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Kulagin DN, Lunina AA, Simakova UV, Vedenin AA, Vereshchaka AL. Revision of the 'Acanthephyra purpurea' species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic. Mol Phylogenet Evol 2024; 195:108070. [PMID: 38574781 DOI: 10.1016/j.ympev.2024.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
We inventoried all nine species of the 'Acanthephyra purpurea' complex, one of the most abundant and cosmopolitan group of mesopelagic shrimps. We used 119 specimens at hand and genetic data for 124 specimens from GenBank and BOLD. Phylogenetic analysis of four genes (COI, 16S, NaK, and enolase) showed that the 'Acanthephyra purpurea' complex is polyphyletic and encompasses two species groups, 'A. purpurea' (mostly Atlantic) and 'A. smithi' (Indo-West Pacific). The 'A. purpurea' species group consists of two major molecular clades A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa. Molecular data suggest that hitherto accepted species A. acanthitelsonis, A. pelagica, and A. sica should be considered as synonyms. The Atlantic is inhabited by at least two cryptic genetic lineages of A. pelagica and A. quadrispinosa. Morphological analyses of qualitative and quantitative (900 measurements) characters resulted in a tabular key to species and in a finding of four evolutionary traits. Atlantic species showed various scenarios of diversification visible on mitochondrial gene level, nuclear gene level, and morphological level. We recorded and discussed similar phylogeographic trends in diversification and in distribution of genetic lineages within two different clades: A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa.
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Affiliation(s)
- Dmitry N Kulagin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Anastasiia A Lunina
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Ulyana V Simakova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | | | - Alexander L Vereshchaka
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia.
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Shen ZY, Terada T, Landry JF, Hoare RJB, Kuo LY, Chou MH, Hsu YF, Huang JP. Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae). Mol Phylogenet Evol 2024; 194:108040. [PMID: 38395320 DOI: 10.1016/j.ympev.2024.108040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonodagen. nov., Petalagen. nov., and Pediformisgen. nov., and revalidating five genera: Cuprina, Calicotis, Thylacosceles, Actinoscelis, Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae.
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Affiliation(s)
- Zong-Yu Shen
- Biodiversity Research Center, Academic Sinica, Taipei, Taiwan; Department of Life Science, National Taiwan Normal University, Taipei, Taiwan; Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Takeshi Terada
- Okayama Prefectural Environmental Conservation Foundation, Inc., Okayama, Japan
| | - Jean-François Landry
- Canadian National Collection of Insects, Arachnids, and Nematodes, Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, C.E.F., Ottawa, Ontario, Canada
| | - Robert J B Hoare
- New Zealand Arthropod Collection, Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, New Zealand
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Hsun Chou
- Department of Biological Sciences, Northern Arizona University, AZ, USA
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
| | - Jen-Pan Huang
- Biodiversity Research Center, Academic Sinica, Taipei, Taiwan.
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Tchoumbou M, Harl J, Souaibou A, Iezhova T, Valkiūnas G. Molecular characterization of Haemoproteus enucleator with emphasis on the host and geographic distribution. Acta Trop 2024; 253:107154. [PMID: 38373526 DOI: 10.1016/j.actatropica.2024.107154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Haemoproteus species (Haemosporida, Haemoproteidae) are cosmopolitan and highly diverse blood parasites of birds that have been neglected in avian medicine. However, recent discoveries based on molecular diagnostic markers show that these pathogens often cause marked damage to various internal organs due to exo-erythrocytic development, sometimes resulting in severe and even lethal avian haemoproteosis, including cerebral pathologies. Molecular markers are essential for haemoproteosis diagnostics, but the data is limited, particularly for parasites transmitted in tropical ecosystems. This study combined microscopic and molecular approaches to characterize Haemoproteus enucleator morphologically and molecularly. Blood samples were collected from the African pygmy kingfisher Ispidina picta in Cameroon, and the parasite was identified using morphological characters of gametocytes. The analysis of partial cytochrome b sequences (cytb) identified a new Haemoproteus lineage (hISPIC03), which was linked to the morphospecies H. enucleator. Illustrations of blood stages were provided and the phylogenetic analysis showed that the new lineage clustered with five other closely related lineages belonging to the same morphospecies (hALCLEU01, hALCLEU02, hALCLEU03, hISPIC01, and hALCQUA01), with a maximum genetic distance between these lineages of 1.5 % (7 bp difference) in the 478 bp cytb sequences. DNA haplotype network was developed and identified geographic and host distribution of all lineages belonging to H. enucleator group. These lineages were almost exclusively detected in African kingfishers from Gabon, Cameroon, South Africa, and Botswana. This study developed the molecular characterization of H. enucleator and provides opportunities for diagnostics of this pathogen at all stages of its life cycle, which remains undescribed in all its closely related lineages.
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Affiliation(s)
- Mélanie Tchoumbou
- Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania; Biodiversity Initiative, Houghton, MI, USA.
| | - Josef Harl
- Institute of Pathology, Department for Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Aladji Souaibou
- Vector Borne Parasitic & Infectious Diseases Laboratory of the Applied Biology and Ecology Research Unit, University of Dschang, Cameroon
| | - Tatjana Iezhova
- Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
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Reinecke A, Flaig IC, Lozano YM, Rillig MC, Hilker M. Drought induces moderate, diverse changes in the odour of grassland species. Phytochemistry 2024; 221:114040. [PMID: 38428627 DOI: 10.1016/j.phytochem.2024.114040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Plants react to drought stress with numerous changes including altered emissions of volatile organic compounds (VOC) from leaves, which provide protection against oxidative tissue damage and mediate numerous biotic interactions. Despite the share of grasslands in the terrestrial biosphere, their importance as carbon sinks and their contribution to global biodiversity, little is known about the influence of drought on VOC profiles of grassland species. Using coupled gas chromatography-mass spectrometry, we analysed the odorants emitted by 22 European grassland species exposed to an eight-week-lasting drought treatment (DT; 30% water holding capacity, WHC). We focused on the odorants emitted during the light phase from whole plant shoots in their vegetative stage. Emission rates were standardised to the dry weight of each shoot. Well-watered (WW) plants (70% WHC) served as control. Drought-induced significant changes included an increase in total emission rates of plant VOC in six and a decrease in three species. Diverging effects on the number of emitted VOC (chemical richness) or on the Shannon diversity of the VOC profiles were detected in 13 species. Biosynthetic pathways-targeted analyses revealed 13 species showing drought-induced higher emission rates of VOC from one, two, three, or four major biosynthetic pathways (lipoxygenase, shikimate, mevalonate and methylerythritol phosphate pathway), while six species exhibited reduced emission rates from one or two of these pathways. Similarity trees of odorant profiles and their drought-induced changes based on a biosynthetically informed distance metric did not match species phylogeny. However, a phylogenetic signal was detected for the amount of terpenoids released by the studied species under WW and DT conditions. A comparative analysis of emission rates of single compounds released by WW and DT plants revealed significant VOC profile dissimilarities in four species only. The moderate drought-induced changes in the odorant emissions of grassland species are discussed with respect to their impact on trophic interactions across the food web. (294 words).
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Affiliation(s)
- Andreas Reinecke
- Freie Universität Berlin, Inst. of Biology, Applied Zoology/Animal Ecology, Haderslebener Str. 9, 12163, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195, Berlin, Germany.
| | - Isabelle C Flaig
- Freie Universität Berlin, Inst. of Biology, Applied Zoology/Animal Ecology, Haderslebener Str. 9, 12163, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195, Berlin, Germany
| | - Yudi M Lozano
- Freie Universität Berlin, Inst. of Biology, Plant Ecology, Altensteinstr. 6, 14195, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195, Berlin, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Inst. of Biology, Plant Ecology, Altensteinstr. 6, 14195, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195, Berlin, Germany
| | - Monika Hilker
- Freie Universität Berlin, Inst. of Biology, Applied Zoology/Animal Ecology, Haderslebener Str. 9, 12163, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195, Berlin, Germany
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Powell VCR, Barr WA, Hammond AS, Wood BA. Behavioral and phylogenetic correlates of limb length proportions in extant apes and monkeys: Implications for interpreting hominin fossils. J Hum Evol 2024; 190:103494. [PMID: 38564844 DOI: 10.1016/j.jhevol.2024.103494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 04/04/2024]
Abstract
The body proportions of extant animals help inform inferences about the behaviors of their extinct relatives, but relationships between body proportions, behavior, and phylogeny in extant primates remain unclear. Advances in behavioral data, molecular phylogenies, and multivariate analytical tools make it an opportune time to perform comprehensive comparative analyses of primate traditional limb length proportions (e.g., intermembral, humerofemoral, brachial, and crural indices), body size-adjusted long bone proportions, and principal components. In this study we used a mix of newly-collected and published data to investigate whether and how the limb length proportions of a diverse sample of primates, including monkeys, apes, and modern humans, are influenced by behavior and phylogeny. We reconfirm that the intermembral index, followed by the first principal component of traditional limb length proportions, is the single most effective variable distinguishing hominoids and other anthropoids. Combined limb length proportions and positional behaviors are strongly correlated in extant anthropoid groups, but phylogeny is a better predictor of limb length proportion variation than of behavior. We confirm convergences between members of the Atelidae and extant apes (especially Pan), members of the Hylobatidae and Pongo, and a potential divergence of Presbytis limb proportions from some other cercopithecoids, which correlate with adaptations for forelimb-dominated behaviors in some colobines. Collectively, these results substantiate hypotheses indicating that extinct hominins and other hominoid taxa can be distinguished by analyzing combinations of their limb length proportions at different taxonomic levels. From these results, we hypothesize that fossil skeletons characterized by notably disparate limb length proportions are unlikely to have exhibited similar behavioral patterns.
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Affiliation(s)
- Vance C R Powell
- Department of Anatomy, Howard University College of Medicine, 520 W St. N.W., Washington, D.C., 20059, USA; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, D.C., 20052, USA.
| | - W Andrew Barr
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, D.C., 20052, USA
| | - Ashley S Hammond
- Division of Anthropology, American Museum of Natural History (AMNH), New York, N.Y., 10024, USA; New York Consortium in Evolutionary Primatology at AMNH, New York, N.Y., 10024, USA
| | - Bernard A Wood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, D.C., 20052, USA
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Torday JS. The synchronic, diachronic cell as the holism of consciousness. Prog Biophys Mol Biol 2024; 188:19-23. [PMID: 38408617 DOI: 10.1016/j.pbiomolbio.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/02/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024]
Abstract
The cell is both synchronic and diachronic, based on ontogeny and phylogeny, respectively. As experimental evidence for this holism, absent gravitational force, differentiated lung and bone cells devolve, losing their phenotypes, losing their evolutionary status, reverting to their nonlocal status. Thus, when evolution is seen as serial homeostasis, it is homologous with Quantum Entanglement as the nonlocal means of maintaining homeostatic balance between particles. This monadic perspective on consciousness is one-hundred and eighty degrees out of synch with the conventional way of thinking about consciousness as a diad, or mind and brain. There have been many attempts to explain consciousness, virtually all of them based on the brain as mind. The working hypothesis is that consciousness is a holism constituted by the unicell, the lipid cell membrane forming a barrier between inside and outside of the cell's environment as a topology. Conceptually, both the unicell and 'two hands clapping' are holisms, but because the cell is constituted by the ambiguity of negative entropy, and 'one hand clapping' requires two hands, they are both pseudo-holisms, constantly striving to be whole again. In the case of the cell, it is incomplete in the sense that there are factors in the ever-changing environment that can homeostatically complete it. That process results in biochemical modification of specific DNA codes in the egg or sperm so that the offspring is able to adapt in subsequent generations epigenetically. The opportunity to trace the evolution of the breath from humans to fish opens up to the further revelation of the interplay between evolution and geological change, tracing it back to invertebrates, sponges, and ultimately to unicellular organisms. And therein is evidence that the Cosmos itself 'breathes', providing the ultimate celestial fundament for this trail of holisms.
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Affiliation(s)
- John S Torday
- University of California- Los Angeles, Los Angeles, CA, USA.
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Shohana NN, Dey AR, Rony SA, Akter S, Karmakar BC, Alam MZ. Comparison of the first time detected Oesophagostomum asperum with Oesophagostomum columbianum in sheep and goats in Bangladesh based on the trinity: Morphology, morphometry and genetic diversity. Saudi J Biol Sci 2024; 31:103980. [PMID: 38500816 PMCID: PMC10945262 DOI: 10.1016/j.sjbs.2024.103980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Oesophagostomum spp. (Family: Chabertiidae) is keeping a low profile in terms of severity in Bangladesh while maintaining economic loss through disguise within sheep and goats. The study was performed to identify prevalence, confirmation of species through morphology and morphometry followed by phylogeny using ITS2 and COX1 genes. In total 384 slaughterhouse-sourced small and large intestines were pooled from Mymensingh, Kishoreganj, Netrokona, Sherpur and Tangail districts of Mymensingh division. Followed by isolation, O. columbianum and O. asperum were identified following their key morphological features. Notably, O. asperum was first time detected in Bangladesh. The overall prevalence of Oesophagostomum spp. was found 60.93%. The prevalence of O. columbianum (64.95%) was almost double than that of O. asperum (35.04%). Among several characters, only the distance between anus to tail tip showed a significant morphological disparity in female. The Neighbor-joining (NJ) phylogenic trees based on ITS2 and COX1 genes confirmed the study species. The first time identified O. asperum along with morphometry and phylogeny will add value to the fact that nematodes are invisibly present with high prevalence in this country. This study will help to draw specific attention to command a practical control strategy for intervening in economic loss.
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Affiliation(s)
- Nusrat Nowrin Shohana
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Anita Rani Dey
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Sharmin Aqter Rony
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Shirin Akter
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Bimal Chandra Karmakar
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mohammad Zahangir Alam
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Kumar TP, Gireesh-Babu P, Vasudevan D, Pavan-Kumar A, Chaudhari A. Characterization of Kiss/Kissr system and expression profiling through developmental stages indicate kiss1 to be the active isotype in Clarias magur. Fish Physiol Biochem 2024:10.1007/s10695-024-01343-4. [PMID: 38647980 DOI: 10.1007/s10695-024-01343-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Kisspeptin (Kiss) and kisspeptin receptor (Kissr) system is a key regulator of GnRH expression in several vertebrates. The Indian catfish, Clarias magur, is popular in the Indian sub-continent, and a neo-type of the Asian catfish, C. batrachus. Catfish breeding is constrained as males do not release milt captivity with/without stimulation. Magur Kiss/Kissr system comprising of kiss1, kiss2, kissr1, and kissr2 genes was characterized for the first time. Full-length mRNA was sequenced using RACE PCR. Neighbor-joining tree of predicted proteins shows one clade of teleost orthologs. Magur whole genome (NCBI GenBank) has single copies of each gene, though yet unannotated/misannotated. Anomalies in the nomenclature of earlier sequences in GenBank were noted. Relative gene expression was profiled during various ontogenic stages, in six tissues including brain and gonads at maturity, and also in brains and gonads of premature and spent fish. Expression of gnrh1, gnrhr1, and gnrhr2 was estimated concomitantly. The kiss1 was the first to be twofold upregulated (P < 0.05) at 12 h post fertilization. Kiss/Kissr genes expressed primarily in the brain, ovary, and testis. Though kiss2 was 10 times higher than kiss1, only kiss1 showed significant modulation across stages and appears to be the active isotype that regulates GnRH in magur.
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Affiliation(s)
- Thushar P Kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | | | - Dileep Vasudevan
- RGCB-Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Annam Pavan-Kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Aparna Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India.
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Pushpavathi D, Krishnamurthy YL. Study on endolichenic fungal assemblage in Parmotrema and Heterodermia lichens of Shivamoga, Karnataka. Mol Biol Rep 2024; 51:549. [PMID: 38642168 DOI: 10.1007/s11033-024-09497-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Lichen is a symbiotic association of algae and fungi, recognized as a self-sustaining ecosystem that constitutes an indeterminant number of bacteria, actinomycetes, fungi, and protozoa. We evaluated the endolichenic fungal assemblage given the dearth of knowledge on endolichenic fungi (ELFs), particularly from part of the Central Western Ghats, Karnataka, and conducted a phylogenetic analysis of xylariaceous fungi, the most diversified group of fungi using ITS and ITS+Tub2 gene set. RESULTS Out of 17 lichen thalli collected from 5 ecoregions, 42 morphospecies recovered, belong to the class Sordariomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes, Saccharomycetes. About 19 and 13 ELF genera have been reported from Parmotrema and Heterodermia thallus. Among the ecoregions EC2 showing highest species diversity (Parmotrema (1-D) = 0.9382, (H) = 2.865, Fisher-α = 8.429, Heterodermia (1-D) = 0.8038, H = 1.894, F-α = 4.57) followed the EC3 and EC1. Xylariales are the predominant colonizer reported from at least one thallus from four ecoregions. The morphotypes ELFX04, ELFX05, ELFX08 and ELFX13 show the highest BLAST similarity (> 99%) with Xylaria psidii, X. feejeensis, X. berteri and Hypoxylon fragiforme respectively. Species delimitation and phylogenetic position reveal the closest relation of Xylariaceous ELFs with plant endophytes. CONCLUSIONS The observation highlights that the deciduous forest harness a high number of endolichenic fungi, a dominant portion of these fungi are non-sporulating and still exist as cryptic. Overall, 8 ELF species recognized based on phylogenetic analysis, including the two newly reported fungi ELFX03 and ELFX06 which are suspected to be new species based on the present evidence. The study proved, that the lichen being rich source to establish fungal diversity and finding new species. Successful amplification of most phylogenetic markers like RPB2, building of comprehensive taxonomic databases and application of multi-omics data are further needed to understand the complex nature of lichen-fungal symbiosis.
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Affiliation(s)
- D Pushpavathi
- Department of PG Studies and Research in Applied Botany, Kuvempu University, Jnanasahyadri, Shankaraghatta, Karnataka, 577451, India
| | - Y L Krishnamurthy
- Department of PG Studies and Research in Applied Botany, Kuvempu University, Jnanasahyadri, Shankaraghatta, Karnataka, 577451, India.
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Carvalho APS, Owens HL, St Laurent RA, Earl C, Dexter KM, Messcher RL, Willmott KR, Aduse-Poku K, Collins SC, Homziak NT, Hoshizaki S, Hsu YF, Kizhakke AG, Kunte K, Martins DJ, Mega NO, Morinaka S, Peggie D, Romanowski HP, Sáfián S, Vila R, Wang H, Braby MF, Espeland M, Breinholt JW, Pierce NE, Kawahara AY, Lohman DJ. Comprehensive phylogeny of Pieridae butterflies reveals strong correlation between diversification and temperature. iScience 2024; 27:109336. [PMID: 38500827 PMCID: PMC10945170 DOI: 10.1016/j.isci.2024.109336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/28/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Temperature is thought to be a key factor influencing global species richness patterns. We investigate the link between temperature and diversification in the butterfly family Pieridae by combining next generation DNA sequences and published molecular data with fine-grained distribution data. We sampled nearly 600 pierid butterfly species to infer the most comprehensive molecular phylogeny of the family and curated a distribution dataset of more than 800,000 occurrences. We found strong evidence that species in environments with more stable daily temperatures or cooler maximum temperatures in the warm seasons have higher speciation rates. Furthermore, speciation and extinction rates decreased in tandem with global temperatures through geological time, resulting in a constant net diversification.
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Affiliation(s)
- Ana Paula S. Carvalho
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | - Hannah L. Owens
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Ryan A. St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Chandra Earl
- Department of Natural Sciences, Bernice Pauahi Bishop Museum, Honolulu, HI, USA
| | - Kelly M. Dexter
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | - Rebeccah L. Messcher
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | - Keith R. Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | | | | | - Nicholas T. Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Sugihiko Hoshizaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, R.O.C
| | - Athulya G. Kizhakke
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Dino J. Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY, USA
- Insect Committee of Nature Kenya, The East Africa Natural History Society, Nairobi, Kenya
| | - Nicolás O. Mega
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Sadaharu Morinaka
- Saitama Study Center, The Open University of Japan, Omiya-ku, Saitama City, Japan
| | - Djunijanti Peggie
- Museum Zoologi Bogor, Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Cibinong, Bogor, Indonesia
| | - Helena P. Romanowski
- Laboratório de Ecologia de Insetos, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Szabolcs Sáfián
- African Butterfly Research Institute, Karen, Nairobi, Kenya
- Institute of Silviculture and Forest Protection, University of Sopron, Sopron, Hungary
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Houshuai Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Michael F. Braby
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Australian National Insect Collection, National Research Collections Australia, Canberra, ACT, Australia
| | - Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Jesse W. Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Intermountain Healthcare, Intermountain Precision Genomics, St. George, UT, USA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - David J. Lohman
- Department of Biology, City University of New York, New York, NY, USA
- PhD Program in Biology, Graduate Center, City University of New York, New York, NY, USA
- Entomology Section, National Museum of Natural History, Manila, Philippines
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11
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Zhou Y, Yu L, Liu M, Liang W, Li Z, Nan Z, Kan B. Virulence, antibiotic resistance phenotypes and molecular characterisation of Vibrio furnissii isolates from patients with diarrhoea. BMC Infect Dis 2024; 24:412. [PMID: 38641583 PMCID: PMC11027346 DOI: 10.1186/s12879-024-09273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/29/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Vibrio furnissii is an emerging human pathogen closely related to V. fluvialis that causes acute gastroenteritis. V. furnissii infection has been reported to be rarer than V. fluvialis, but a multi-drug resistance plasmid has recently been discovered in V. furnissii. METHODS During daily monitoring at a general hospital in Beijing, China, seven V. furnissii strains were collected from patients aged over 14 years who presented with acute diarrhoea between April and October 2018. Genome analysis and comparison were performed for virulence and antimicrobial resistance genes, plasmids and transposon islands, together with phylogenetic analysis. Antimicrobial resistance to 19 antibiotics was investigated using the microbroth dilution method. Virulence phenotypes were investigated based on type VI secretion system (T6SS) expression and using a bacterial killing assay and a haemolysin assay. RESULTS Phylogenetic analysis based on single-nucleotide polymorphisms revealed a closer relationship between V. furnissii and V. fluvialis than between other Vibrio spp. The seven V. furnissii isolates were in different monophyletic clades in the phylogenetic tree, suggesting that the seven cases of gastroenteritis were independent. High resistance to cefazolin, tetracycline and streptomycin was found in the V. furnissii isolates at respective rates of 100.0%, 57.1% and 42.9%, and intermediate resistance to ampicillin/sulbactam and imipenem was observed at respective rates of 85.7% and 85.7%. Of the tested strains, VFBJ02 was resistant to both imipenem and meropenem, while VFBJ01, VFBJ02, VFBJ05 and VFBJ07 were multi-drug resistant. Transposon islands containing antibiotic resistance genes were found on the multi-drug resistance plasmid in VFBJ05. Such transposon islands also occurred in VFBJ07 but were located on the chromosome. The virulence-related genes T6SS, vfh, hupO, vfp and ilpA were widespread in V. furnissii. The results of the virulence phenotype assays demonstrated that our isolated V. furnissii strains encoded an activated T6SS and grew in large colonies with strong beta-haemolysis on blood agar. CONCLUSION This study showed that diarrhoea associated with V. furnissii occurred sporadically and was more common than expected in the summer in Beijing, China. The antibiotic resistance of V. furnissii has unique characteristics compared with that of V. fluvialis. Fluoroquinolones and third-generation cephalosporins, such as ceftazidime and doxycycline, were effective at treating V. furnissii infection. Continua laboratory-based surveillance is needed for the prevention and control of V. furnissii infection, especially the dissemination of the antibiotic resistance genes in this pathogen.
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Affiliation(s)
- Yanyan Zhou
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100052, China
| | - Li Yu
- Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, China
| | - Ming Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Weili Liang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Zhenpeng Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Zheng Nan
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100052, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China.
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12
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Ghimire P, Palacios C, Trimble J, Lamichhaney S. Museum Genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens. G3 (Bethesda) 2024:jkae081. [PMID: 38626302 DOI: 10.1093/g3journal/jkae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/16/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia sps.) and examine their genetic composition, taxonomic status, and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences, however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollyneck are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian sub-species C. e. neglecta and C. e. episcopus suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.
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Affiliation(s)
- Prashant Ghimire
- Department of Biological Sciences, Kent State University, Kent, OH, USA, 44240
| | - Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH, USA, 44240
| | - Jeremiah Trimble
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA, 02138
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH, USA, 44240
- School of Biomedical Sciences, Kent State University, Kent, OH, USA, 44240
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13
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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. Water Res 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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14
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Dementieva NV, Shcherbakov YS, Stanishevskaya OI, Vakhrameev AB, Larkina TA, Dysin AP, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbach NR, Griffin DK, Romanov MN. Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds. J Zhejiang Univ Sci B 2024; 25:324-340. [PMID: 38584094 PMCID: PMC11009443 DOI: 10.1631/jzus.b2300443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/10/2023] [Indexed: 04/09/2024]
Abstract
The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
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Affiliation(s)
- Natalia V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia.
| | - Yuri S Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Tatiana A Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Artem P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga A Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anna E Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anastasiia I Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Grigoriy K Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Natalia R Reinbach
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. ,
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. ,
- L K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, 142132, Russia. ,
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15
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Irwin LN. Behavioral indicators of heterogeneous subjective experience in animals across the phylogenetic spectrum: Implications for comparative animal phenomenology. Heliyon 2024; 10:e28421. [PMID: 38623251 PMCID: PMC11016586 DOI: 10.1016/j.heliyon.2024.e28421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 04/17/2024] Open
Abstract
This behavioral study was undertaken to provide empirical evidence in favor of or opposed to the notion that animals across a wide breadth of the animal kingdom have subjective (personal) experience that varies with their lifestyles, ecological constraints, or phylogeny. Twelve species representing two invertebrate phyla and six vertebrate classes were observed unobtrusively in 15-min episodes, during which three modes of behavior (volitional, interactive, and egocentric) were quantified according to the frequency, variety, and dynamism of each mode. Volitional behavior was the most prevalent and dynamic mode for nearly all species, largely without regard to phylogenetic position. Interactive behavior likewise varied inconsistently across the entire evolutionary spectrum. Egocentric behavior was concentrated among the avian and mammalian species, but evidence of it were observed in the invertebrate species as well. Diagrams of the matrix constructed from the three qualitative modes and three quantitative attributes for each mode provide a metaphorical representation of the unique experiential profile of each species. To the extent that these behavioral measures correlate with the nature of the animal's subjective experience, they support the growing view that phenomenology is heterogeneous, multimodal, and non-linear in extent across the animal kingdom.
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Affiliation(s)
- Louis N. Irwin
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
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16
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Wong Chin JM, Puchooa D, Bahorun T, Alrefaei AF, Neergheen VS, Jeewon R. Multigene phylogeny, bioactive properties, enzymatic and dye decolorization potential of selected marine fungi from brown algae and sponges of Mauritius. Heliyon 2024; 10:e28955. [PMID: 38623192 PMCID: PMC11016617 DOI: 10.1016/j.heliyon.2024.e28955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Marine fungi represent an important proportion of the microbial diversity in the oceans. They are attractive candidates for biotechnological purposes and industrial applications. Despite an increasing interest in mycology, marine fungi associated with sponges and algae have been poorly studied in Mauritius. The objectives of this study were to: 1) use multigene phylogenetic analyses to identify isolated marine fungi; 2) determine the differences in the antimicrobial and antioxidant properties of the fungal extracts; and 3) assess their enzyme activities and dye decolorization potential. Five fungal isolates viz Aspergillus chevalieri, Aspergillus iizukae, Aspergillus ochraceus, Exserohilum rostratum and Biatriospora sp. were identified based on phylogenetic analyses. There was no significant difference in the antimicrobial properties of the liquid and solid media extracts unlike the antioxidant properties (p < 0.05). The solid media extract of Aspergillus chevalieri (F2-SF) had a minimum inhibitory concentration of 0.156 mg/ml against Staphylococcus aureus while Aspergillus ochraceus (F25-SF) had a minimum inhibitory concentration of 0.313 and 2.5 mg/ml against Enterococcus faecalis and Salmonella typhi. The solid media extract of Biatriospora sp. (F34-SF) had a minimum inhibitory concentration of 0.195 and 1.563 mg/ml against Bacillus cereus, Escherichia coli and Enterobacter cloacae. An IC50 of 78.92 ± 4.71 μg/ml in the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) scavenging assay, ferric reducing antioxidant power (FRAP) value of 11.17 ± 0.20 mM Fe2+/g dry weight extract (DWE) and total phenolic content 360.35 ± 10.31 mg GAE/g DWE was obtained with the solid media extract of Aspergillus chevalieri (F2-SF). Aspergillus ochraceus (F25-SF) and Biatriospora sp. (F34-SF) solid media extracts showed lower IC50 values in the DPPH assay and higher total phenolic content as compared to the liquid media extracts. Aspergillus chevalieri was a good producer of the enzymes DNAse and lipase and had maximum percentage dye decolorization of 79.40 ± 17.72% on Congo red. An enzymatic index ≥ 2 was found for the DNAse and lipase and the maximum percentage dye decolorization of 87.18 ± 3.80% was observed with Aspergillus ochraceus on Methylene blue. Regarding Biatriospora sp., it was a moderate producer of the three enzymes amylase, DNAse and protease and had a maximum dye decolorization potential of 56.29 ± 6.51% on Crystal violet. This study demonstrates that Mauritian marine fungi possess good bioactive properties, enzymatic and dye decolorization potentials, that can potentially be considered for use in pharmaceutical and industrial applications.
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Affiliation(s)
- Jessica Mélanie Wong Chin
- Biopharmaceutical Unit, Center for Biomedical and Biomaterials Research (CBBR), University of Mauritius, Réduit, Mauritius
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit, Mauritius
| | - Daneshwar Puchooa
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit, Mauritius
| | - Theeshan Bahorun
- Biopharmaceutical Unit, Center for Biomedical and Biomaterials Research (CBBR), University of Mauritius, Réduit, Mauritius
- Department of Biosciences and Ocean Studies, Faculty of Science, University of Mauritius, Réduit, Mauritius
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Vidushi S. Neergheen
- Biopharmaceutical Unit, Center for Biomedical and Biomaterials Research (CBBR), University of Mauritius, Réduit, Mauritius
| | - Rajesh Jeewon
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit, Mauritius
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Shi YJ, Mi JX, Huang JL, Tian FF, He F, Zhong Y, Yang HB, Wang F, Xiao Y, Yang LK, Zhang F, Chen LH, Wan XQ. A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau. Mol Phylogenet Evol 2024:108072. [PMID: 38615706 DOI: 10.1016/j.ympev.2024.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
While the diversity of species formation is broadly acknowledged, significant debate exists regarding the universal nature of hybrid species formation. Through an 18-year comprehensive study of all Populus species on the Qinghai-Tibet Plateau, 23 previously recorded species and 8 new species were identified. Based on morphological characteristics, these can be classified into three groups: species in section Leucoides, species with large leaves, and species with small leaves in section Tacamahaca. By conducting whole-genome re-sequencing of 150 genotypes from these 31 species, 2.28 million single nucleotide polymorphisms (SNPs) were identified. Phylogenetic analysis utilizing these SNPs not only revealed a highly intricate evolutionary network within the large-leaf species of section Tacamahaca but also confirmed that a new species, P. curviserrata, naturally hybridized with P. cathayana, P. szechuanica, and P. ciliata, resulting in 11 hybrid species. These findings indicate the widespread occurrence of hybrid species formation within this genus, with hybridization serving as a key evolutionary mechanism for Populus on the plateau. A novel hypothesis, "Hybrid Species Exterminating Their Ancestral Species (HSEAS)," is introduced to explain the mechanisms of hybrid species formation at three different scales: the entire plateau, the southeastern mountain region, and individual river valleys.
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Affiliation(s)
- Yu-Jie Shi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China
| | - Jia-Xuan Mi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin-Liang Huang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fei-Fei Tian
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fang He
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhong
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China
| | - Han-Bo Yang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China
| | - Fang Wang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Xiao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin-Kai Yang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fan Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang-Hua Chen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China
| | - Xue-Qin Wan
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China.
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18
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Zhao R, Li H, Wu G, Wang YF. Codon usage bias analysis in the mitochondrial genomes of five Rhingia Scopoli (Diptera, Syrphidae, Eristalinae) species. Gene 2024; 917:148466. [PMID: 38615984 DOI: 10.1016/j.gene.2024.148466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/26/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
This study presents the sequencing and annotation of mitochondrial genomes from five Rhingia species of the family Syrphidae, focusing on codon bias. Each species possessed 22 tRNAs genes, 13 protein-coding genes, 2 rRNAs genes, and a control region, without any observed gene rearrangements. Nucleotide composition analysis revealed a higher AT content compared with GC content, indicating AT enrichment. Neutrality plot, Parity rule 2 bias, and effective number of codons plot analyses collectively indicated that natural selection primarily influences the codon usage bias in the five Rhingia species. Relative synonymous codon usage analysis identified the optimal codons for Rhingia binotata, R. fromosana, R. campestris, R. louguanensis, and R. xanthopoda as 10, 14, 10, 11, and 12, respectively, all ending with A/U and exhibiting AT preference. Phylogenetic analysis, based on maximum likelihood and Bayesian inference methods applied to three datasets, confirmed the monophyly of Rhingia. In conclusion, this research establishes a foundation for understanding the phylogenetic evolution and codon usage patterns in Rhingia, offering valuable for future studies.
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Affiliation(s)
- Rui Zhao
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Hu Li
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China.
| | - Gang Wu
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Yi-Fan Wang
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
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Lindsey CR, Knoll AH, Herron MD, Rosenzweig F. Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae. BMC Biol 2024; 22:79. [PMID: 38600528 PMCID: PMC11007952 DOI: 10.1186/s12915-024-01878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. RESULTS Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae. CONCLUSIONS Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.
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Affiliation(s)
- Charles Ross Lindsey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
| | - Matthew D Herron
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, GA, 30332, USA.
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20
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Marwaha S, Ranjan R, Nath K, Singh M, Sawal RK, Sahoo A. Molecular epidemiology of anaplasmosis in Indian dromedary camels. Vet Res Commun 2024:10.1007/s11259-024-10373-5. [PMID: 38589771 DOI: 10.1007/s11259-024-10373-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
The present study aimed to investigate the molecular epidemiology, risk factors, and haemato-biochemical changes in anaplasmosis in Indian dromedary camels. Blood samples collected from 103 camels were analysed using blood smear examination and semi-nested PCR based on the 16s rRNA gene to diagnose anaplasmosis. The prevalence of anaplasmosis was estimated to be 42.72% (95% CI: 33.59-52.37) by PCR assay and 16.5% (95% CI: 10.47-24.95%) by blood smear examination. Phylogenetic analysis of six partial sequences of 16s rRNA gene obtained in the present study indicated the involvement of multiple Anaplasma species, including A. marginale and A. platys, showing genetic similarity with cattle strains. A novel genotype related to A. camelii/A. cinensis/A. platys group was also identified. Hemato-biochemical examination revealed mild anaemia, increased serum urea nitrogen and creatinine levels, and decreased total protein and albumin levels in Anaplasma-positive animals. The infections were largely subclinical in nature, except in one camel that revealed fever, inappetence, and pale mucous membrane and responded well to treatment with oxytetracycline. To our knowledge, this is the first molecular study on camel anaplasmosis in India, indicating a high prevalence of infection and involvement of multiple Anaplasma species with potential risk for interspecies transmission.
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Affiliation(s)
- Sumnil Marwaha
- ICAR-National Research Centre on Camel, Bikaner, Rajasthan, 334001, India
| | - Rakesh Ranjan
- ICAR-National Research Centre on Camel, Bikaner, Rajasthan, 334001, India.
| | - Kashi Nath
- ICAR-National Research Centre on Camel, Bikaner, Rajasthan, 334001, India
| | - Meetpal Singh
- ICAR-National Research Centre on Camel, Bikaner, Rajasthan, 334001, India
| | - R K Sawal
- ICAR-National Research Centre on Camel, Bikaner, Rajasthan, 334001, India
| | - Artabandhu Sahoo
- ICAR-National Research Centre on Camel, Bikaner, Rajasthan, 334001, India
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21
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Dolatabad HK, Mahjenabadi VAJ. Geographical and climatic distribution of lentil-nodulating rhizobia in Iran. FEMS Microbiol Ecol 2024:fiae046. [PMID: 38587812 DOI: 10.1093/femsec/fiae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
Lentil is one of the most important legumes cultivated in various provinces of Iran. However, there is limited information about the symbiotic rhizobia of lentils in this country. In this study, molecular identification of lentil-nodulating rhizobia was performed based on 16S-23S rRNA intergenic spacer (IGS) and recA, atpD, glnII, and nodC gene sequencing. Using PCR-RFLP analysis of 16S-23S rRNA IGS, a total of 116 rhizobia isolates were classified into 20 groups, leaving seven strains unclustered. Phylogenetic analysis of representative isolates revealed that the rhizobia strains belonged to Rhizobium leguminosarum and Rhizobium laguerreae, and the distribution of the species is partially related to geographical location. R. leguminosarum was the dominant species in North Khorasan and Zanjan, while R. laguerreae prevailed in Ardabil and East Azarbaijan. The distribution of the species was also influenced by agroecological climates; R. leguminosarum thrived in cold semi-arid climates, whereas R. laguerreae adapted to humid continental climates. Both species exhibited equal dominance in the Mediterranean climate, characterized by warm, dry summers and mild, wet winters, in Lorestan and Kohgiluyeh-Boyer Ahmad provinces.
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Affiliation(s)
- Hossein Kari Dolatabad
- Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Karaj, Iran
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22
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Armand A, Khodaparast SA, Nazari S, Zibaee A. Morpho-molecular study of entomopathogenic fungi associated with citrus orchard pests in Northern Iran. Arch Microbiol 2024; 206:202. [PMID: 38568380 DOI: 10.1007/s00203-024-03944-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Entomopathogenic fungi play a significant role in regulating insect populations in nature and have potential applications in pest management strategies in different regions. Citrus spp. are among the important horticultural products in northern Iran, and the orchards are affected by different insect pests, especially mealybugs. This study aimed to isolate and identify entomopathogenic fungi associated with citrus orchard pests in northern Iran, focusing on Akanthomyces and Lecanicillium species on mealybugs. Through the samples collected from different regions within Guilan province, 12 fungal isolates were collected and identified based on the combination of morphological characteristics and molecular data. Akanthomyces lecanii, A. muscarius, Engyodontium rectidentatum, Lecanicillium aphanocladii and Lecanicillium rasoulzarei sp. nov. were identified. Of these, A. muscarius on Lepidosaphes sp., E. rectidentatum on Coccidae, and L. aphanocladii on Tetranychus urticae are reported as new fungal-host records from Iran. Moreover, a new species, Lecanicillium rasoulzarei, is illustrated, described, and compared with closely related species.
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Affiliation(s)
- Alireza Armand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Seyed Akbar Khodaparast
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
| | - Saeed Nazari
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Arash Zibaee
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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23
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Bedsted AE, Rasmussen TB, Martinenghi LD, Bøtner A, Nauwynck H, Belsham GJ. Porcine respiratory coronavirus genome sequences; comparisons and relationships to transmissible gastroenteritis viruses. Virology 2024; 595:110072. [PMID: 38599031 DOI: 10.1016/j.virol.2024.110072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/14/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
Porcine respiratory coronavirus (PRCV) was initially detected in Europe, and later in the United States of America (US), in the 1980s. In this study we obtained and compared PRCV sequences from Europe and the US, and investigated how these are related to transmissible gastroenteritis virus (TGEV) sequences. The whole genome sequences of Danish (1/90-DK), Italian (PRCV15087/12 III NPTV Parma), and Belgian PRCV (91V44) strains are presented. These sequences were aligned with nine other PRCV sequences from Europe and the US, and 43 TGEV sequences. Following alignment of the PRCV sequences, it was apparent that multiple amino acid variations in the structural proteins were distinct between the European and US strains. The alignments were used to build phylogenetic trees to infer the evolutionary relationships between the strains. In these trees, the European PRCV strains clustered as a separate group, whereas the US strains of PRCV all clustered with TGEVs.
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Affiliation(s)
- Amalie Ehlers Bedsted
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Laura D Martinenghi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Hans Nauwynck
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, University of Ghent, 9820, Merelbeke, Belgium
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark.
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Omonhinmin CA, Alonge KO. Intra-specific genetic diversity, phylogenetic analysis and ecological preferences of Pentaclethra macrophylla Benth ., across Nigeria based on rbcL dataset. Data Brief 2024; 53:110213. [PMID: 38419771 PMCID: PMC10900092 DOI: 10.1016/j.dib.2024.110213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Pentaclethra macrophylla Benth., commonly referred to as "African oil bean"; is a leguminous tree species that belongs to the subfamily Caesalpinioideae of the family Fabaceae and it is native to the dry tropical rainforest forest of West to Central Africa. It is widely used as a resource for food, medicine, firewood, construction, arts, and craft and particularly of socio-economic and cultural value to indigenous people of southern, Nigeria. Despite its significant potential, it is considered underutilized in the aspect of research attention and global trade. The dataset highlights the distribution pattern, genetic diversity, phylogenetic relationship, and ecological preferences of P. macrophylla accessions collected across the various agro-ecological zones in Nigeria where it is distributed, using the Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase (rbcL) gene.
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Affiliation(s)
- Conrad Asotie Omonhinmin
- Department of Biological Sciences, Biotechnology Cluster, College of Science and Technology, Covenant University, Canaan land Ota, Ogun State, Nigeria
| | - Kristen Oluwafunmilola Alonge
- Department of Biological Sciences, Biotechnology Cluster, College of Science and Technology, Covenant University, Canaan land Ota, Ogun State, Nigeria
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Nakajima H, Fukui A, Suzuki K, Tirta RYK, Furuya H. HOST SWITCHING IN DICYEMIDS (PHYLUM DICYEMIDA). J Parasitol 2024; 110:159-169. [PMID: 38629270 DOI: 10.1645/23-52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Dicyemids (phylum Dicyemida) are the most common and most characteristic endosymbionts in the renal sacs of benthic cephalopod molluscs: octopuses and cuttlefishes. Typically, 2 or 3 dicyemid species are found in a single specimen of the host, and most dicyemids have high host specificity. Host-specific parasites are restricted to a limited range of host species by ecological barriers that impede dispersal and successful establishment; therefore, phylogenies of interacting groups are often congruent due to repeated co-speciation. Most frequently, however, host and parasite phylogenies are not congruent, which can be explained by processes such as host switching and other macro-evolutionary events. Here, the history of dicyemids and their host cephalopod associations were studied by comparing their phylogenies. Dicyemid species were collected from 8 decapodiform species and 12 octopodiform species in Japanese waters. Using whole mitochondrial cytochrome c oxidase subunit 1 (COI) sequences, a phylogeny of 37 dicyemid species, including 4 genera representing the family Dicyemidae, was reconstructed. Phylogenetic trees derived from analyses of COI genes consistently suggested that dicyemid species should be separated into 3 major clades and that the most common genera, Dicyema and Dicyemennea, are not monophyletic. Thus, morphological classification does not reflect the phylogenetic relationships of these 2 genera. Divergence (speciation) of dicyemid species seems to have occurred within a single host species. Possible host-switching events may have occurred between the Octopodiformes and Decapodiformes or within the Octopodiformes or the Decapodiformes. Therefore, the mechanism of dicyemid speciation may be a mixture of host switching and intra-host speciation. This is the first study in which the process of dicyemid diversification involving cephalopod hosts has been evaluated with a large number of dicyemid species and genera.
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Affiliation(s)
- Hiroaki Nakajima
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ayako Fukui
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kazutaka Suzuki
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - R Yusrifar Kharisma Tirta
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hidetaka Furuya
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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26
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Vintsek L, Klichowska E, Nowak A, Nobis M. Insight into the phylogeny and responses of species from the genus Sergia (Campanulaceae) to the climate changes predicted for the Mountains of Central Asia (a world biodiversity hotspot). BMC Plant Biol 2024; 24:228. [PMID: 38561665 PMCID: PMC10986085 DOI: 10.1186/s12870-024-04938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Together with other elevated areas, the Mountains of Central Asia are significantly threatened by ongoing climate change. The presence of refuges during the glaciations makes the region extremely rich in species, especially endemic ones. However, the limited potential for colonisation of other habitats makes rocky-related species with 'island-like' distribution, particularly vulnerable to climate change. To understand the processes underlying species response to climate warming, we assessed differences in ecological niches and phylogenetic relationship of two geographically disjunctive alpine species belonging to the genus Sergia. The taxa are considered Tertiary relicts, endemic to the Tian Shan and Pamir-Alai Mountains. To illustrate range dynamics and differences in occupied niches of Sergia species, we used Ecological Niche Modelling of current and future distribution. Whereas, to reconstruct the phylogenetic relationship within and between Sergia and other related Campanulaceae species from the region we used molecular data (ITS, cpDNA, DArTseq-derived SNPs). RESULTS The results reveal that the genus Sergia is a polyphyletic group, and its representatives differ geographically, ecologically and genetically. Both S. regelii and S. sewerzowii constitute a common clade with Asyneuma group, however, S. sewerzowii is more closely related to Campanula alberti (a species that has never previously been considered closely related to the genus Asyneuma or Sergia) than to S. regelii. Sergia sewerzowii is adapted to lower elevations with higher temperatures, while S. regelii prefers higher elevations with lower temperatures. The future distribution models demonstrate a dramatic loss of S. regelii range with a shift to suitable habitats in higher elevations, while the potential range of S. sewerzowii increases and shifts to the north. CONCLUSIONS This study shows that S. regelii and S. sewerzowii have a long and independent evolution history. Sergia regelii and S. sewerzowii significantly differ in realised niches. These differences are mirrored in the response of the studied endemics to future climate warming. As suitable habitats shrink, rapid changes in distribution can lead to species' range loss, which is also directly related to declines in genetic variability. The outcomes of this paper will help to more precisely assess the impact of climate changes on rocky-related plant species found in this world's biodiversity hotspot.
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Affiliation(s)
- Lizaveta Vintsek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland.
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, Warsaw, 02-973, Poland
- Botanical Garden of the Wrocław University, Sienkiewicza 23, 50-335, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland.
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Foučková M, Uhrová K, Kubánková A, Pánek T, Čepička I. Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea). Eur J Protistol 2024; 93:126052. [PMID: 38302295 DOI: 10.1016/j.ejop.2024.126052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Psalteriomonadidae are a small family of anaerobic free-living protists belonging to Heterolobosea, Discoba. We cultured 74 new strains of mostly amoeboid Psalteriomonadidae obtained from mainly freshwater habitats and sequenced their 18S rRNA gene. Based on the phylogenetic analysis and genetic distances, we report multiple novel species, four of which we formally describe based on the light-microscopic morphology (Psalteriomonas minuta, P. australis, P. fimbriata, and P. parva). We also examined the ultrastructure of two Psalteriomonas species using transmission electron microscopy. We transfer Sawyeria marylandensis into the genus Psalteriomonas and synonymize Sawyeria with Psalteriomonas. In addition, we studied the flagellate stage of P. marylandensis comb. nov. for the first time, using light and scanning electron microscopy.
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Affiliation(s)
- Martina Foučková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Kristýna Uhrová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Aneta Kubánková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic.
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Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024; 54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Ivan Jakovlić
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fei Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Institute of Aquatic Sciences, Tibet Academy of Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China
| | - Chuan-Yu Xiang
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qunzong Gusang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Sonam Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Shenggui Xue
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Wen-Jin Zhu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Zhenxin Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Jihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Upadhyay S, Das K, Ghosal A, Saito-Nakano Y, Dutta S, Nozaki T, Ganguly S. Short tandem repeat (STR) based sequence typing of Entamoeba histolytica identifies S TGA-D locus as a genetic marker, associated with disease outcomes. Parasitol Int 2024; 99:102846. [PMID: 38110172 DOI: 10.1016/j.parint.2023.102846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023]
Abstract
Amoebiasis, caused by the enteric parasite Entamoeba histolytica has differential disease outcomes. The association of parasite genotypes with outcomes of amoebic infection is still a paradox and requires to be explored. The genetic information of infecting strains from endemic settings of different geographical regions is essential to evaluate the relation. Comparative genetics of E. histolytica clinical isolates from different disease outcomes have been explored based on two tRNA-linked STR loci (STGA-D and A-L). All of the repeat patterns in the A-L locus were newly identified and unique to Indian isolates. The majority of newly identified repeat patterns in STGA-D locus have outcome-specific distributions, predicting the emergence of disease-specific mutations in this target locus. Statistical analysis further reinforces this observation, as identified repeat patterns only from STGA-D but not A-L locus were significantly associated with disease outcomes. Phylogenetic analysis indicates independent segregation and divergence of tRNA-linked STR arrays for each STR locus.
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Affiliation(s)
- Shashi Upadhyay
- Department of Allied Health Sciences, School of Health Science and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Koushik Das
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India.
| | - Ajanta Ghosal
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Sandipan Ganguly
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India.
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Escarcega-Bata A, Núñez Resendiz ML, Zamudio-Resendiz ME, Dreckmann KM, Cuevas Sánchez E, Sentíes A. Morpho-molecular and environmental evidence of the ocurrence of Karenia longicanalis (Dinophyceae: Kareniaceae) as a bloom former in the Eastern Pacific Ocean. Protist 2024; 175:126022. [PMID: 38350283 DOI: 10.1016/j.protis.2024.126022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/15/2024]
Abstract
Karenia longicanalis, an athecate dinoflagellate, was first described during a bloom in Victoria Harbour (Hong Kong, China). This study confirms the presence of K. longicanalis as a bloom former in the eastern Pacific Ocean. Specimens were collected in March 2019 at three sampling stations in Acapulco Bay, Mexico. Water temperature, salinity, dissolved oxygen, and pH were measured in situ at the time of sample collection. Cell morphology was examined by optical and scanning electron microscopy. A molecular analysis based on the amplification of the large subunit (LSU) rDNA region revealed that the LSU sequences formed a monophyletic group with other GenBank sequences belonging to K. longicanalis. The resulting phylogeny demonstrates that Karenia is closely related to Asterodinium, Gertia, and Shimiella. The morphology of the specimens was consistent with previous descriptions.
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Affiliation(s)
- Alexis Escarcega-Bata
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico; Universidad Autónoma Metropolitana, Unidad Iztapalapa, Departamento de Hidrobiología, Laboratorio de Macroalgas Marinas y Salobres, 09340, CdMx, Mexico.
| | - María Luisa Núñez Resendiz
- Universidad Autónoma Metropolitana, Unidad Iztapalapa, Departamento de Hidrobiología, Laboratorio de Macroalgas Marinas y Salobres, 09340, CdMx, Mexico
| | - María Eugenia Zamudio-Resendiz
- Universidad Autónoma Metropolitana, Unidad Iztapalapa, Departamento de Hidrobiología, Laboratorio de Fitoplancton Marino y Salobre, 09340, CdMx, Mexico
| | - Kurt M Dreckmann
- Universidad Autónoma Metropolitana, Unidad Iztapalapa, Departamento de Hidrobiología, Laboratorio de Macroalgas Marinas y Salobres, 09340, CdMx, Mexico
| | - Estefany Cuevas Sánchez
- Universidad Autónoma Metropolitana, Unidad Iztapalapa, Departamento de Hidrobiología, Laboratorio de Macroalgas Marinas y Salobres, 09340, CdMx, Mexico
| | - Abel Sentíes
- Universidad Autónoma Metropolitana, Unidad Iztapalapa, Departamento de Hidrobiología, Laboratorio de Macroalgas Marinas y Salobres, 09340, CdMx, Mexico
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Hämmerle M, Rymbekova A, Gelabert P, Sawyer S, Cheronet O, Bernardi P, Calvignac-Spencer S, Kuhlwilm M, Guellil M, Pinhasi R. Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak. Emerg Infect Dis 2024; 30:816-818. [PMID: 38526306 PMCID: PMC10977839 DOI: 10.3201/eid3004.231546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
We used pathogen genomics to test orangutan specimens from a museum in Bonn, Germany, to identify the origin of the animals and the circumstances of their death. We found monkeypox virus genomes in the samples and determined that they represent cases from a 1965 outbreak at Rotterdam Zoo in Rotterdam, the Netherlands.
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Affiliation(s)
- Michelle Hämmerle
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
| | - Aigerim Rymbekova
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
| | - Pere Gelabert
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
| | - Susanna Sawyer
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
| | - Olivia Cheronet
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
| | - Paolo Bernardi
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
| | - Sébastien Calvignac-Spencer
- University of Vienna, Vienna, Austria (M. Hämmerle, A. Rymbekova, P. Gelabert, S. Sawyer, O. Cheronet, P. Bernardi, M. Kuhlwilm, M. Guellil, R. Pinhasi)
- Helmholtz Centre for Infection Research, Greifswald, Germany (S. Calvignac-Spencer)
- University of Greifswald, Greifswald (S. Calvignac-Spencer)
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Fathi A, Nabavi R, Noaman V, Sarani A, Saadati D, Ben Said M, Ghafar A, Jabbar A, Sazmand A. Molecular identification, risk factor assessment, and phylogenetic analysis of tick-borne pathogens in symptomatic and asymptomatic cattle from South-Eastern Iran. Exp Appl Acarol 2024; 92:479-506. [PMID: 38457048 DOI: 10.1007/s10493-023-00886-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 12/29/2023] [Indexed: 03/09/2024]
Abstract
Tick-borne pathogens (TBPs) represent a substantial threat to cattle globally, exerting adverse impacts on production, health, and economic viability. This study delves into the prevalence and implications of TTBPs in cattle sourced from resource-limited smallholder livestock farms situated in southeastern Iran, proximate to Afghanistan and Pakistan. Blood and tick specimens were systematically collected from a cohort of 230 cattle, comprising 150 asymptomatic and 80 symptomatic individuals. Genomic DNA isolated from blood samples underwent rigorous examination for the presence of key TBPs, including Anaplasma marginale, A. phagocytophilum, A. bovis, A. centrale, Babesia bigemina, and Theileria annulata, utilizing multiple genetic markers. Nucleotide sequence analysis facilitated the reconstruction of phylogenetic relationships. The study also evaluated various potential risk factors, such as clinical status, gender, age, breed, tick infestation, and management practices, to elucidate their associations with TTBPs. Among the cattle cohort, a staggering 87.8% (202/230) tested positive for at least one pathogen. Prevalence statistics encompassed A. marginale (72.2%), T. annulata (68.3%), A. phagocytophilum/A. platys-like complex (66.1%), A. centrale (16.7%), B. bigemina (10.0%), and A. bovis (6.1%). Remarkably, mixed infections involving two, three, and four pathogens were detected in 23%, 52.1%, and 2.2% of animals, respectively. Notably, all asymptomatic cattle were positive for at least one TBP. Tick infestation was observed in 62.2% (143/230) of cattle, predominantly caused by Hyalomma anatolicum (82.5%), Rhipicephalus (Boophilus) annulatus (13.1%), and R. sanguineus sensu lato (4.4%). Risk factors linked to TBPs encompassed tick infestation, older age, and crossbred animals. Clinical presentations among symptomatic cattle encompassed fever, anemia, weight loss, anorexia, jaundice, and enlarged superficial lymph nodes. This study underscores the pivotal role of asymptomatic carriers in the propagation of TTBPs within endemic regions. Furthermore, it emphasizes the potential for the implementation of molecular diagnostics to unmask subclinical infections, thereby affording the opportunity for targeted interventions aimed at ameliorating the burden of TTBPs in resource-constrained smallholder dairy farms.
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Affiliation(s)
- Atefeh Fathi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Zabol, Zabol, Iran
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Reza Nabavi
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran.
| | - Vahid Noaman
- Department of Parasitic Disease Research, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Ali Sarani
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Zabol, Bonjar Road, Zabol, 9861335856, Iran
| | - Dariush Saadati
- Department of Food Hygiene, Faculty of Veterinary Medicine, University of Zabol, Bonjar Road, Zabol, 9861335856, Iran
| | - Mourad Ben Said
- Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
| | - Abdul Ghafar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, 3030, Australia
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, 3030, Australia
| | - Alireza Sazmand
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran
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Khuman A, Yadav V, Chaudhary B. Evolutionary dynamics of the cytoskeletal profilin gene family in Brassica juncea L. reveal its roles in silique development and stress resilience. Int J Biol Macromol 2024; 266:131247. [PMID: 38565371 DOI: 10.1016/j.ijbiomac.2024.131247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Essential to plant adaptation, cell wall (CW) integrity is maintained by CW-biosynthesis genes. Cytoskeletal actin-(de)polymerizing, phospholipid-binding profilin (PRF) proteins play important roles in maintaining cellular homeostasis across kingdoms. However, evolutionary selection of PRF genes and their systematic characterization in family Brassicaceae, especially in Brassica juncea remain unexplored. Here, a comprehensive analysis of genome-wide identification of BjPRFs, their phylogenetic association, genomic localization, gene structure, and transcriptional profiling were performed in an evolutionary framework. Identification of 23 BjPRFs in B. juncea indicated an evolutionary conservation within Brassicaceae. The BjPRFs evolved through paralogous and orthologous gene formation in Brassica genomes. Evolutionary divergence of BjPRFs indicated purifying selection, with nonsynonymous (dN)/synonymous (dS) value of 0.090 for orthologous gene-pairs. Hybrid homology-modeling identified evolutionary distinct and conserved domains in BjPRFs which suggested that these proteins evolved following the divergence of monocot and eudicot plants. RNA-seq profiles of BjPRFs revealed their functional evolution in spatiotemporal manner during plant-development and stress-conditions in diploid/amphidiploid Brassica species. Real-Time PCR experiments in seedling, vegetative, floral and silique tissues of B. juncea suggested their essential roles in systematic plant development. These observations underscore the expansion of BjPRFs in B. juncea, and offer valuable evolutionary insights for exploring cellular mechanisms, and stress resilience.
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Affiliation(s)
| | - Vandana Yadav
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
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Bourland W, Pomahač O, Čepička I. Redescription and molecular phylogeny of the freshwater metopid, Castula strelkowi (Jankowski, 1964) from the Czech Republic and synonymization of Pileometopus with Castula. Protist 2024; 175:126034. [PMID: 38569353 DOI: 10.1016/j.protis.2024.126034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
The relationships of the mainly free living, obligately anaerobic ciliated protists belonging to order Metopida continue to be clarified and now comprise three families: Metopidae, Tropidoatractidae, and Apometopidae. The most species-rich genus of the Metopidae, Metopus has undergone considerable subdivision into new genera in recent years as more taxa are characterized by modern morphologic and molecular methods. The genus, Castula, was established to accommodate setae-bearing species previously assigned to Metopus: C. setosa and C. fusca, and one new species, C. flexibilis. Another new species, C. specialis, has been added since. Here we redescribe another species previously included in Metopus, using morphologic and molecular methods, and transfer it to Castula as C. strelkowi n. comb. (original combination Metopus strelkowi). We also reassess the monotypic genus, Pileometopus, which nests within the strongly supported Castula clade in 18S rRNA gene trees and conclude that it represents a morphologically divergent species of Castula.
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Affiliation(s)
- William Bourland
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic.
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic
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Yilmaz M, Arslan T, Atalay Oral M, Kubilay A. Antibiotic susceptibility and resistance genes profiles of Vagococcus salmoninarum in a rainbow trout ( Oncorhyncus mykiss, Walbaum) farm. PeerJ 2024; 12:e17194. [PMID: 38560471 PMCID: PMC10981890 DOI: 10.7717/peerj.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Disease outbreaks negatively affect fish production. Antimicrobial agents used in the treatment of diseases become ineffective over time because of antibiotic resistance developed by bacteria distributed in the aquaculture environment. This study was conducted for 4 months (cold period) in a fish farm to detect the fish disease, cold water streptococcosis. In the study, four brood stock showing disease signs were detected. Bacteria isolates were obtained and identified as Vagococcus salmoninarum. Antimicrobial susceptibility of V. salmoninarum was tested and antibiotic resistance gene profiles of V. salmoninarum isolates were screened. The phylogenetic relation of the isolates with the previously reported strains was evaluated. Antibiotic resistance developed by pathogenic bacteria is distributed in the aquaculture environment. The transfer of resistance genes from one bacterium to another is very common. This situation causes the antimicrobial agents used in the treatment of diseases to become ineffective over time. The disc diffusion test showed that all four isolates developed resistance to 13 (FFC30, AX25, C30, E15, CF30, L2, OX1, S10, T30, CRO30, CC2, PT15 and TY15) of the evaluated antibiotics and were about to develop resistance to six others (AM 10, FM 300, CFP75, SXT25, APR15 and TE30). Furthermore, antibiotic resistance genes tetA, sul1, sul2, sul3, dhfr1, ereB and floR were detected in the isolated strain. Moreover, the phylogenetic analysis showed that isolated V. salmoninarum strain (ESN1) was closely related to the bacterial strains isolated from USA and Jura.
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Affiliation(s)
- Mesut Yilmaz
- Department of Aquaculture, Faculty of Fisheries, Akdeniz University, Antalya, Turkey
| | - Tulin Arslan
- Faculty of Fisheries, Mugla University, Muğla, Turkey
| | - Mükerrem Atalay Oral
- Elmalı Vocational School of Higher Education, Akdeniz University, Antalya, Turkey
| | - Aysegul Kubilay
- Faculty of Eğirdir Fisheries, Isparta University of Applied Sciences, Isparta, Turkey
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Ebadi M, Ahmadi F, Tahmouresi H, Pazhang M, Mollaei S. Investigation the biological activities and the metabolite profiles of endophytic fungi isolated from Gundelia tournefortii L. Sci Rep 2024; 14:6810. [PMID: 38528041 DOI: 10.1038/s41598-024-57222-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
Endophytic fungi are microorganisms that are considered as a potential source of natural compounds, and can be applied in various industries. The aims of this research were molecular identification of endophytic fungi isolated from the Gundelia tournefortii stems, and investigation their biological activities as well as phenolic and fatty acid profile. Surface sterilized stems of G. tournefortii were placed on potato dextrose agar (PDA) to isolate the fungal endophytes. Genomic DNA was extracted by CTAB method, and PCR amplification was performed by ITS 1 and ITS 4 as primers. The enzyme production of endophytic fungi was determined based on the formation of a clear zone that appeared around the colonies of fungus. The anti-oxidant activity was evaluated by measuring the amount of free radicals DPPH. Also, the total phenol and flavonoid contents were measured obtained by Folin-Ciocalteu and aluminum chloride colorimetric methods, respectively. Moreover, the separation and identification of phenolic acids and fatty acids were done by HPLC and GC, respectively. Phylogenetic analysis was done based on the Internal Transcribed Spacer (ITS) region, and five isolates were identified as following: Aspergillus niger, Penicillium glabrum, Alternaria alternata, A. tenuissima, and Mucor circinelloides. Evaluation of the enzymatic properties showed that P. gabrum (31 ± 1.9 mm), and A. niger (23 ± 1.7) had more ability for producing pectinase and cellulase. The anti-oxidant activity of isolates showed that A. alternata extract (IC50 = 471 ± 29 µg/mL) had the highest anti-oxidant properties, followed by A. tenuissima extract (IC50 = 512 ± 19 µg/mL). Also, the extract of A. alternata had the greatest amount of total phenols and flavonoids contents (8.2 ± 0.4 mg GAL/g and 2.3 ± 0.3 mg QE/g, respectively). The quantification analysis of phenolic acid showed that rosmarinic acid, para-coumaric acid, and meta-coumaric acid (42.02 ± 1.31, 7.53 ± 0.19, 5.41 ± 0.21 mg/g, respectively) were the main phenolic acids in the studied fungi. The analysis of fatty acids confirmed that, in all fungi, the main fatty acids were stearic acid (27.9-35.2%), oleic acid (11.3-17.3%), palmitic acid (16.9-23.2%), linoleic acid (5.8-11.6%), and caprylic acid (6.3-10.9%). Our finding showed that endophytic fungi are a source of bioactive compounds, which could be used in various industries. This is the first report of endophytic fungi associated with G. tournefortii, which provides knowledge on their future use on biotechnological processes.
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Affiliation(s)
- Mostafa Ebadi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Fatemeh Ahmadi
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Hossein Tahmouresi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mohammad Pazhang
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Saeed Mollaei
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran.
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Zhang H, Liu P, Zhang Y, Sun H, Wang Y, Gao Z, Liu X. Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny. BMC Genom Data 2024; 25:34. [PMID: 38528505 PMCID: PMC10962098 DOI: 10.1186/s12863-024-01222-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Calamus tetradactylus, a species primarily distributed in Vietnam, Laos, and southern China, is highly valued for its utilization as a small-diameter rattan material. While its physical and mechanical properties have been extensively studied, the genomic characteristics of C. tetradactylus remain largely unexplored. RESULTS To gain a better understanding of its chloroplast genomic features and evolutionary relationships, we conducted sequencing and assembly of the chloroplast genome of C. tetradactylus. The complete chloroplast genome exhibited the typical highly conserved quartile structure, with specific variable regions identified in the single-copy region (like psbF-psbE, π = 0.10327, ndhF-rpl32, π = 0.10195), as well as genes such as trnT-GGU (π = 0.05764) and ycf1 (π = 0.03345) and others. We propose that these regions and genes hold potential as markers for species identification. Furthermore, phylogenetic analysis revealed that C. tetradactylus formed a distinct clade within the phylogenetic tree, alongside other Calamus species, and C. tetradactylus was most closely related to C. walkeri, providing support for the monophyly of the genus. CONCLUSION The analysis of the chloroplast genome conducted in this study provides valuable insights that can contribute to the improvement of rattan breeding programs and facilitate sustainable development in the future.
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Affiliation(s)
| | - Peng Liu
- BGI Research, Beijing, 102601, China
| | - Yi Zhang
- School of nursing, Chongqing Medical and Pharmaceutical College, P. R, Chongqing, China
| | - Huayu Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Yue Wang
- BGI Research, Beijing, 102601, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Xin Liu
- BGI Research, Beijing, 102601, China.
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Hunter C, Dia K, Boykins J, Perry K, Banerjee N, Cuffee J, Armstrong E, Morgan G, Banerjee HN, Banerjee A, Bhattacharya S. An investigation for phylogenetic characterization of human Pancreatic cancer microbiome by 16SrDNA Sequencing and Bioinformatics techniques. Res Sq 2024:rs.3.rs-4140368. [PMID: 38585738 PMCID: PMC10996791 DOI: 10.21203/rs.3.rs-4140368/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Pancreatic cancer is a significant public health concern, with increasing incidence rates and limited treatment options. Recent studies have highlighted the role of the human microbiome, particularly the gut microbiota, in the development and progression of this disease. Microbial dysbiosis, characterized by alterations in the composition and function of the gut microbiota, has been implicated in pancreatic carcinogenesis through mechanisms involving chronic inflammation, immune dysregulation, and metabolic disturbances. Researchers have identified specific microbial signatures associated with pancreatic cancer, offering potential biomarkers for early detection and prognostication. By leveraging advanced sequencing and bioinformatics tools, scientists have delineated differences in the gut microbiota between pancreatic cancer patients and healthy individuals, providing insights into disease pathogenesis and potential diagnostic strategies. Moreover, the microbiome holds promise as a therapeutic target in pancreatic cancer treatment. Interventions aimed at modulating the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, have demonstrated potential in enhancing the efficacy of existing cancer therapies, including chemotherapy and immunotherapy. These approaches can influence immune responses, alter tumor microenvironments, and sensitize tumors to treatment, offering new avenues for improving patient outcomes and overcoming therapeutic resistance. Overall, understanding the complex interplay between the microbiome and pancreatic cancer is crucial for advancing our knowledge of disease mechanisms and identifying innovative therapeutic strategies. Here we report phylogenetic analysis of the 16S microbial sequences of the pancreatic cancer mice microbiome and corresponding age matched healthy mice microbiome. We successfully identified differentially abundance of microbiota in the pancreatic cancer.
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Affiliation(s)
- Colby Hunter
- Elizabeth City State University campus of The University of North Carolina
| | - Khadimou Dia
- Elizabeth City State University campus of The University of North Carolina
| | - Julia Boykins
- Elizabeth City State University campus of The University of North Carolina
| | - Karrington Perry
- Elizabeth City State University campus of The University of North Carolina
| | - Narendra Banerjee
- Elizabeth City State University campus of The University of North Carolina
| | - Jazmine Cuffee
- Elizabeth City State University campus of The University of North Carolina
| | - Erik Armstrong
- Elizabeth City State University campus of The University of North Carolina
| | - Gabrielle Morgan
- Elizabeth City State University campus of The University of North Carolina
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Pu J, Zhang Y, Zhong D, Chen Q. Detection and genetic characterization of circulating canine parvovirus from stray dogs in Shanghai, China. Virology 2024; 595:110041. [PMID: 38555807 DOI: 10.1016/j.virol.2024.110041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/02/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
Canine parvovirus (CPV) is the main cause of viral diarrhea in dogs. CPV became a global disease in 1978 and was endemic all over the world. CPV-2 was the first strain to be identified, but with genetic mutations, new genotypes such as CPV-2a/2b/2c/new-2a/new-2b have emerged. In this study, 128 fecal samples of stray dogs suspected of CPV-2 infection were collected from January to March 2021 in Shanghai, China. All samples were screened by PCR and further analyzed by VP2 gene. The positive rate of CPV-2 was 9.4% (12/128), of which 6 CPV-2 isolates were successfully isolated. Phylogenetic tree analysis showed that 4 isolates were CPV-2c genotype and 2 were new-CPV-2b genotype. VP-2 is a key protein that determines the antigenic properties, host range and receptor binding of cpv-2. The results of VP2 amino acid sequence analysis in this study showed that the CPV-2c isolated strain was the same as the previous strains reported in China, including F267Y, Y324I, Q370R and A5G mutations in addition to the typical N426E mutations. Similarly, in addition to the conventional N426D, S297A, F267Y and Y324I mutations, the new CPV-2b isolate also had a new mutation of T440A. This study further confirmed the prevalence of CPV-2c and new-CPV-2b in Shanghai, and also found a new mutation site of new-CPV-2c, which provided a theoretical basis for further enriching the epidemiological data of CPV-2 in Shanghai, as well as the development of vaccines and the prevention and control of the disease.
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Affiliation(s)
- Junyi Pu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China; SNLG Precision Medtech (Shanghai) Ltd, Shanghai, 201100, PR China
| | - Yan Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Dengke Zhong
- Shanghai Vocational and Technical College of Agriculture and Forestry, Shanghai, 201600, PR China.
| | - Qiusheng Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Xu DM, Chai FR, Liang XF, Lu K. Knockout of lws1 in zebrafish (Danio rerio) reveals its role in regulating feeding and vision-guided behavior. Funct Integr Genomics 2024; 24:62. [PMID: 38514486 DOI: 10.1007/s10142-024-01333-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Long-wave sensitive (LWS) is a G protein-coupled receptor expressed in the retina, and zebrafish is a better model organism for studying vision, but the role of LWS1 in vision-guided behavior of larvae fish has rarely been reported. In this study, we found that zebrafish lws1 and lws2 are tandemly replicated genes, both with six exons, with lws1 being more evolutionarily conserved. The presence of Y277F in the amino acid sequence of lws2 may have contributed to the shift of λmax to green light. We established a lws1 knockout zebrafish model using CRISPR/Cas9 technology. Lws1-/- larvae showed significantly higher levels of feeding and appetite gene (agrp) expression than WT, and significantly lower levels of anorexia gene (pomc, cart) expression. In addition, green light gene compensation was observed in lws1-/- larvae with significantly increased expression levels of rh2-1. The light-dark movement test showed that lws1-/- larvae were more active under light-dark transitions or vibrational stimuli, and the expression of phototransduction-related genes was significantly up-regulated. This study reveals the important role of lws1 gene in the regulation of vision-guided behavior in larvae.
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Affiliation(s)
- Di-Mei Xu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Fa-Rui Chai
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| | - Ke Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
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Hellekant G. Neuroscience of taste: unlocking the human taste code. BMC Neurosci 2024; 25:19. [PMID: 38515045 PMCID: PMC10956246 DOI: 10.1186/s12868-024-00847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/24/2024] [Indexed: 03/23/2024] Open
Abstract
Since antiquity human taste has been divided into 4-5 taste qualities. We realized in the early 1970s that taste qualities vary between species and that the sense of taste in species closer to humans such as primates should show a higher fidelity to human taste qualities than non-primates (Brouwer et al. in J Physiol 337:240, 1983). Here we present summary results of behavioral and single taste fiber recordings from the distant South American marmoset, through the Old World rhesus monkey to chimpanzee, the phylogenetically closest species to humans. Our data show that in these species taste is transmitted in labelled-lines to the CNS, so that when receptors on taste bud cells are stimulated, the cell sends action potentials through single taste nerve fibers to the CNS where they create taste, whose quality depends on the cortical area stimulated. In human, the taste qualites include, but are perhaps not limited to sweet, sour, salty, bitter and umami. Stimulation of cortical taste areas combined with inputs from internal organs, olfaction, vision, memory etc. leads to a choice to accept or reject intake of a compound. The labelled-line organization of taste is another example of Müller's law of specific nerve energy, joining other somatic senses such as vision (Sperry in J Neurophysiol 8:15-28, 1945), olfaction (Ngai et al. in Cell 72:657-666, 1993), touch, temperature and pain to mention a few.
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Affiliation(s)
- Göran Hellekant
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Wisconsin-Madison, 1656 Linden Drive, Madison, WI, 53706, USA.
- School of Medicine, Department of Biomedical Sciences, University of Minnesota Duluth Campus, 1035 University Drive, Duluth, MN, 55812, USA.
- School of Veterinary Medicine, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Sánchez Reyes LL, McTavish EJ, O'Meara B. DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life. Syst Biol 2024:syae015. [PMID: 38507308 DOI: 10.1093/sysbio/syae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 03/22/2024] Open
Abstract
Chronograms -phylogenies with branch lengths proportional to time- represent key data on timing of evolutionary events for the study of natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www .datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as sec- ondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8 and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.
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Affiliation(s)
- Luna L Sánchez Reyes
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
| | - Emily Jane McTavish
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
| | - Brian O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
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Amir Afzali Y, Naderloo R, Keikhosravi A, Klaus S. Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species? J Hered 2024:esae016. [PMID: 38501510 DOI: 10.1093/jhered/esae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Indexed: 03/20/2024] Open
Abstract
The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum, utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late-Holocene, accompanied by a recent population bottleneck. Species distribution modelling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance.
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Affiliation(s)
- Yaser Amir Afzali
- School of Biology, College of Science, University of Tehran, Tehran, 1417935840, Iran
| | - Reza Naderloo
- School of Biology, College of Science, University of Tehran, Tehran, 1417935840, Iran
| | - Alireza Keikhosravi
- Department of Biology, Hakim Sabzevari University, Sabzevar, 9617976487, Iran
| | - Sebastian Klaus
- Environmental Resources Management, ERM GmbH, Neu-Isenburg, Siemensstr. 9 · 63263, Germany
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Chiu CC, Yao CT, Liao BY, Li SH. Convergent evolution of kidney sizes and supraorbital salt glands for birds living in saline habitats. iScience 2024; 27:109169. [PMID: 38433889 PMCID: PMC10904986 DOI: 10.1016/j.isci.2024.109169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/30/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Only a small number of avian species inhabit salty environments. To understand how they adapted, we examined the evolution of kidney sizes, supraorbital salt glands (SSGs), and the utilization of salty habitats across 230 species spanning 25 avian orders. Phylogenetic analysis indicates that SSGs, large kidneys, and thriving in salty habitats emerged convergently in birds. Transition rate analysis reveals that species possessing SSGs and large kidneys tended to move from low-to high-salinity environments, while others moved in the opposite direction. However, habitat salinity also influenced kidney evolution; lineages residing in high-salinity environments tended to develop larger kidneys than those in low-salinity environments. Our findings suggest that SSGs and large kidneys may have evolved through adaptation to high salinity. Overall, habitat conditions and physiological traits influenced avian adaptation to salty environments in a reciprocal manner. These results shed the new light on the evolutionary mechanisms underlying functional diversity in birds.
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Affiliation(s)
- Chi-Cheng Chiu
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Cheng-Te Yao
- High altitude research station, Taiwan Endemic Species Research Institute, Nantou 55244, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan
| | - Shou-Hsien Li
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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Pei X, Chen Z, Li Q, Li X, Pu C, Luo K, Luo J, Pu M, Wang H, Khanal L, Jiang X. A new species of the genus Soriculus (Soricidae, Eulipotyphla, Mammalia) from Medog in the eastern Himalaya. Zookeys 2024; 1195:139-155. [PMID: 38525353 PMCID: PMC10958163 DOI: 10.3897/zookeys.1195.115699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/08/2024] [Indexed: 03/26/2024] Open
Abstract
Himalayan shrews of the genus Soriculus (Soricidae, Eulipotyphla), currently represented by four nominal species, are endemic to the Himalayas and the Gaoligong Mountains. In April 2022 and April 2023, a total of 10 specimens of Soriculus were collected from Beibeng and Damu, Medog County, Tibet, China. The morphology of the specimens was compared with the four recognised species of the genus Soriculus. Additionally, two mitochondrial (Cyt b and 12S) and three nuclear (APOB, BRCAI and RAG2) genes were sequenced to test the phylogenetic relationships of these specimens with the other species. Our results indicate that these specimens represent a distinct species, Soriculusbeibengensissp. nov., which is formally described here. The new species is distinguished from the other Soriculus species by the combination of darker pelages, smaller size, the relatively stubby nasal and the widened posterior processes of incisors. Phylogenetic analyses revealed the new species is sister to S.minor. The p-distance of Cyt b gene between S.beibengensis sp. nov. and other nominal Soriculus species ranges from 9.1-16.3%. This new species has a known distribution at an elevation of 1,500-2,125 m in Medog County, Tibet, China. The discovery of this new species from Medog County has important implications for interpreting small mammal biogeographic patterns in the eastern Himalaya and the mountain chains of south-west China.
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Affiliation(s)
- Xiaoxin Pei
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, ChinaUniversity of Chinese Academy of SciencesKunmingChina
| | - Zhongzheng Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, ChinaAnhui Normal UniversityWuhuChina
| | - Quan Li
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Xueyou Li
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Changzhe Pu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Kang Luo
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Jing Luo
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Mingjin Pu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Hongjiao Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Laxman Khanal
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, NepalTribhuvan UniversityKathmanduNepal
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
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Zhu R, Jin L, Sang Y, Hu S, Wang BT, Jin FJ. Characterization of potassium-solubilizing fungi, Mortierella spp., isolated from a poplar plantation rhizosphere soil. Arch Microbiol 2024; 206:157. [PMID: 38480543 DOI: 10.1007/s00203-024-03912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 04/16/2024]
Abstract
Potassium-solubilizing microorganisms are capable of secreting acidic chemicals that dissolve and release potassium from soil minerals, thus facilitating potassium uptake by plants. In this study, three potassium-dissolving filamentous fungi were isolated from the rhizosphere soil of a poplar plantation in Jiangsu Province, China. Phylogenetic analyses based on ITS, 18 S, and 28 S showed that these three isolates were most similar to Mortierella. These strains also possessed spherical or ellipsoidal spores, produced sporangia at the hyphal tip, and formed petal-like colonies on PDA media resembling those of Mortierella species. These findings, along with further phenotypic observations, suggest that these isolates were Mortierella species. In addition, the potassium-dissolution experiment showed that strain 2K4 had a relatively high potassium-solubilizing capacity among these isolated fungi. By investigating the influences of different nutrient conditions (carbon source, nitrogen source, and inorganic salt) and initial pH values on the potassium-dissolving ability, the optimal potassium-solubilization conditions of the isolate were determined. When potassium feldspar powder was used as an insoluble potassium source, isolate 2K4 exhibited a significantly better polysaccharide aggregation ability on the formed mycelium-potassium feldspar complex. The composition and content of organic acids secreted by strain 2K4 were further detected, and the potassium-dissolution mechanism of the Mortierella species and its growth promotion effect were discussed, using maize as an example.
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Affiliation(s)
- Rui Zhu
- College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Long Jin
- College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yue Sang
- College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Shuang Hu
- College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Bao-Teng Wang
- College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Feng-Jie Jin
- College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
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Yang H, Jo H, Kim SH, Yun CS, Park SH, Park DS. Veillonella faecalis sp. nov., a propionic acid-producing bacterium isolated from the faeces of an infant. Antonie Van Leeuwenhoek 2024; 117:50. [PMID: 38472420 DOI: 10.1007/s10482-024-01951-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
A strictly anaerobic, Gram-stain-negative, catalase-negative, cocci-shaped, and propionate-producing bacterial strain, named Ds1651T was isolated from the fecal sample collected from a South Korean infant. Through a comparison of 16S rRNA gene sequences, it was revealed that Ds1651T had the highest phylogenetic affinity with Veillonella nakazawae KCTC 25297 T (99.86%), followed by Veillonella infantium KCTC 25370 T (99.80%), and Veillonella dispar KCTC 25309 T (99.73%) in the family Veillonellaceae. Average nucleotide identity values between Ds1651T and three reference species were 95.48% for Veillonella nakazawae KCTC 25297 T, 94.46% for Veillonella infantium KCTC 25370 T, and 92.81% for Veillonella dispar KCTC 25309 T. The G + C content of Ds1651T was 38.58 mol%. Major fermentation end-products were acetic and propionic acids in Trypticase peptone glucose yeast extract broth with 1% (v/v) sodium lactate. The predominant cellular fatty acids that account for more than 10% were summed in Feature 8 (C17:1 ω8c and/or C17:2) and C13:0. Based on the findings from phylogenetic, genomic, phenotypic, and chemotaxonomic studies, we propose that the type strain Ds1651T (= KCTC 25477 T = GDMCC 1.3707 T) represents a novel bacterial species within the genus Veillonella, with the proposed name Veillonella faecalis sp. nov.
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Affiliation(s)
- Haneol Yang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hana Jo
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Seung Hyun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Chan-Seok Yun
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea.
| | - Doo-Sang Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea.
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Fan F, Pei L, Jiang L, Ye Y, Liu Y, Liu B. Gene Rearrangements in the Mitochondrial Genome of Gonatopsis borealis and Onychoteuthis compacta Reveal Their Phylogenetic Implications for Oegopsida. Biochem Genet 2024:10.1007/s10528-024-10707-7. [PMID: 38466493 DOI: 10.1007/s10528-024-10707-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/16/2024] [Indexed: 03/13/2024]
Abstract
The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida.
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Affiliation(s)
- Fan Fan
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yifan Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bilin Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
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Song Y, Liang Y, Ma W, Crabbe MJC, Ren Z. Complete Mitochondrial Genome and Phylogenetic Position of Nurudea zhengii Ren (Insecta, Hemiptera, Aphididae). Biochem Genet 2024:10.1007/s10528-024-10717-5. [PMID: 38456973 DOI: 10.1007/s10528-024-10717-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/24/2024] [Indexed: 03/09/2024]
Abstract
Nurudea zhengii Ren was identified by aphid morphological characteristics as well as the gall shape and host plant species, and placed in the tribe Fordini (Hemiptera, Aphididae, Eriosomatinae). Here, its whole genome was firstly sequenced by a genome-skimming method and its mitochondrial genome (mitogenome) was assembled to examine its genetic variation and phylogenetic position. The complete mitogenome of Nurudea zhengii is 15,392 bp in length, and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs and one D-loop region. The gene order follows the mitogenomes of the other Rhus gall aphids, and similarly has an AT bias with the content of 83.9%. The majority strand is A-skewed and C-skewed, and shows opposite skewness for G-skewed in the minority strands. The ratios of nonsynonymous to synonymous substitution rates of protein-coding genes are lower than one except for ATP8, which indicated that ATP8 was undergoing positive selection. Phylogenetic analysis among the Rhus gall aphids based on 13 protein-coding genes and two rRNA genes showed that N. zhengii was sister to N. shiraii, and then clustered with N. yanoniella as a group with high support value. The two species, N. shiraii and N. yanoniella, share the same host plant Rhus chinensis, while the host of N. zhengii is R. hypoleuca. However, the phylogenetic relationship indicated that the taxa sharing the same host plant were not absolutely clustered as the closest taxa at least at species level.
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Affiliation(s)
- Yuzhen Song
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Yukang Liang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Wenli Ma
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
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50
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Giorgi FM, Pozzobon D, Di Meglio A, Mercatelli D. Genomic and transcriptomic analysis of the recent Mpox outbreak. Vaccine 2024; 42:1841-1849. [PMID: 38311533 DOI: 10.1016/j.vaccine.2023.12.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 02/06/2024]
Abstract
The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare them with all available Mpox sequences of historical relevance, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Mpox, with >99 % sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We analyze specific mutations occurring in viral proteins between the current outbreak, previous Mpox and Cowpox sequences, and the historical Variola virus. Genome-wide sequence analysis of the recent outbreak and other Mpox/Cowpox/Variola viruses shows a very high conservation, with 97.9 % (protein-based) and 97.8 % (nucleotide-based) sequence identity. We identified significant correlation in human transcriptional responses as well, with a conserved immune pathway response induced in human cell cultures by the three families of Pox virus. The similarities identified between the major strains of Pox viruses, as well as within the Mpox clades, both at the genomic and transcriptomic levels, provide a molecular basis for the observed efficacy of Variola vaccines in other Poxviruses.
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Affiliation(s)
- Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Daniele Pozzobon
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Antonio Di Meglio
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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