DOI: 10.11609/jott.6508.13.14.20218-20248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Uttar Pradesh is an active center for algal research in India, but regional checklists are not available. Checklists of algae reported from class Chlorophyceae (sensu Fritsch, 1935) are presented here, with taxonomic status updated per AlgaeBase. The checklist covers algae from 17 types of habitats and includes 749 species, 166 varities and six forma, belonging to four phyla, 11 classes, 26 orders, 64 families and 161 genera. Charophyta is the dominant phylum with 519 infrageneric taxa (species, varities, forma), while Chlorophyta is represented by 389 taxa. Zygnematophyceae is the dominant class with 465 infrageneric taxa under two orders, six families and 29 genera. Chlorophyceae has 305 infrageneric taxa under five orders, 33 families, and 76 genera. Cosmarium is the most speciose genus with 163 taxa, followed by Oedogonium (79), Spirogyra (72), and Closterium (54). Our study revealed that of 75 districts in Uttar Pradesh only 40 are explored for algae, with Prayagraj and Lucknow recording 266 and 144 taxa respectively.
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Vicuña R, González B. The microbial world in a changing environment. REVISTA CHILENA DE HISTORIA NATURAL 2021. [DOI: 10.1186/s40693-021-00099-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abstract
Background
In this article we would like to touch on the key role played by the microbiota in the maintenance of a sustainable environment in the entire planet. For obvious reasons, this article does not intend to review thoroughly this extremely complex topic, but rather to focus on the main threats that this natural scenario is presently facing.
Methods
Recent literature survey.
Results
Despite the relevance of microorganisms have in our planet, the effects of climate change on microbial communities have been scarcely and not systematically addressed in literature. Although the role of microorganisms in emissions of greenhouse gases has received some attention, there are several microbial processes that are affected by climate change with consequences that are presently under assessment. Among them, host-pathogen interactions, the microbiome of built environment, or relations among plants and beneficial microbes.
Conclusions
Further research is required to advance in knowledge of the effect of climate change on microbial communities. One of the main targets should be a complete evaluation of the global microbial functional diversity and the design of new strategies to cope with limitations in methods to grow microorganisms in the laboratory. These efforts should contribute to raise a general public awareness on the major role played by the microbiota on the various Earth ecosystems.
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Hobern D, Barik SK, Christidis L, T.Garnett S, Kirk P, Orrell TM, Pape T, Pyle RL, Thiele KR, Zachos FE, Bánki O. Towards a global list of accepted species VI: The Catalogue of Life checklist. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00516-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pyle RL, Barik SK, Christidis L, Conix S, Costello MJ, van Dijk PP, Garnett ST, Hobern D, Kirk PM, Lien AM, Orrell TM, Remsen D, Thomson SA, Wambiji N, Zachos FE, Zhang ZQ, Thiele KR. Towards a global list of accepted species V. The devil is in the detail. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00504-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ulaszewski B, Jankowska-Wróblewska S, Świło K, Burczyk J. Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112534. [PMID: 34834899 PMCID: PMC8618278 DOI: 10.3390/plants10112534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.
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Han X, Shen D, Xiong Q, Bao B, Zhang W, Dai T, Zhao Y, Borriss R, Fan B. The Plant-Beneficial Rhizobacterium Bacillus velezensis FZB42 Controls the Soybean Pathogen Phytophthora sojae Due to Bacilysin Production. Appl Environ Microbiol 2021; 87:e0160121. [PMID: 34550751 PMCID: PMC8580012 DOI: 10.1128/aem.01601-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Soybean root rot caused by the oomycete Phytophthora sojae is a serious soilborne disease threatening soybean production in China. Bacillus velezensis FZB42 is a model strain for Gram-positive plant growth-promoting rhizobacteria and is able to produce multiple antibiotics. In this study, we demonstrated that B. velezensis FZB42 can efficiently antagonize P. sojae. The underlying mechanism for the inhibition was then investigated. The FZB42 mutants deficient in the synthesis of lipopeptides (bacillomycin D and fengycin), known to have antifungal activities, and polyketides (bacillaene, difficidin, and macrolactin), known to have antibacterial activities, were not impaired in their antagonism toward P. sojae; in contrast, mutants deficient in bacilysin biosynthesis completely lost their antagonistic activities toward P. sojae, indicating that bacilysin was responsible for the activity. Isolated pure bacilysin confirmed this inference. Bacilysin was previously shown to be antagonistic mainly toward prokaryotic bacteria rather than eukaryotes. Here, we found that bacilysin could severely damage the hyphal structures of P. sojae and lead to the loss of its intracellular contents. A device was invented allowing interactions between P. sojae and B. velezensis FZB42 on nutrient agar. In this manner, the effect of FZB42 on P. sojae was studied by transcriptomics. FZB42 significantly inhibited the expression of P. sojae genes related to growth, macromolecule biosynthesis, pathogenicity, and ribosomes. Among them, the genes for pectate lyase were the most significantly downregulated. Additionally, we showed that bacilysin effectively prevents soybean sprouts from being infected by P. sojae and could antagonize diverse Phytophthora species, such as Phytophthora palmivora, P. melonis, P. capsici, P. litchi, and, most importantly, P. infestans. IMPORTANCEPhytophthora spp. are widespread eukaryotic phytopathogens and often extremely harmful. Phytophthora can infect many types of plants important to agriculture and forestry and thus cause large economic losses. Perhaps due to inappropriate recognition of Phytophthora as a common pathogen in history, research on the biological control of Phytophthora is limited. This study shows that B. velezensis FZB42 can antagonize various Phytophthora species and prevent the infection of soybean seedlings by P. sojae. The antibiotic produced by FZB42, bacilysin, which was already known to have antibacterial effectiveness, is responsible for the inhibitory action against Phytophthora. We further showed that some Phytophthora genes and pathways may be targeted in future biocontrol studies. Therefore, our data provide a basis for the development of new tools for the prevention and control of root and stem rot in soybean and other plant diseases caused by Phytophthora.
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Affiliation(s)
- Xingshan Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Dongxia Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Beihua Bao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenbo Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Tingting Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yinjuan Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Greifswald, Germany
| | - Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Mahapatra A, Mukherjee J. Taxonomy classification using genomic footprint of mitochondrial sequences. Comb Chem High Throughput Screen 2021; 25:401-413. [PMID: 34382517 DOI: 10.2174/1386207324666210811102109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Advancement in the sequencing technology yields a huge number of genomes of a multitude of organisms in our planet. One of the fundamental tasks for processing and analyzing these sequences is to organize them in the existing taxonomic orders. <P> Method: Recently we proposed a novel approach, GenFooT, of taxonomy classification using the concept of genomic footprint (GFP). The technique is further refined and enhanced in this work leading to improved accuracies in the task of taxonomic classification on various benchmark datasets. GenFooT maps a genome sequence in a 2D coordinate space and extracts features from that representation. It uses two hyper-parameters, namely block size and number of fragments of genomic sequence while computing the feature. In this work, we propose an analysis for choosing values of those parameters adaptively from the sequences. The enhanced version of GenFooT is named GenFooT2. <P> Results and Conclusion: We have experimented GenFooT2 on ten different biological datasets of genomic sequences of various organisms belonging to different taxonomy ranks. Our experimental results indicate more than 3% improved classification performance of the proposed features with Logistic regression classifier than the GenFooT. We also performed the statistical test to compare the performance of GenFooT2 with the state-of-the-art methods including our previous method GenFooT. The experimental results as well as the statistical test exhibit that the performance of the proposed GenFooT2 is significantly better.
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Affiliation(s)
- Aritra Mahapatra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur. India
| | - Jayanta Mukherjee
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur. India
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Li S, Tan H, Liu B, Zhu H, Hu Z, Liu G. Watanabeales ord. nov. and twelve novel species of Trebouxiophyceae (Chlorophyta). JOURNAL OF PHYCOLOGY 2021; 57:1167-1186. [PMID: 33713360 DOI: 10.1111/jpy.13165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/04/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
The Trebouxiophyceae include Chlorellales, Prasiolales, Trebouxiales, Microthamniales, and numerous members for which taxonomic locations have not been determined. The Watanabea clade is a group in the Trebouxiophyceae of Chlorella-like taxa, which are predominantly solitary and terrestrial. With the increase in descriptions of new species within the Watanabea clade in recent years, it is necessary to define the boundary and taxonomic status of the clade. In this study, nineteen strains of terrestrial algae collected from China were investigated based on molecular and morphological data, involving phylogenetic analyses, light and electron microscopy, and ITS-2 secondary structures. These 19 strains were described as five known species and 12 novel ones. Based on the consistent topological structures of the phylogenetic analyses for three taxonomic levels (the core Chorophyta, Trebouxiophyceae based on 18S sequences, Watanabeales and Symbiochloris based on 18S, 5.8S, ITS2 and rbcL gene sequences) and common morphological characteristics, especially the key phenotypic feature of unequally sized autospores, the Watanabea clade was defined as a new order, Watanabeales ord. nov., with one family, Watanabeaceae fam. nov. The boundary of Watanabeales was delineated and included the genera Chloroidium, Calidiella, Jaagichlorella, Kalinella, Massjukichlorella, Mysteriochloris, Polulichloris, Phyllosiphon, Watanabea, and Viridiella. Symbiochloris did not belong to Watanabeales according to the phylogenetic analyses and the reproduction by equal-sized autospores, aplanospores, or zoospores. The Watanabeales were separated into four groups during the phylogenetic analyses, but no regular differences in habitats or morphology could be used as the morphological basis to split Watanabeales into the four groups.
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Affiliation(s)
- Shuyin Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Haochen Tan
- Xiashan Reservoir Administration, Weifang, 261325, China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices. Polar Biol 2021. [DOI: 10.1007/s00300-021-02896-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractPhagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.
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Sakamoto T, Ortega JM. Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. BMC Bioinformatics 2021; 22:388. [PMID: 34325658 PMCID: PMC8323199 DOI: 10.1186/s12859-021-04304-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, an alternative representation of data as a table would facilitate the use of information for processing bioinformatics data. To do so, since some taxonomic-ranks are missing in some lineages, an algorithm might propose provisional names for all taxonomic-ranks. RESULTS To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic table, maintaining its compatibility with the original tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic-rank to an existing clade or "no rank" node when possible, using its name as part of the created taxonomic-rank name (e.g. Ord_Ornithischia) or interpolating parent nodes when needed (e.g. Cla_of_Ornithischia), both examples given for the dinosaur Brachylophosaurus lineage. The new hierarchical structure was named Taxallnomy because it contains names for all taxonomic-ranks, and it contains 41 hierarchical levels corresponding to the 41 taxonomic-ranks currently found in the NCBI Taxonomy database. From Taxallnomy, users can obtain the complete taxonomic lineage with 41 nodes of all taxa available in the NCBI Taxonomy database, without any hazard to the original tree information. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree and by producing metagenomics profiles. CONCLUSION Taxallnomy applies to any bioinformatics analyses that depend on the information from NCBI Taxonomy. Taxallnomy is updated periodically but with a distributed PERL script users can generate it locally using NCBI Taxonomy as input. All Taxallnomy resources are available at http://bioinfo.icb.ufmg.br/taxallnomy .
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Affiliation(s)
- Tetsu Sakamoto
- BioME - Bioinformatics Multidisciplinary Environment, Instituto Metrópole Digital (IMD), Universidade Federal Do Rio Grande Do Norte (UFRN), Natal, RN, Brazil
- Laboratório de Biodados, Departamento de Bioquímica E Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - J Miguel Ortega
- Laboratório de Biodados, Departamento de Bioquímica E Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
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Progression of asexual to sexual stages of Cystoisospora suis in a host cell-free environment as a model for Coccidia. Parasitology 2021; 148:1475-1481. [PMID: 34193323 PMCID: PMC8426156 DOI: 10.1017/s0031182021001074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
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40
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Del Risco AA, Montoya ÁM, García V, Currea S, Rivera YA, Moreno D, Rodríguez ÁT. Data synthesis and dynamic visualization converge into a comprehensive biotic interaction network: a case study of the urban and rural areas of Bogotá D.C. Urban Ecosyst 2021. [DOI: 10.1007/s11252-021-01133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bourgoin T, Bailly N, Zaragueta R, Vignes-Lebbe R. Complete formalization of taxa with their names, contents and descriptions improves taxonomic databases and access to the taxonomic knowledge they support. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1915895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Thierry Bourgoin
- Muséum national d'Histoire naturelle, Institut Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 MNHN-CNRS-Sorbonne Université-EPHE-Université des Antilles, Paris, 75005 France
| | - Nicolas Bailly
- Beaty Biodiversity Museum - Department of Zoology, University of British Columbia, Vancouver, Canada
| | - René Zaragueta
- Sorbonne Université, Muséum national d’Histoire naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique Évolution Biodiversité (ISYEB), Paris, 75005 France
| | - Régine Vignes-Lebbe
- Sorbonne Université, Muséum national d’Histoire naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique Évolution Biodiversité (ISYEB), Paris, 75005 France
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Sterner BW, Gilbert EE, Franz NM. Decentralized but Globally Coordinated Biodiversity Data. Front Big Data 2021; 3:519133. [PMID: 33693407 PMCID: PMC7931950 DOI: 10.3389/fdata.2020.519133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Centralized biodiversity data aggregation is too often failing societal needs due to pervasive and systemic data quality deficiencies. We argue for a novel approach that embodies the spirit of the Web (“small pieces loosely joined”) through the decentralized coordination of data across scientific languages and communities. The upfront cost of decentralization can be offset by the long-term benefit of achieving sustained expert engagement, higher-quality data products, and ultimately more societal impact for biodiversity data. Our decentralized approach encourages the emergence and evolution of multiple self-identifying communities of practice that are regionally, taxonomically, or institutionally localized. Each community is empowered to control the social and informational design and versioning of their local data infrastructures and signals. With no single aggregator to exert centralized control over biodiversity data, decentralization generates loosely connected networks of mid-level aggregators. Global coordination is nevertheless feasible through automatable data sharing agreements that enable efficient propagation and translation of biodiversity data across communities. The decentralized model also poses novel integration challenges, among which the explicit and continuous articulation of conflicting systematic classifications and phylogenies remain the most challenging. We discuss the development of available solutions, challenges, and outline next steps: the global effort of coordination should focus on developing shared languages for data signal translation, as opposed to homogenizing the data signal itself.
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Affiliation(s)
- Beckett W Sterner
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Edward E Gilbert
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Nico M Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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Ciobanu D, Clum A, Ahrendt S, Andreopoulos WB, Salamov A, Chan S, Quandt CA, Foster B, Meier-Kolthoff JP, Tang YT, Schwientek P, Benny GL, Smith ME, Bauer D, Deshpande S, Barry K, Copeland A, Singer SW, Woyke T, Grigoriev IV, James TY, Cheng JF. A single-cell genomics pipeline for environmental microbial eukaryotes. iScience 2021; 24:102290. [PMID: 33870123 PMCID: PMC8042348 DOI: 10.1016/j.isci.2021.102290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 12/05/2022] Open
Abstract
Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. We optimized single-cell methodology using a broad sample range, for EME We combined bioinformatic and bench protocols into a concise workflow We benchmarked the pipeline and used it on environmental samples We selected a set of QC criteria for best genome quality prediction
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Affiliation(s)
- Doina Ciobanu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Sandy Chan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.,Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Jan P Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Yung Tsu Tang
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Patrick Schwientek
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Shweta Deshpande
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | | | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
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Abstract
Understanding how species’ thermal limits have evolved across the tree of life is central to predicting species’ responses to climate change. Here, using experimentally-derived estimates of thermal tolerance limits for over 2000 terrestrial and aquatic species, we show that most of the variation in thermal tolerance can be attributed to a combination of adaptation to current climatic extremes, and the existence of evolutionary ‘attractors’ that reflect either boundaries or optima in thermal tolerance limits. Our results also reveal deep-time climate legacies in ectotherms, whereby orders that originated in cold paleoclimates have presently lower cold tolerance limits than those with warm thermal ancestry. Conversely, heat tolerance appears unrelated to climate ancestry. Cold tolerance has evolved more quickly than heat tolerance in endotherms and ectotherms. If the past tempo of evolution for upper thermal limits continues, adaptive responses in thermal limits will have limited potential to rescue the large majority of species given the unprecedented rate of contemporary climate change. Historical climate adaptation can give insight into the potential for adaptation to contemporary changing climates. Here Bennett et al. investigate thermal tolerance evolution across much of the tree of life and find different effects of ancestral climate on the subsequent evolution of ectotherms vs. endotherms.
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Aeles J, Horst F, Lapuschkin S, Lacourpaille L, Hug F. Revealing the unique features of each individual's muscle activation signatures. J R Soc Interface 2021; 18:20200770. [PMID: 33435843 DOI: 10.1098/rsif.2020.0770] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is growing evidence that each individual has unique movement patterns, or signatures. The exact origin of these movement signatures, however, remains unknown. We developed an approach that can identify individual muscle activation signatures during two locomotor tasks (walking and pedalling). A linear support vector machine was used to classify 78 participants based on their electromyographic (EMG) patterns measured on eight lower limb muscles. To provide insight into decision-making by the machine learning classification model, a layer-wise relevance propagation (LRP) approach was implemented. This enabled the model predictions to be decomposed into relevance scores for each individual input value. In other words, it provided information regarding which features of the time-varying EMG profiles were unique to each individual. Through extensive testing, we have shown that the LRP results, and by extent the activation signatures, are highly consistent between conditions and across days. In addition, they are minimally influenced by the dataset used to train the model. Additionally, we proposed a method for visualizing each individual's muscle activation signature, which has several potential clinical and scientific applications. This is the first study to provide conclusive evidence of the existence of individual muscle activation signatures.
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Affiliation(s)
- Jeroen Aeles
- Laboratory 'Movement, Interactions, Performance' (EA 4334), University of Nantes, Nantes, France
| | - Fabian Horst
- Department of Training and Movement Science, Institute of Sport Science, Johannes Gutenberg-University Mainz, Mainz, Rhineland-Palatinate, Germany
| | - Sebastian Lapuschkin
- Department of Artificial Intelligence, Fraunhofer Heinrich Hertz Institute, Berlin, Germany
| | - Lilian Lacourpaille
- Laboratory 'Movement, Interactions, Performance' (EA 4334), University of Nantes, Nantes, France
| | - François Hug
- Laboratory 'Movement, Interactions, Performance' (EA 4334), University of Nantes, Nantes, France.,The University of Queensland, School of Health and Rehabilitation Sciences, Brisbane, Australia.,Institut Universitaire de France (IUF), Paris, France
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Sato S. Plasmodium-a brief introduction to the parasites causing human malaria and their basic biology. J Physiol Anthropol 2021; 40:1. [PMID: 33413683 PMCID: PMC7792015 DOI: 10.1186/s40101-020-00251-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
Malaria is one of the most devastating infectious diseases of humans. It is problematic clinically and economically as it prevails in poorer countries and regions, strongly hindering socioeconomic development. The causative agents of malaria are unicellular protozoan parasites belonging to the genus Plasmodium. These parasites infect not only humans but also other vertebrates, from reptiles and birds to mammals. To date, over 200 species of Plasmodium have been formally described, and each species infects a certain range of hosts. Plasmodium species that naturally infect humans and cause malaria in large areas of the world are limited to five—P. falciparum, P. vivax, P. malariae, P. ovale and P. knowlesi. The first four are specific for humans, while P. knowlesi is naturally maintained in macaque monkeys and causes zoonotic malaria widely in South East Asia. Transmission of Plasmodium species between vertebrate hosts depends on an insect vector, which is usually the mosquito. The vector is not just a carrier but the definitive host, where sexual reproduction of Plasmodium species occurs, and the parasite’s development in the insect is essential for transmission to the next vertebrate host. The range of insect species that can support the critical development of Plasmodium depends on the individual parasite species, but all five Plasmodium species causing malaria in humans are transmitted exclusively by anopheline mosquitoes. Plasmodium species have remarkable genetic flexibility which lets them adapt to alterations in the environment, giving them the potential to quickly develop resistance to therapeutics such as antimalarials and to change host specificity. In this article, selected topics involving the Plasmodium species that cause malaria in humans are reviewed.
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Affiliation(s)
- Shigeharu Sato
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia. .,Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
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申 琪. The Distributional Patterns of Medical Insects in the World and Its Relation with other Biota. INTERNATIONAL JOURNAL OF ECOLOGY 2021. [DOI: 10.12677/ije.2021.104064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ortúzar-Ferreira CN, Genovez-Oliveira JL, de Souza Oliveira M, de Mello ER, Thode-Filho S, de Oliveira ÁA, de Lima VM, Ferreira I, Berto BP. Isospora oliveirai n. sp. (Chromista: Miozoa: Eimeriidae) from the Greenish Schiffornis Schiffornis virescens (Lafresnaye, 1838) (Passeriformes: Tyranni: Tityridae) in South America. Acta Parasitol 2020; 65:843-851. [PMID: 32494953 DOI: 10.1007/s11686-020-00237-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/27/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Coccidia are obligatory intracellular parasites with at least one intestinal phase in their life cycles, being Isospora Schneider, 1881 the main coccidian genus related to the order Passeriformes. However, there is no record of isosporans from the passerine family Tityridae, which is the family of the greenish schiffornis Schiffornis virescens (Lafresnaye, 1838). PURPOSE This study aimed to examine the faeces from a greenish schiffornis S. virescens captured in the Itatiaia National Park, State of Rio de Janeiro, Southeastern Brazil, to determine what coccidian parasites were present. METHODS Only one specimen of Schiffornis virescens was captured with mist nets. Coccidian oocysts were recovered from the fecal samples by flotation in Sheather's saturated solution. Morphological observations, line drawings, photomicrographs and measurements were made in optical microscopy and digitally edited. The molecular analysis included the study of the sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene, with phylogenetic reconstructions based on the Neighbor-Joining and Maximum Likelihood analysis. RESULTS An Isospora sp. considered as new to science is described and identified from Schiffornis virescens (Lafresnaye, 1838). Isospora oliveirai n. sp. has oocysts that are subspheroidal, 26.0 × 24.8 μm, with rough, bilayered wall, c.2.5 μm thick. Micropyle and oocyst residuum absent, but one to six polar granules are present. Sporocysts lemon-shaped, 18.1 × 10.9 μm. The Stieda body is knob-like to half-moon-shaped and sub-Stieda is rounded. Sporocyst residuum is present, composed of scattered spherules of different sizes. Sporozoites are vermiform, with refractile bodies and nucleus. Molecular analysis at the COI gene exhibited similarity of 97% with Isospora serinuse Yang, Brice, Elliot et Ryan, 2015 from island canaries Serinus canaria (Linnaeus, 1758), and Isospora spp. from great tits Parus major (Linnaeus, 1758) and European robins Erithacus rubecula (Linnaeus, 1758). CONCLUSION Based on the morphological and molecular features, I. oliveirai is considered as new to science and the first coccidian species recorded from Tityridae.
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Antiproliferative Activity, Proapoptotic Effect, and Cell Cycle Arrest in Human Cancer Cells of Some Marine Natural Product Extract. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7948705. [PMID: 33294124 PMCID: PMC7714591 DOI: 10.1155/2020/7948705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/27/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023]
Abstract
Bioactive constituents of numerous marine organisms have been investigated recently for their preclinical and clinical anticancer activity. Three marine organisms: black-spotted sea cucumber: Pearsonothuria graeffei (Pg), lollyfish: Holothuria atra (Ha), and sea hare: Aplysia dactylomela (Ad), were collected during winter 2019 from Gulf of Aqaba, Red Sea, Egypt, and macerated with ethanol into three different extracts: PgE, HaE, and AdE, where each was in vitro assessed for its antiproliferative and proapoptotic properties on HepG2, HCT-116, and MCF-7 cancer cells. PgE dose-dependently inhibited the growth of HepG2, HCT-116, and MCF-7 cells within IC50 values 16.22, 13.34, and 18.09 μg/mL, respectively, while the IC50 values for the antiproliferative activity of HaE were 12.48, 10.45, and 10.36 μg/mL, respectively, and the IC50 values of AdE were 6.51, 5.33, and 6.87 μg/mL, respectively. All extracts were found to induce G0/G1 cell cycle arrest for HepG2 cells side by side with their inhibition of CDK2 on all three cell lines while all extracts were also showed to induce apoptosis in HepG2 cell line at pre-G 1 phase supplemented by their anticancer activity via proapoptotic protein Bax, caspase-3, and cleavage PARP increase, and antiapoptotic protein Bcl-2 downturn. Moreover, necrosis has been relatively noticed in HepG2 cell line as an additional anticancer activity for each extract. Our data introduced three ethanolic marine extracts as natural chemotherapeutic agents to be further developed for cancer control.
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Duarte S, Vieira PE, Costa FO. Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.55162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.
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