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Fu YT, Deng YP, Xie Y, Wang HM, Peng YY, Liu GH, Wu X. Impact factors and genetic characteristics of head lice infestation in schoolchildren: a cross-sectional study from 2018 to 2023 in central China. Parasit Vectors 2025; 18:184. [PMID: 40399977 PMCID: PMC12096793 DOI: 10.1186/s13071-025-06825-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Accepted: 05/02/2025] [Indexed: 05/23/2025] Open
Abstract
BACKGROUND Head lice (Pediculus humanus capitis) infestation is a worldwide public health concern, especially in school-aged children. However, its main impact factors and genetic characteristics remain poorly understood in China. Hence, the purpose of the study was to explore the precise association between multiple impact factors and head lice infestation, characterize the genetic variation of the head lice, and develop a sensitive and specific mitochondrial (mt) DNA duplex polymerase chain reaction (PCR) for accurately distinguishing clades A and B. METHODS A cross-sectional study was conducted in Hunan Province, central China from January 2018 to July 2023. A total of 9254 schoolchildren from 48 primary schools in each administrative region were examined for head lice. Impact factors for infestation were analyzed using the data collected by a questionnaire. The mt cytb gene sequences of head lice collected in the current study were used for sequence analysis, then were added to the global pool to conduct the phylogenetic analyses. Primers designed on the basis of this gene sequence were used in duplex PCR to diagnose head lice clades A and B by amplicon size. RESULTS Head lice infestation was found in 93.8% (45/48) of the primary schools included in the study. Overall, 6.8% (630/9254) of the examined schoolchildren harbored head lice, with 94.6% (596/630) being girls. A total of 2132 adult head lice were collected from 630 infested cases. The impact factors for head lice infestation included gender, school location, family situation, per capita income, study mode, and hair washing per week (p < 0.01). However, season and age were not considered as impact factors for head lice prevalence (p > 0.05). Phylogenetic analysis based on mt cytb gene sequences showed that head lice are classified into two clades (A and B), with clade B being more dominant in Hunan Province, central China. The newly developed duplex PCR was able to differentiate clades A from B in China with 100% sensitivity and specificity. CONCLUSIONS Our findings revealed that head lice infestation is mostly associated with poverty and poor hygiene in Hunan Province, central China. It is crucial to consider the simultaneous surveillance of head lice infestation in schoolchildren in regions with low level of socioeconomic status; however, datasets from other provinces are warranted to confirm the findings. It further showed that clades A and B are common in central China and that the latter has emerged and become the dominant one.
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Affiliation(s)
- Yi-Tian Fu
- Department of Parasitology, Xiangya School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China.
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Yuan-Ping Deng
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hui-Mei Wang
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yan-Yan Peng
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Guo-Hua Liu
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China.
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Casimiro-Soriguer CS, Lara M, Aguado A, Loucera C, Ortuño FM, Lorusso N, Navarro-Marí JM, Sanbonmatsu-Gámez S, Camacho-Martinez P, Merino-Diaz L, de Salazar A, Fuentes A, The Andalusian COVID-19 Sequencing Initiative, Lepe JA, García F, Dopazo J, Perez-Florido J. A Genomic Surveillance Circuit for Emerging Viral Pathogens. Microorganisms 2025; 13:912. [PMID: 40284750 PMCID: PMC12029405 DOI: 10.3390/microorganisms13040912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Revised: 04/07/2025] [Accepted: 04/14/2025] [Indexed: 04/29/2025] Open
Abstract
Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27 hospitals, which act as regional hubs within their respective health districts. Sequencing is performed at three reference laboratories, with downstream data analysis and reporting centralized at a bioinformatics platform. From 2021 to 2025, over 42,500 SARS-CoV-2 genomes were sequenced, enabling the identification of major variants and their evolutionary dynamics. The circuit tracked the transition from Alpha and Delta to successive Omicron waves, including both recombinant and non-recombinant clades. The integration of genomic and epidemiological data facilitated rapid variant detection, outbreak investigation, and public health decision making. This surveillance framework at a regional granularity demonstrates the feasibility of large-scale sequencing within a decentralized healthcare system and has expanded to monitor other pathogens, reinforcing its value for epidemic preparedness. Continued investment in genomic surveillance is critical for tracking viral evolution, guiding interventions, and mitigating future public health threats.
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Affiliation(s)
- Carlos S. Casimiro-Soriguer
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain;
| | - Maria Lara
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Andrea Aguado
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Carlos Loucera
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain;
| | - Francisco M. Ortuño
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Department of Computer Engineering, Automatics and Robotics, University of Granada, 18071 Granada, Spain
| | - Nicola Lorusso
- Dirección General de Salud Pública, Consejería de Salud y Consumo, Junta de Andalucía, 41020 Sevilla, Spain
| | - Jose M. Navarro-Marí
- Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain (F.G.)
| | - Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain (F.G.)
| | - Pedro Camacho-Martinez
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Laura Merino-Diaz
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Adolfo de Salazar
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain (F.G.)
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Ana Fuentes
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain (F.G.)
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | | | - Jose A. Lepe
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain;
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Federico García
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain (F.G.)
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Joaquín Dopazo
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain;
| | - Javier Perez-Florido
- Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain;
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Gil N, Leurs N, Martinand-Mari C, Debiais-Thibaud M. The vertebrate small leucine-rich proteoglycans: amplification of a clustered gene family and evolution of their transcriptional profile in jawed vertebrates. G3 (BETHESDA, MD.) 2025; 15:jkaf003. [PMID: 39774651 PMCID: PMC11917481 DOI: 10.1093/g3journal/jkaf003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 12/18/2024] [Indexed: 01/11/2025]
Abstract
Small Leucine-Rich Proteoglycans (SLRPs) are a major family of vertebrate proteoglycans. In bony vertebrates, SLRPs have a variety of functions from structural to signaling and are found in extracellular matrices, notably in skeletal tissues. However, there is little or no data on the diversity, function and expression patterns of SLRPs in cartilaginous fishes, which hinders our understanding of how these genes evolved with the diversification of vertebrates, in particular regarding the early events of whole-genome duplications that shaped gnathostome and cyclostome genomes. We used a selection of chromosome-level assemblies of cartilaginous fish and other vertebrate genomes for phylogeny and synteny reconstructions, allowing better resolution and understanding of the evolution of this gene family in vertebrates. Novel SLRP members were uncovered together with specific loss events in different lineages. Our reconstructions support that the canonical SLRPs have originated from different series of tandem duplications that preceded the extant vertebrate last common ancestor, one of them even preceding the extant chordate last common ancestor. They then further expanded with additional tandem and whole-genome duplications during the diversification of extant vertebrates. Finally, we characterized the expression of several SLRP members in the small-spotted catshark Scyliorhinus canicula and from this, inferred conserved and derived SLRP expression in several skeletal and connective tissues in jawed vertebrates.
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Affiliation(s)
- Nathan Gil
- Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France
| | - Nicolas Leurs
- Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France
| | - Camille Martinand-Mari
- Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France
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He Y, Mok K, Chumnanpuen P, Nakphaichit M, Vongsangnak W. Dissecting Metabolic Functions and Sugar Transporters Using Genome and Transportome of Probiotic Limosilactobacillus fermentum KUB-D18. Genes (Basel) 2025; 16:348. [PMID: 40149499 PMCID: PMC11942490 DOI: 10.3390/genes16030348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Revised: 03/04/2025] [Accepted: 03/13/2025] [Indexed: 03/29/2025] Open
Abstract
Background/Objectives:Limosilactobacillus fermentum KUB-D18, a heterofermentative lactic acid bacterium with promising probiotic properties, is known for promoting gut health and nutrient absorption. Originally isolated from chicken intestines, this strain demonstrates versatile metabolic capabilities in diverse gastrointestinal environments. However, the metabolic functions and sugar transport-related genes remain largely unexplored. This study thus aimed to dissect metabolic functions and sugar transports of L. fermentum KUB-D18. Methods: Next-generation and third-generation sequencing techniques using integrative genomic platform towards transportome analysis were performed. Results: The complete genome, sized at 2.12 Mbps with a GC content of 51.36%, revealed 2079 protein-encoding genes, of which 1876 protein functions were annotated and identified in top categories involved in amino acids, nucleotide, energy, and carbohydrate transports and metabolisms. Comparative genes analysis identified 50 core and 12 strain-specific genes linked to probiotic properties, e.g., acid resistances and bile tolerances, antioxidant functions, or anti-inflammatory properties. Further, sugar transportome analysis uncovered 57 transporter genes, demonstrating diverse carbon utilization and phosphotransferase (PTS) systems, corroborated by API 50 CHL test results for carbohydrate metabolism profile. Conclusions: These findings enhance the comprehensive metabolic understanding of L. fermentum KUB-D18, supporting its industrial potential and applications in engineered probiotics.
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Affiliation(s)
- Yuke He
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Kevin Mok
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
- Center of Excellence for Microbiota Innovation, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
- Center of Excellence for Microbiota Innovation, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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Yan J, Xiong L, Yang LX, He ZM, Zhang P, Liao K. Morphological and multi-locus phylogenetic analyses reveal three new branched species of Clavaria (Clavariaceae, Agaricales) from China. MycoKeys 2025; 115:137-153. [PMID: 40114980 PMCID: PMC11923793 DOI: 10.3897/mycokeys.115.145774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Accepted: 02/24/2025] [Indexed: 03/22/2025] Open
Abstract
Based on morphological and molecular evidence, 12 specimens have been identified as belonging to three previously unrecognized species of Clavaria, which are here described as C.divergens, C.orientalis, and C.tongdaoensis. Clavariadivergens is characterized by its branched, white basidiomata. Clavariaorientalis and C.tongdaoensis are very similar to C.zollingeri in the field. However, C.orientalis is distinguished by its more robust branches, while C.tongdaoensis differs by its varied or paler color of basidiomata. A concatenated sequence dataset (ITS-nrLSU-RPB2) was used for multi-locus phylogenetic analysis. The phylogenetic tree of Clavaria showed that the three branched species each formed a distinct lineage with strong support. A key to the known branched species of Clavaria in China is provided.
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Affiliation(s)
- Jun Yan
- College of Life Science, Hunan Normal University, Changsha 410081, China Hunan Normal University Changsha China
- Hunan Provincial Demonstration Center of Forestry Seeding Breeding, Changsha 410329, China Hunan Provincial Demonstration Center of Forestry Seeding Breeding Changsha China
| | - Li Xiong
- Hunan Provincial Demonstration Center of Forestry Seeding Breeding, Changsha 410329, China Hunan Provincial Demonstration Center of Forestry Seeding Breeding Changsha China
| | - Li-Xun Yang
- Bureau of Forestry, Tongdao Dong Autonomous County, Huaihua 418500, China Bureau of Forestry, Tongdao Dong Autonomous County Huaihua China
| | - Zheng-Mi He
- College of Life Science, Hunan Normal University, Changsha 410081, China Hunan Normal University Changsha China
| | - Ping Zhang
- College of Life Science, Hunan Normal University, Changsha 410081, China Hunan Normal University Changsha China
| | - Ke Liao
- Hunan Provincial Demonstration Center of Forestry Seeding Breeding, Changsha 410329, China Hunan Provincial Demonstration Center of Forestry Seeding Breeding Changsha China
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Graham MR, Kaur N, Jones CS, Lamour K, Connolly BA. A phoenix in the greenhouse: characterization and phylogenomics of complete chloroplast genomes sheds light on the putatively extinct-in-the-wild Solanum ensifolium (Solanaceae). BMC PLANT BIOLOGY 2025; 25:320. [PMID: 40075255 PMCID: PMC11900257 DOI: 10.1186/s12870-025-06338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 03/04/2025] [Indexed: 03/14/2025]
Abstract
BACKGROUND The genus Solanum is a diverse group of flowering plants with significant economic importance. Within this genus, the subgenus Leptostemonum, comprising spiny solanums, is particularly noteworthy due to its high species diversity and endemism. Solanum ensifolium, a member of this subgenus, is a critically endangered species endemic to Puerto Rico and known locally as erubia. The species survives in greenhouses and botanical gardens and is thought to be extinct in the wild, but with reintroduction efforts in progress. Despite its conservation status, genomic data for S. ensifolium remains scarce, limiting our understanding of its evolutionary history and potential adaptations. RESULTS The S. ensifolium chloroplast genome (155,295 bp) exhibits a typical quadripartite structure and encodes 151 genes, including 95 protein-coding genes involved in photosynthesis, transcription, translation, and other essential cellular functions. Gene content and genome organization are similar to those observed in closely related Solanum species. Comparative genomic analysis of the annotated genome with that of closely related Solanum species revealed differences in nucleotide diversity between the large single-copy (LSC) and small single-copy regions (SSC), and the inverted repeat (IR) regions. Additionally, phylogenetic analyses confirmed placement of S. ensifolium within the Leptostemonum subgenus, affirming its suspected close relationship with S. crotonoides and S. aturense. Furthermore, of the three individuals of S. ensifolium for which chloroplast genomes were obtained, no genetic variation was observed. CONCLUSIONS The availability of the S. ensifolium chloroplast genome provides insights into its evolutionary history and conservation needs. Comparative genomics uncovered evolutionary differences in Solanum chloroplast genomes, including nucleotide diversity and structural variations. Phylogenetic analyses confirmed the close relationship between S. ensifolium and other Leptostemonum species. These findings enhance our understanding of this critically endangered species' evolution, guiding effective conservation strategies like using chloroplast variation to assess genetic diversity for ex situ conservation and reintroduction programs. The uniformity of the chloroplast genome in S. ensifolium may reveal that this species has undergone a genetic bottleneck. To prevent inbreeding depression and maintain evolutionary adaptability, efforts should be made to generate and preserve as much genetic diversity as possible.
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Affiliation(s)
- Matthew R Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, 06226, USA
| | - Noorpreet Kaur
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Cynthia S Jones
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Bryan A Connolly
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, 06226, USA.
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Jia S, Shen T, Cai W, Zhang J, Chen S. Complete Mitochondrial Genome of Platygyra daedalea and Characteristics Analysis of the Mitochondrial Genome in Merulinidae. Genes (Basel) 2025; 16:304. [PMID: 40149455 PMCID: PMC11942114 DOI: 10.3390/genes16030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 02/20/2025] [Accepted: 02/26/2025] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND The Merulinidae family belonging to the order Scleractinia is mainly distributed in the Indo-Pacific and Caribbean regions and often constitute the most dominant species of coral reefs. Mitochondrial genome is a key tool for studying the phylogeny and adaptation. Only a few studies have conducted the characteristics analyses of mitochondrial genome in the Merulinidae family. METHODS Therefore, we used high-throughput sequencing technology to describe the mitochondrial genome of Platygyra daedalea, a member of this family. Bioinformatics was used to analyze the composition characteristics of the mitochondrial genome of 10 Merulinidae species. RESULTS The mitochondrial genome of P. daedalea had a total length of 16,462 bp and a GC content of 33.0%. Thirteen unique protein-coding genes (PCGs), two transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes were annotated. Each species of Merulinidae had 13 unique PCGs in the mitochondrial genome. In contrast, the number of tRNAs and rRNAs significantly varied in Merulinidae species. Collinearity and gene rearrangement analyses indicated that the mitochondrial evolution of species in the Merulinidae family was relatively conserved. Divergence time analysis indicated that Merulinidae originated in the Oligocene, whereas the Platygyra genus originated in the Miocene. The formation and intraspecific divergence of coral species were consistent with geological changes in the ocean. CONCLUSIONS The results of this study help better understand the characteristics of the mitochondrial genome in the Merulinidae family and provide insights into the utility of mitochondrial genes as molecular markers of phylogeny.
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Affiliation(s)
- Shuwen Jia
- Qukou Scientific Research Base, Institute of Marine Ecology, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571136, China; (S.J.); (T.S.); (W.C.); (J.Z.)
- Key Laboratory for Coastal Marine Eco-Environment Process and Carbon Sink of Hainan Province, Yazhou Bay Innovation Institute, College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572000, China
- Dongzhaigang, Conservation and Restoration of Seagrass Bed Resources, Hainan Observation and Research Station, Haikou 571136, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya 572022, China
| | - Tongtong Shen
- Qukou Scientific Research Base, Institute of Marine Ecology, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571136, China; (S.J.); (T.S.); (W.C.); (J.Z.)
- Key Laboratory for Coastal Marine Eco-Environment Process and Carbon Sink of Hainan Province, Yazhou Bay Innovation Institute, College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572000, China
- Dongzhaigang, Conservation and Restoration of Seagrass Bed Resources, Hainan Observation and Research Station, Haikou 571136, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya 572022, China
| | - Wenqi Cai
- Qukou Scientific Research Base, Institute of Marine Ecology, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571136, China; (S.J.); (T.S.); (W.C.); (J.Z.)
- Key Laboratory for Coastal Marine Eco-Environment Process and Carbon Sink of Hainan Province, Yazhou Bay Innovation Institute, College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572000, China
- Dongzhaigang, Conservation and Restoration of Seagrass Bed Resources, Hainan Observation and Research Station, Haikou 571136, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya 572022, China
| | - Jian Zhang
- Qukou Scientific Research Base, Institute of Marine Ecology, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571136, China; (S.J.); (T.S.); (W.C.); (J.Z.)
- Key Laboratory for Coastal Marine Eco-Environment Process and Carbon Sink of Hainan Province, Yazhou Bay Innovation Institute, College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572000, China
- Dongzhaigang, Conservation and Restoration of Seagrass Bed Resources, Hainan Observation and Research Station, Haikou 571136, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya 572022, China
| | - Shiquan Chen
- Qukou Scientific Research Base, Institute of Marine Ecology, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571136, China; (S.J.); (T.S.); (W.C.); (J.Z.)
- Key Laboratory for Coastal Marine Eco-Environment Process and Carbon Sink of Hainan Province, Yazhou Bay Innovation Institute, College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572000, China
- Dongzhaigang, Conservation and Restoration of Seagrass Bed Resources, Hainan Observation and Research Station, Haikou 571136, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya 572022, China
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Chen KY, Wang JD, Xiang RQ, Yang XD, Yun QZ, Huang Y, Sun H, Chen JH. Backbone phylogeny of Salix based on genome skimming data. PLANT DIVERSITY 2025; 47:178-188. [PMID: 40182486 PMCID: PMC11963080 DOI: 10.1016/j.pld.2024.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 09/04/2024] [Accepted: 09/08/2024] [Indexed: 04/05/2025]
Abstract
The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of Salix is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs (SCOs) from 66 Salix accessions, along with publicly available plastome and sequence read archive (SRA) datasets to obtain a robust backbone phylogeny of Salix, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved Salix into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of Salix into five subgenera: Salix, Urbaniana, Triandrae, Longifoliae and Vetrix. We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade, while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of Salix. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies, enabling the comprehensive elucidation of Salix relationships.
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Affiliation(s)
- Kai-Yun Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Jin-Dan Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Rui-Qi Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xue-Dan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Quan-Zheng Yun
- Beijing Ori-Gene Science and Technology Co Ltd, Beijing 102206, PR China
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming 650092, Yunnan, PR China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Jia-Hui Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
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9
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Giombini E, Schiavoni I, Ambrosio L, Lo Presti A, Di Martino A, Fiore S, Leone P, Fortunato F, Prato R, Fedele G, Palamara AT, Stefanelli P. JN.1 variants circulating in Italy from October 2023 to April 2024: genetic diversity and immune recognition. BMC Infect Dis 2025; 25:291. [PMID: 40022017 PMCID: PMC11871800 DOI: 10.1186/s12879-025-10685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 02/19/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND The continuous emergence of SARS-CoV-2 variants and subvariants poses significant public health challenges. The latest designated subvariant JN.1, with all its descendants, shows more than 30 mutations in the spike gene. JN.1 has raised concerns due to its genomic diversity and its potential to enhance transmissibility and immune evasion. This study aims to analyse the molecular characteristics of JN.1-related lineages (JN.1*) identified in Italy from October 2023 to April 2024 and to evaluate the neutralization activity against JN.1 of a subsample of sera from individuals vaccinated with XBB.1.5 mRNA. METHODS The genomic diversity of the spike gene of 794 JN.1* strain was evaluated and phylogenetic analysis was conducted to compare the distance to XBB.1.5. Moreover, serum neutralization assays were performed on a subsample of 19 healthcare workers (HCWs) vaccinated with the monovalent XBB.1.5 mRNA booster to assess neutralizing capacity against JN.1. RESULTS Sequence analysis displayed high spike variability between JN.1* and phylogenetic investigation confirmed a substantial differentiation between JN.1* and XBB.1.5 spike regions with 29 shared mutations, of which 17 were located within the RBD region. Pre-booster neutralization activity against JN.1 was observed in 42% of HCWs sera, increasing significantly post-booster, with all HCWs showing neutralization capacity three months after vaccination. A significant correlation was found between anti-trimeric Spike IgG levels and neutralizing titers against JN.1. CONCLUSIONS The study highlights the variability of JN.1* in Italy. Results on a subsample of sera from HCWs vaccinated with XBB.1.5 mRNA booster vaccine suggested enhanced neutralization activity against JN.1.
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Affiliation(s)
- Emanuela Giombini
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Ilaria Schiavoni
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | | | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Stefano Fiore
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Pasqualina Leone
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Francesca Fortunato
- Department of Medical and Surgical Sciences, Hygiene Unit, Policlinico Foggia Hospital, University of Foggia, Foggia, Italy
| | - Rosa Prato
- Department of Medical and Surgical Sciences, Hygiene Unit, Policlinico Foggia Hospital, University of Foggia, Foggia, Italy
| | - Giorgio Fedele
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | | | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy.
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10
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Sun Y, Jin Y, Sun M, Wang L, Liu Q. Whole plastome sequence of Hibiscus moscheutos L. 1753 (Malvaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2025; 10:239-243. [PMID: 39981318 PMCID: PMC11841096 DOI: 10.1080/23802359.2025.2466604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Accepted: 02/09/2025] [Indexed: 02/22/2025] Open
Abstract
Hibiscus moscheutos, a perennial herb in the Malvaceae family, has medicinal properties but lacks molecular data. This study sequenced and analyzed its first complete plastome using next-generation sequencing. The 160,208 bp circular plastome has a typical quadripartite structure with 130 genes and 36.93% GC content. Phylogenetic analysis showed that H. mutabilis is sister to H. taiwanensis. This study provides essential molecular data for future research on Hibiscus phylogeny, taxonomy, and evolution.
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Affiliation(s)
- Yu Sun
- College of Pharmacy, Heze University, Heze, PR China
| | - Yutian Jin
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - Maoyin Sun
- College of Pharmacy, Heze University, Heze, PR China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, PR China
| | - Qianqian Liu
- College of Pharmacy, Heze University, Heze, PR China
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11
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Wittmers F, Poirier C, Bachy C, Eckmann C, Matantseva O, Carlson CA, Giovannoni SJ, Goodenough U, Worden AZ. Symbionts of predatory protists are widespread in the oceans and related to animal pathogens. Cell Host Microbe 2025; 33:182-199.e7. [PMID: 39947132 DOI: 10.1016/j.chom.2025.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/06/2024] [Accepted: 01/15/2025] [Indexed: 05/09/2025]
Abstract
Protists are major predators of ocean microbial life, with an ancient history of entanglements with prokaryotes, but their delicate cell structures and recalcitrance to culturing hinder exploration of marine symbioses. We report that tiny oceanic protistan predators, specifically choanoflagellates-the closest living unicellular relatives of animals-and uncultivated MAST-3 form symbioses with four bacterial lineages related to animal symbionts. By targeting living phagotrophs on ship expeditions, we recovered genomes from physically associated uncultivated Legionellales and Rickettsiales. The evolutionary trajectories of Marinicoxiellaceae, Cosmosymbacterales, Simplirickettsiaceae, and previously named Gamibacteraceae vary, including host-engagement mechanisms unknown in marine bacteria, horizontally transferred genes that mediate pathogen-microbiome interactions, and nutritional pathways. These symbionts and hosts occur throughout subtropical and tropical oceans. Related bacteria were detected in public data from freshwater, fish, and human samples. Symbiont associations with animal-related protists, alongside relationships to animal pathogens, suggest an unexpectedly long history of shifting associations and possibilities for host expansion as environments change.
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Affiliation(s)
- Fabian Wittmers
- Marine Biological Laboratory, Woods Hole, MA, USA; Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - Olga Matantseva
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Craig A Carlson
- The Marine Science Institute, Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | | | - Ursula Goodenough
- Department of Biology, Washington University St. Louis, St. Louis, MO, USA
| | - Alexandra Z Worden
- Marine Biological Laboratory, Woods Hole, MA, USA; Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany; Department of Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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12
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Saraf A, Blondet E, Boullié A, Criscuolo A, Gugger M. Insight on the heterocyte patterning and the proheterocyte division in the toxic cyanobacterium Kaarinaea lacus gen. nov., sp. nov., and its genomic potential for natural products. HARMFUL ALGAE 2025; 142:102792. [PMID: 39947850 DOI: 10.1016/j.hal.2024.102792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 11/06/2024] [Accepted: 12/23/2024] [Indexed: 05/09/2025]
Abstract
Nostoc sp. 152 (= PCC 9237T), a toxic cyanobacterium, isolated from mixed cyanobacterial bloom in a Finnish freshwater lake was reassessed using phylogenetic, morphological and genomic analyses. Multilocus and 16S rRNA gene phylogenetic analyses confirmed that this strain represents a novel Nostocalean genus for which we propose the name Kaarinaea lacus gen. nov., sp. nov., in accordance with the International Code of Nomenclature of Prokaryotes. The most intriguing morphological feature exhibited by PCC 9237T is the occasional division of proheterocytes. Based on our observations, we propose a hypothesis for the sequence of events taking place leading to this phenomenon. The other interesting feature includes the unusual heterocyte patterning resulting in the development of heterocytes in series in the old culture followed by its fragmentation at this site. Among the genes involved in heterocyte differentiation and patterning, patC and three homologs of hetP were not found from the genome of PCC 9237T. Furthermore, genomic investigations revealed a variant of heterocyte glycolipid gene cluster with a reduced hglB, but having additional gene coding for a protein with TubCN terminal docking domain. Finally, the presence of a pks2-like gene cluster, whose product may interfere with the cellular differentiation, and an anachelin-like gene cluster demands further investigations.
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Affiliation(s)
- Aniket Saraf
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris F-75015, France
| | - Eddy Blondet
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris F-75015, France
| | - Anne Boullié
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris F-75015, France
| | - Alexis Criscuolo
- Institut Pasteur, Université Paris Cité, GIPhy - Genome Informatics and Phylogenetics, Biological Resource Center of Institut Pasteur, Paris F-75015, France
| | - Muriel Gugger
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris F-75015, France.
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13
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Guo F, Tan H, Yang J, Jia R, Wang R, Wu L, Pan F, Kang K, Xie W, Li Y, Fan K. Insight into the codon usage patterns and adaptation of Tembusu Virus. Poult Sci 2025; 104:104651. [PMID: 39667183 PMCID: PMC11699206 DOI: 10.1016/j.psj.2024.104651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 12/05/2024] [Accepted: 12/06/2024] [Indexed: 12/14/2024] Open
Abstract
Since its emergence in 2010, Tembusu virus (TMUV) has rapidly spread across poultry populations in Asia, leading to substantial economic losses in these areas. Here, we investigate the codon usage patterns (CUPs) underlying TMUV's adaptation and evolutionary dynamics within host environments. Phylogenetic and compositional analyses consistently classify TMUV into four evolutionary lineages-Clusters 1, 2, 3, and ancestral TMUV-with Cluster 2 emerging as the dominant lineage. Codon adaptation index (CAI) analysis reveals that this lineage of TMUV show best adapted to the CUPs of duck than other lineages, underscoring the role of natural selection in shaping viral evolution, a finding in line with evidence that CUPs in the TMUV genome is predominantly shaped by natural selection. Furthermore, TMUV exhibits markedly higher adaptation to the CUPs of poultry hosts (duck, goose, and chicken) compared to potential host humans or vector mosquito. Thus, species-specific adaptability to the host environment may be a reason account for the distinct infectivity and clinic outcome of TMUV acted on hosts. Analysis of dinucleotide distribution reveals significant suppression of CpG and UpA dinucleotides in the TMUV genome, reflecting adaptive pressures to evade vertebrate immune responses. During transmission, TMUV shows increasing alignment with host CUPs and a continuous reduction in CpG dinucleotides, potentially enhancing its fitness within host microenvironments. This work advances our understanding of the basic biology underlying TMUV epidemiology, pathogenicity, and species-specific adaptation.
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Affiliation(s)
- Fucheng Guo
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China; Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Huiming Tan
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jinjin Yang
- Technology Center of Zhanjiang Customs District, Zhanjiang, 524000, Guangdong, China
| | - Rumin Jia
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ruichen Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lie Wu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Fengzhi Pan
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Kai Kang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Weitian Xie
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Youquan Li
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Kewei Fan
- Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China.
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14
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Schulz F, Yan Y, Weiner AK, Ahsan R, Katz LA, Woyke T. Protists as mediators of complex microbial and viral associations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.29.630703. [PMID: 39803511 PMCID: PMC11722414 DOI: 10.1101/2024.12.29.630703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
Abstract
Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments. Our findings reveal unique microbiome compositions and hint at an intricate network of complex interactions and associations with bacterial symbionts and viruses. We observed stark differences between ciliates and amoebae in terms of microbiome and virome compositions, highlighting the specificity of protist-microbe interactions. Over 115 of the recovered microbial genomes were affiliated with known endosymbionts of eukaryotes, including diverse members of the Holosporales, Rickettsiales, Legionellales, Chlamydiae, Dependentiae , and more than 250 were affiliated with possible host-associated bacteria of the phylum Patescibacteria. We also identified more than 80 giant viruses belonging to diverse viral lineages, of which some were actively expressing genes in single cell transcriptomes, suggesting a possible association with the sampled protists. We also revealed a wide range of other viruses that were predicted to infect eukaryotes or host-associated bacteria. Our results provide further evidence that protists serve as mediators of complex microbial and viral associations, playing a critical role in ecological networks. The frequent co-occurrence of giant viruses and diverse microbial symbionts in our samples suggests multipartite associations, particularly among amoebae. Our study provides a preliminary assessment of the microbial diversity associated with lesser-known protist lineages and paves the way for a deeper understanding of protist ecology and their roles in environmental and human health.
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Affiliation(s)
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | - Agnes K.M. Weiner
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | - Ragib Ahsan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, California, USA
- University of California Merced, Life and Environmental Sciences, Merced, California, USA
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15
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Yang F, Xiao J, Zhang X, Shang Y, Guo Y. First Report and Phylogenetic Analysis of Mitochondrial Genomes of Chrysomya villeneuvi and Sarcophaga genuforceps. INSECTS 2024; 16:26. [PMID: 39859606 PMCID: PMC11766282 DOI: 10.3390/insects16010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 12/26/2024] [Accepted: 12/28/2024] [Indexed: 01/27/2025]
Abstract
The mitochondrial genome, highly conserved across species, is crucial for species identification, phylogenetic analysis, and evolutionary research. Chrysomya villeneuvi and Sarcophaga genuforceps, two species with significant forensic value, have been understudied in terms of genetic data. In this study, the complete mitochondrial genomes of C. villeneuvi (15,623 bp) and S. genuforceps (15,729 bp) were sequenced and analyzed. All thirteen protein-coding genes (PCGs) exhibited Ka/Ks ratios below one, indicating purifying selection and supporting their utility as barcoding markers. Phylogenetic analysis and genetic distance calculations based on PCGs showed that C. villeneuvi is closely related to Chrysomya rufifacies and Chrysomya albiceps, and S. genuforceps aligns more closely with Sarcophaga kentejana and Sarcophaga schuetzei. This research is the first to provide mitochondrial genome data for C. villeneuvi and S. genuforceps, expanding the genetic resources available for Calliphoridae and Sarcophagidae and offering a foundation for further forensic and evolutionary studies.
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Affiliation(s)
| | | | | | | | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (F.Y.); (J.X.)
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16
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Kämpfer P, Glaeser SP, McInroy JA, Busse HJ, Clermont D, Criscuolo A. Description of Cohnella rhizoplanae sp. nov., isolated from the root surface of soybean (Glycine max). Antonie Van Leeuwenhoek 2024; 118:41. [PMID: 39718652 PMCID: PMC11668882 DOI: 10.1007/s10482-024-02051-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 12/03/2024] [Indexed: 12/25/2024]
Abstract
A Gram-staining-positive, aerobic bacterium, designated strain JJ-181 T, was isolated from the root surface of soybean. Based on the 16S rRNA gene sequence similarities, strain JJ-181 T was grouped into the genus Cohnella, most closely related to Cohnella hashimotonis F6_2S_P_1T (98.85%) and C. ginsengisoli GR21-5 T (98.3%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-181 T genome assembly against publicly available Cohnella type strain genomes were below 84% and 28%, respectively. The fatty acid profile from whole cell hydrolysates, the cell wall diaminoacid, the quinone system, the polar lipid profile, and the polyamine pattern supported the allocation of strain JJ-181 T to the genus Cohnella. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain JJ-181 T from its closely-related Cohnella species. Functional analysis revealed that strain JJ-181 T has different gene clusters related to swarming motility, chemotaxis ability, and endospore and biofilm formations. The gene content also suggests the ability of strain JJ-181 T to synthesise biotin and riboflavin, as well as indole-3-acetic acid, an important phytohormone for plant growth. Based on polyphasic analyses, strain JJ-181 T can be classified as a new species of the genus Cohnella, for which we propose the name Cohnella rhizoplanae sp. nov., with strain JJ-181 T (= LMG 31678 T = CIP 112018 T = CCM 9031 T = DSM 110650 T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - John A McInroy
- Division - Entomology and Plant Pathology Dept., Auburn University, Alabama, USA
| | - Hans-Jürgen Busse
- Division of Clinical Microbiology and Infection Biology, Institut Für Bakteriologie, Mykologie Und Hygiene, Veterinärmedizinische Universität, Vienna, Austria
| | - Dominique Clermont
- Institut Pasteur, Université de Paris, CIP - Collection of Institut Pasteur, 75015, Paris, France
| | - Alexis Criscuolo
- GIPhy - Genome Informatics and Phylogenetics, Biological Resource Center of Institut Pasteur, Institut Pasteur, Université de Paris, 75015, Paris, France
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17
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Nishiura H, Kumagai A, Mine J, Takadate Y, Sakuma S, Tsunekuni R, Uchida Y, Miyazawa K. Phylogenetic and Pathogenic Analysis of H5N1 and H5N6 High Pathogenicity Avian Influenza Virus Isolated from Poultry Farms (Layer and Broiler Chickens) in Japan in the 2023/2024 Season. Viruses 2024; 16:1956. [PMID: 39772262 PMCID: PMC11680161 DOI: 10.3390/v16121956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 12/06/2024] [Accepted: 12/18/2024] [Indexed: 01/11/2025] Open
Abstract
During the 2023-2024 winter, 11 high pathogenicity avian influenza (HPAI) outbreaks caused by clade 2.3.4.4b H5N1 and H5N6 HPAI viruses were confirmed in Japanese domestic poultry among 10 prefectures (n = 10 and 1, respectively). In this study, we aimed to genetically and pathologically characterize these viruses. Phylogenetic analysis revealed that H5N1 viruses were classified into the G2d-0 genotype, whereas the H5N6 virus was a novel genotype in Japan, designated as G2c-12. The G2c-12 virus shared PB2, PB1, PA, HA, and M genes with previous G2c viruses, but had NP and NS genes originating from avian influenza viruses in wild birds abroad. The N6 NA gene was derived from an H5N6 HPAI virus that was different from the viruses responsible for the outbreaks in Japan in 2016-2017 and 2017-2018. Experimental infections in chickens infected with H5N1(G2d-0) and H5N6(G2c-12) HPAI viruses showed no significant differences in the 50% chicken lethal dose, mean death time, or virus shedding from the trachea and cloaca, or in the histopathological findings. Different genotypes of the viruses worldwide, their introduction into the country, and their stable lethality in chickens may have triggered the four consecutive seasons of HPAI outbreaks in Japan.
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Affiliation(s)
| | | | | | | | | | | | | | - Kohtaro Miyazawa
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba 3050856, Japan; (H.N.); (A.K.); (J.M.); (Y.T.); (S.S.); (R.T.); (Y.U.)
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18
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Kaur A, Minsavage GV, Potnis N, Jones JB, Goss EM. Evolution of copper resistance in Xanthomonas euvesicatoria pv. perforans population. mSystems 2024; 9:e0142724. [PMID: 39584814 DOI: 10.1128/msystems.01427-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Accepted: 10/29/2024] [Indexed: 11/26/2024] Open
Abstract
The widespread use of antimicrobials that target bacterial pathogens has driven evolution of resistance, compromising the efficacy of these bactericides. Understanding the emergence and spread of resistance genes via mobile genetic elements is crucial for combating antimicrobial resistance. Copper resistance (CuR) in Xanthomonas euvesicatoria pv. perforans has severely affected the efficacy of copper-based bactericides for controlling bacterial leaf spot disease of tomato and pepper. Here, we investigated the evolutionary pathways of CuR acquisition and dissemination in X. euvesicatoria pv. perforans using an extensive collection of strains. We determined that chromosomally encoded CuR predominates over plasmid-borne CuR in multiple distinct phylogenetic groups of X. euvesicatoria pv. perforans. Our analysis revealed a single site of chromosomal integration by a CuR genomic island, although the genomic island showed sequence variation among phylogenetic groups. While chromosomal CuR was more prevalent, strains with plasmid-borne resistance conferred greater copper tolerance. Additionally, we identified strains carrying two copies of CuR genes, on plasmid and chromosome, that exhibited increased copper tolerance. Strains of X. euvesicatoria pv. perforans from the USA shared identical CuR gene sequences whether on plasmids or chromosome while different alleles were found in strains from other countries. In contrast to X. euvesicatoria pv. perforans, plasmid-borne CuR predominated in closely related pathovar, X. euvesicatoria pv. euvesicatoria. Overall, these findings contribute to a better understanding of the evolution and persistence of CuR in X. euvesicatoria pv. perforans and its closest relatives.IMPORTANCEThe emergence of antimicrobial resistance is a significant threat to agricultural production as it reduces the efficacy of various antimicrobials including copper-based bactericides that are widely used to control plant diseases. The challenge of increasing antimicrobial resistance entering a production system necessitates a deeper understanding of the dynamics and mechanisms by which pathogens acquire resistance. As a result of this research, we have identified different mechanisms of copper resistance acquisition as well as levels of copper resistance in a devastating plant pathogen, X. euvesicatoria pv. perforans. The evolution and dissemination of copper resistance in strains through plasmid or chromosomally integrated genomic island or both presents barriers to current management approaches, where growers rely heavily on copper-based bactericides to manage disease outbreaks. This knowledge is crucial when considering the continued use of existing antimicrobials or adopting alternative antimicrobials in efforts to implement enhanced antimicrobial stewardship strategies in agriculture.
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Affiliation(s)
- Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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Zhu L, Bau T. Biodiversity of Herbivores Triggers Species Differentiation of Coprophilous Fungi: A Case Study of Snow Inkcap ( Coprinopsis sect. Niveae). J Fungi (Basel) 2024; 10:835. [PMID: 39728330 DOI: 10.3390/jof10120835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 11/24/2024] [Accepted: 11/26/2024] [Indexed: 12/28/2024] Open
Abstract
Coprophilous species of Coprinopsis sect. Niveae, commonly known as "snow inkcap", are widespread in pastoral areas; however, wide sampling approaches are needed to discover new taxa and to clarify the taxonomic status of the so-called "snow inkcap". Nationwide field work was conducted in China with a detailed record collected of the distribution and the animal origin of the dung. A four-loci phylogenetic study of Coprinopsis sect. Niveae was conducted based on the internal transcribed spacer regions (ITS), the ribosomal large subunit (LSU), and translation elongation factor 1-α (tef1-α)], and the mitochondria small ribosomal RNA subunit (mtSSU). Fourteen phylogenetic species were assigned to this section, including six novel species, namely Coprinopsis furfuracea, C. iliensis, C. khorqinensis, C. sericivia, C. subigarashii, and C. tenuipes. Macro-, micro-, and ultramicro-morphological observations of species collected from China were also conducted and the detailed descriptions and illustrations of the novel species are provided. Our studies revealed that the different origin of herbivore dung, the distribution, the color and thickness of the pileus, the shape of stipes, the shape and size of basidiospores, and the presence or absence of pleurocystidia can be used as characteristics for distinguishing species in sect. Niveae. The key to species belonging to this section is also provided.
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Affiliation(s)
- Liyang Zhu
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture, Changchun 130118, China
| | - Tolgor Bau
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture, Changchun 130118, China
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20
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Deng PT, Liu XF, Yan J, Chen ZH, Zhang P. Update on the taxonomy of Clavulina in China II: description of four new species from Hainan Island. Mycol Prog 2024; 23:48. [DOI: 10.1007/s11557-024-01988-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 01/05/2025]
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21
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Su L, Yu T, Xue R, Zhang W, Xu C, Xia X, Li J, Lei H, Dong Y, Zhang G, Tang L. New Contributions on Species Diversity of Genus Hydnum and Lentaria s.l. in China. J Fungi (Basel) 2024; 10:824. [PMID: 39728320 DOI: 10.3390/jof10120824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/18/2024] [Accepted: 11/25/2024] [Indexed: 12/28/2024] Open
Abstract
Southwest China is extremely rich in fungal resources, and a large number of new taxa have been discovered in recent years. In the present study, we examined 26 specimens of the genera Hydnum and Lentaria sensu lato, most of which were obtained in Yunnan Province. Through ITS-nrLSU-tef1 phylogenetic analysis, combined with morphological studies and geographic analyses, five new species were described, viz. H. cremeum (), H. flavoquamosum (), H. roseoalbum (), H. roseotangerinum (), and L. subalpina (). Furthermore, we also supplied new information on some known species, including host plants and new distribution records. We re-examined the holotype sequences of two known taxa, H. flabellatum and H. pallidomarginatum, treating H. flabellatum as a synonym of H. pallidomarginatum. Additionally, a key to Lentaria s.l. in China was provided.
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Affiliation(s)
- Linjie Su
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Taijie Yu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Rou Xue
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Wenhao Zhang
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Chang Xu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Xing Xia
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Jia Li
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Hanchi Lei
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Yang Dong
- Forestry Bureau of Shitai County, Shitai 245100, China
| | - Guoli Zhang
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Liping Tang
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
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22
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Lin J, Dai H, Yuan J, Tang C, Ma B, Xu J. Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere. Nat Commun 2024; 15:10003. [PMID: 39562570 PMCID: PMC11577039 DOI: 10.1038/s41467-024-54392-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 11/07/2024] [Indexed: 11/21/2024] Open
Abstract
Heavy metal contamination poses an escalating global challenge to soil ecosystems, with hyperaccumulators playing a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.
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Affiliation(s)
- Jiahui Lin
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Hengyi Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Jing Yuan
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Caixian Tang
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant & Soil Sciences, Bundoora, VIC, Australia
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
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23
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Escuer P, Guirao-Rico S, Arnedo MA, Sánchez-Gracia A, Rozas J. Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands. Mol Ecol 2024; 33:e17547. [PMID: 39400446 DOI: 10.1111/mec.17547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/26/2024] [Accepted: 09/24/2024] [Indexed: 10/15/2024]
Abstract
The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage-based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterised genome-wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems.
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Affiliation(s)
- Paula Escuer
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sara Guirao-Rico
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miquel A Arnedo
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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24
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Zou M, Al-Otibi F, Hyde KD, Wang Y, Pan XJ. New Helminthosporium (Massarinaceae, Dothideomycetes) and Nigrospora (Incertae sedis, Sordariomycetes) species associated with walnut ( Juglansregia L.) in China. MycoKeys 2024; 109:265-284. [PMID: 39430416 PMCID: PMC11489710 DOI: 10.3897/mycokeys.109.133431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 09/22/2024] [Indexed: 10/22/2024] Open
Abstract
Six collections of ascomycetes were obtained from samples collected from dead branches and leaves of Juglansregia in Guizhou and Yunnan provinces, China. By incorporating multigene phylogenetic analysis (ITS, LSU, rpb2, SSU, tef1-α, tub2) supplemented by morphological data, we establish two novel species, namely Helminthosporiumguizhouense and Nigrosporayunnanensis. In morphology, H.guizhouense can be distinguished from H.caespitosum by its narrower conidia (13-16 µm vs. 27.3-35.5 µm), and N.yunnanensis is characterized by black, globose conidia (16.2 × 14.4 µm). The phylogenetic results further substantiated them as novel taxa. The present study contributes to our comprehension of the range of fungi found in Juglansregia, thereby expanding our knowledge of the diversity of fungi within this host.
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Affiliation(s)
- Mengting Zou
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550025, China
| | - Fatimah Al-Otibi
- Institute of Plant Health and Medicine, College of Agriculture, Guizhou University, Guiyang Guizhou 550025, China
| | - Kevin David Hyde
- Institute of Plant Health and Medicine, College of Agriculture, Guizhou University, Guiyang Guizhou 550025, China
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia
| | - Yong Wang
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550025, China
| | - Xue-Jun Pan
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550025, China
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25
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Han M, Na Q, Wei R, Zeng H, Hu Y, Zhang L, Du J, Zou L, Tang W, Cheng X, Ge Y. Phylogenetic and Morphological Perspectives on Crepidotus subg. Dochmiopus: Exploratively Unveiling Hidden Diversity in China. J Fungi (Basel) 2024; 10:710. [PMID: 39452662 PMCID: PMC11508588 DOI: 10.3390/jof10100710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 10/26/2024] Open
Abstract
Crepidotus subg. Dochmiopus contributes to more than half of Crepidotus species and exhibits highly hidden diversity. However, C. subg. Dochmiopus is challenging to study because the basidiomata of C. subg. Dochmiopus species are usually small and white, inconspicuous interspecific distinctions, and possess a familiar complex. In this study, we utilized a variety of characteristics for species identification, including habitat, presence or absence of a stipe in mature specimens, pileipellis and cheilocystidia patterns, whether the lamellae edges are fimbriated, and other characteristics. Above all, cheilocystidia and pileipellis patterns will be important in C. subg. Dochmiopus research. Based on the present specimens, we constructed a multigene phylogenetic tree (ITS + LSU) and recognized four new species: C. lamellomaculatus sp. nov., C. capitatocystidiatus sp. nov., C. succineus sp. nov., C. clavocystidiatustustus sp. nov. Detailed morphological descriptions, photographs, line drawings and comparisons with closely related taxa for the new species are provided. The current phylogenetic analysis does not support the previously classifications, indicating that the classification of Crepidotus requires re-evaluation. But the existing molecular datasets and species' descriptions are insufficient to fully resolve the classification. Further integration of new gene segments and a comprehensive review of morphological characteristics will reveal a natural classification for Crepidotus.
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Affiliation(s)
- Menghui Han
- Institute of Mycological Science and Technology, School of Horticulture, Ludong University, Yantai 264025, China; (M.H.); (Q.N.); (R.W.); (X.C.)
| | - Qin Na
- Institute of Mycological Science and Technology, School of Horticulture, Ludong University, Yantai 264025, China; (M.H.); (Q.N.); (R.W.); (X.C.)
| | - Renxiu Wei
- Institute of Mycological Science and Technology, School of Horticulture, Ludong University, Yantai 264025, China; (M.H.); (Q.N.); (R.W.); (X.C.)
| | - Hui Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China;
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, China
| | - Yaping Hu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, China;
| | - Libo Zhang
- Institute of Ecology, Chinese Research Academy of Environmental Science, Beijing 100012, China; (L.Z.); (J.D.)
| | - Jinhong Du
- Institute of Ecology, Chinese Research Academy of Environmental Science, Beijing 100012, China; (L.Z.); (J.D.)
| | - Li Zou
- College of Forestry, Northeast Forestry University, Harbin 150040, China;
| | - Weimin Tang
- Wufeng Tujia Autonomous County Environmental Monitoring Station, Yichang 443400, China;
| | - Xianhao Cheng
- Institute of Mycological Science and Technology, School of Horticulture, Ludong University, Yantai 264025, China; (M.H.); (Q.N.); (R.W.); (X.C.)
| | - Yupeng Ge
- Institute of Mycological Science and Technology, School of Horticulture, Ludong University, Yantai 264025, China; (M.H.); (Q.N.); (R.W.); (X.C.)
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China;
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, China
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26
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Niu C, Liu T, Zhao S, Ren J, Zhao Y, Kang X, Qin W, Xie X, Zhang X, Wei T, Tian J, Li X, Li M, Li S, Li G. Multi-gene analysis of the Russula crown clade (Russulales, Basidiomycota) revealed six new species and Alboflavinae subsect. nov. from Fagaceae forests in China. FRONTIERS IN PLANT SCIENCE 2024; 15:1454035. [PMID: 39439511 PMCID: PMC11494609 DOI: 10.3389/fpls.2024.1454035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 09/09/2024] [Indexed: 10/25/2024]
Abstract
Introduction The crown clade is one of two major groups in the Russula subg. Russula. Methods/material An analysis of Chinese samples was performed based on the morphology, internal transcribed spacer (ITS) sequences, and multi-gene phylogenies of 28S nrLSU, 16S mtSSU, rpb1, rpb2, and tef1-α. Results The results supported the independence of six new species: Russula alboflava (sect. Amethystinae), R. chrysantha (subsect. Chamaeleontinae), R. liyui (subsect. Laricinae), R. lutescens (subsect. Olivaceinae), R. paraxerampelina, and R. prunicolor (subsect. Xerampelinae) from Fagaceae forest habitats. Subsect. Alboflavinae was newly proposed in sect. Amethystinae. Members of the new subsection include R. alboflava, R. burlinghamiae, and possibly R. ballouii. Discussion Our analyses also supported the claim that two species of R. fulvograminea (subsect. Laricinae) and R. subrubens (subsect. Xerampelinae) have a Eurasian distribution. The habitat and primary hosts of the main phylogenetic clades within related subsections were summarized and discussed.
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Affiliation(s)
- Caiyun Niu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Tiezhi Liu
- College of Chemistry and Life Sciences, Chifeng University, Chifeng, China
| | - Shiyi Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Jing Ren
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Yi Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Xia Kang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | | | - Xuejiao Xie
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Xu Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Tiezheng Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinghua Tian
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Xiao Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Ming Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Shoumian Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
| | - Guojie Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China
- Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China
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27
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Zhou X, Wang F, Xie Y, Ning J, Xiao Y, Jiang C, Ding G, Tang Y. The complete chloroplast genome of Camellia huulungensis Rosmann et Ninh, a golden Camellia species endemic to Vietnam. Mitochondrial DNA B Resour 2024; 9:1365-1369. [PMID: 39381362 PMCID: PMC11459732 DOI: 10.1080/23802359.2024.2412227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 09/29/2024] [Indexed: 10/10/2024] Open
Abstract
Camellia huulungensis Rosmann & Ninh 1997, belonging to the sect. Chrysantha, holds important ornamental value and medicinal value. In this study, the complete chloroplast genome sequence of C. huulungensis was assembled using high-throughput sequencing technology. The entire length of chloroplast genome is 156,546 bp and contains a small single-copy region (18,257 bp), a large single-copy region (86,219 bp), and a pair of inverted repeat regions (26,035 bp). A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 37.33%. The phylogenetic analysis showed that C. huulungensis is sister to C. aurea. The results can provide genetic data for further phylogenetic studies of Camellia.
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Affiliation(s)
- Xingwen Zhou
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, China
| | - Fangyi Wang
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, China
| | - Yiqing Xie
- Institute of Economic Forestry, Fujian Academy of Forestry, Fuzhou, China
| | - Jing Ning
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, China
| | - Yuanfeng Xiao
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, China
| | - Changjie Jiang
- Golden Camellia Park of Nanning, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guochang Ding
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunxia Tang
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
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28
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Xu G, Zeng W, Zhang X, Hu J, Lei J. The complete chloroplast genome of Tabebuia rosea (Bignoniaceae). Mitochondrial DNA B Resour 2024; 9:1350-1354. [PMID: 39377036 PMCID: PMC11457379 DOI: 10.1080/23802359.2024.2412238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/28/2024] [Indexed: 10/09/2024] Open
Abstract
Tabebuia rosea is a world-renowned woody plant with colorful flowers in full bloom. In addition to its high ornamental value, it also has ecological and medicinal value. In this study, the complete circular chloroplast genome of T. rosea was reconstructed and annotated using Illumina sequencing. The chloroplast genome was 158,919 bp in size with GC content of 38.21%, including a large single-copy region of 85,823 bp, a small single-copy region of 12,816 bp, and a pair of inverted repeats of 30,140 bp. It encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Based on current available chloroplast genome sequences, the phylogenetic analysis indicated that T. rosea was clustered with T. nodosa and H. chrysanthus. This study provided insights into the evolutionary relationships among different species of Bignoniaceae.
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Affiliation(s)
- Guihong Xu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, China
| | - Wei Zeng
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, China
| | - Xiaofeng Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, China
| | - Jiayu Hu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, China
| | - Jiangli Lei
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, China
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Van Herzele C, Coppens S, Vereecke N, Theuns S, de Graaf DC, Nauwynck H. New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honey bee haemolymph. Vet Res 2024; 55:118. [PMID: 39334245 PMCID: PMC11430211 DOI: 10.1186/s13567-024-01382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/21/2024] [Indexed: 09/30/2024] Open
Abstract
Honey bees are rapidly declining, which poses a significant threat to our environment and agriculture industry. These vital insects face a disease complex believed to be caused by a combination of parasites, viruses, pesticides, and nutritional deficiencies. However, the real aetiology is still enigmatic. Due to the conventional analysis methods, we still lack complete insights into the honey bee virome and the presence of pathogenic bacteria. To fill this knowledge gap, we employed third-generation nanopore metagenomic sequencing on honey bee haemolymph to monitor the presence of pathogens over almost a year. This study provides valuable insights into the changes in bacterial and viral loads within honey bee colonies. We identified different pathogens in the honey bee haemolymph, which are not included in honey bee screenings. These pathogens comprise the Apis mellifera filamentous virus, Apis rhabdoviruses, and various bacteria such as Frischella sp. and Arsenophonus sp. Furthermore, a sharp contrast was observed between young and old bees. Our research proposes that transgenerational immune priming may play a role in shaping infection patterns in honey bees. We observed a significant increase in pathogen loads in the spring, followed by a notable decrease in pathogen presence during the summer and autumn months. However, certain pathogens seem to be able to evade this priming effect, making them particularly intriguing as potential factors contributing to mortality. In the future, we aim to expand our research on honey bee transgenerational immune priming and investigate its potential in natural settings. This knowledge will ultimately enhance honey bee health and decrease colony mortality.
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Affiliation(s)
- Cato Van Herzele
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium.
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | | | - Nick Vereecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
- PathoSense BV, Pastoriestraat 10, 2500, Lier, Belgium
| | | | - Dirk C de Graaf
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Hans Nauwynck
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
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Wang X, Wang L, Kong J, Li H, Kong N. The complete plastome of Rorippa palustris Besser 1821 and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:1273-1277. [PMID: 39328353 PMCID: PMC11425686 DOI: 10.1080/23802359.2024.2406929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
Rorippa palustris Besser 1821, a species of Brassicaceae, is widely distributed around the world and used for both food and traditional Chinese medicinal purposes. Despite the plant's significance, its genetic diversity must be better understood. In this study, we have successfully assembled and characterized a complete plastome of R. palustris, marking a significant advancement toward comprehending its genetic composition. The plastome is 154,674 bp long and harbors 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Our phylogenomic analysis indicated that R. palustris is closely related to R. curvipes. These findings are crucial for conserving and utilizing this important plant species. They also highlight the potential for future research into the evolution and preservation of R. palustris, which could be advantageous in pharmaceutical applications.
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Affiliation(s)
- Xinhua Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Jiaojiao Kong
- Personnel Office, Heze Medical College, Heze, Shandong Province, P. R. China
| | - Hongqin Li
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Na Kong
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
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31
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Zhang Y, Zhang J, Chen Z, Huang Y, Liu J, Liu Y, Yang Y, Jin X, Yang Y, Chen Y. Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1442178. [PMID: 39376234 PMCID: PMC11457174 DOI: 10.3389/fpls.2024.1442178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 09/02/2024] [Indexed: 10/09/2024]
Abstract
Dolichandrone spathacea is a mangrove associate with high medicinal and ecological values. However, due to the dual-pressure of climate change and human activities, D. spathacea has become endangered in China. Moreover, misidentification between D. spathacea and its terrestrial relative D. cauda-felina poses further challenges to field protection and proper medicinal usage of D. spathacea. Thus, to address these problems, we sequenced and assembled mitochondrial (mt) and chloroplast (cp) genomes for both D. spathacea and D. cauda-felina. Comparative analysis revealed apparently different size and scaffold number between the two mt genomes, but a high similarity between the cp genomes. Eight regions with high sequence divergence were identified between the two cp genomes, which might be used for developing candidate DNA markers for distinguishing the two species. The splitting between D. spathacea and D. cauda-felina was inferred to occur at ~6.8 - 7.7 million years ago (Mya), which may be driven by the environment fluctuations in late Miocene. In the cp genome, 12 genes related to the expression of photosynthesis-associated proteins were detected with signatures of positive selection, which may contribute to the origin and evolutionary adaptation of Dolichandrone mangrove species. These new findings do not only enrich organelle genomic resources of Dolichandrone species, but also provide important genetic clues for improving the conservation and proper usage of endangered mangrove associate D. spathacea.
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Affiliation(s)
- Ying Zhang
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Zewei Chen
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Yanni Huang
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jiaxuan Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yiqing Chen
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
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Dorji K, Klungthong C, Dorji T, Wangchuk T, Yuden P, Pelki T, Ghishing TD, Gyemiry G, Gyeltshen S, Chinnawirotpisan P, Manasatienkij W, Wangchuk S, Farmer A. Epidemiology and genetic characterization of influenza viruses circulating in Bhutan in 2022. PLoS One 2024; 19:e0304849. [PMID: 39288111 PMCID: PMC11407632 DOI: 10.1371/journal.pone.0304849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/21/2024] [Indexed: 09/19/2024] Open
Abstract
INTRODUCTION Influenza (Flu) causes considerable morbidity and mortality globally, and in Bhutan, Flu viruses are a leading cause of acute respiratory infection and cause outbreaks during Flu seasons. In this study, we aim to analyze the epidemiology and the genetic characterization of Flu viruses circulated in Bhutan in 2022. METHOD Respiratory specimens were collected from patients who meet the case definition for influenza-like illness (ILI) and severe acute respiratory infection (SARI) from sentinel sites. Specimens were tested for Flu and SARS-CoV-2 viruses by RT-PCR using the Multiplex Assay. Selected positive specimens were utilized for Flu viral genome sequencing by next-generation sequencing. Descriptive analysis was performed on patient demographics to see the proportion of Flu-associated ILI and SARI. All data were analyzed using Epi Info7 and QGIS 3.16 software. RESULT A weekly average of 16.2 ILI cases per 1000 outpatient visits and 18 SARI cases per 1000 admitted cases were reported in 2022. The median age among ILI was 12 years (IQR: 5-28) and SARI was 6.2 (IQR: 2.5-15) years. Flu A(H3N2) (70.2%) subtype was the most predominant circulating strain. Flu A(H1N1)pdm09 and Flu B viruses belonged to subclades that were mismatched to the vaccine strains recommended for the 2021-2022 season but matched the vaccine strain for the 2022-2023 season with vaccine efficacy 85.14% and 88.07% respectively. Flu A(H3N2) virus belonged to two subclades which differed from the vaccine strains recommended in both the 2021-2022 and 2022-2023 seasons with vaccine efficacy 68.28%. CONCLUSION Flu virus positivity rates were substantially elevated during the Flu season in 2022 compared to 2021. Flu A(H3N2) subtype was the most predominant circulating strain in the country and globally. Genetic characterization of the Flu viruses in Bhutan showed a close relatedness of high vaccine efficacy with the vaccine strain that WHO recommended for the 2022-23 season.
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Affiliation(s)
- Kunzang Dorji
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tshering Dorji
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Tandin Wangchuk
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Pema Yuden
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Tshering Pelki
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Tara Devi Ghishing
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Govinda Gyemiry
- ICT, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Sonam Gyeltshen
- National Influenza Centre, Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | | | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sonam Wangchuk
- Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Aaron Farmer
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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Dearlove BL, Fries AC, Epsi NJ, Richard SA, Ganesan A, Huprikar N, Lindholm DA, Mende K, Colombo RE, Colombo C, Bai H, Larson DT, Ewers EC, Lalani T, Smith AG, Berjohn CM, Maves RC, Jones MU, Saunders D, Maldonado CJ, Mody RM, Bazan SE, Tribble DR, Burgess T, Simons MP, Agan BK, Pollett SD, Rolland M. SARS-CoV-2 variant replacement constrains vaccine-specific viral diversification. Virus Evol 2024; 10:veae071. [PMID: 39386074 PMCID: PMC11463026 DOI: 10.1093/ve/veae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/03/2024] [Accepted: 08/31/2024] [Indexed: 10/12/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) vaccine breakthrough infections have been important for all circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant periods, but the contribution of vaccine-specific SARS-CoV-2 viral diversification to vaccine failure remains unclear. This study analyzed 595 SARS-CoV-2 sequences collected from the Military Health System beneficiaries between December 2020 and April 2022 to investigate the impact of vaccination on viral diversity. By comparing sequences based on the vaccination status of the participant, we found limited evidence indicating that vaccination was associated with increased viral diversity in the SARS-CoV-2 spike, and we show little to no evidence of a substantial sieve effect within major variants; rather, we show that rapid variant replacement constrained intragenotype COVID-19 vaccine strain immune escape. These data suggest that, during past and perhaps future periods of rapid SARS-CoV-2 variant replacement, vaccine-mediated effects were subsumed with other drivers of viral diversity due to the massive scale of infections and vaccinations that occurred in a short time frame. However, our results also highlight some limitations of using sieve analysis methods outside of placebo-controlled clinical trials.
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Grants
- Walter Reed National Military Medical Center, Bethesda, MD
- Defense Health Program
- Walter Reed Army Institute of Research, Silver Spring, MD
- National Institute of Allergy and Infectious Diseases at the National Institutes of Health
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF)
- U.S. Department of Defense (DOD)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc.
- Infectious Disease Clinical Research Program (IDCRP)
- National Institute of Allergy and Infectious Disease
- Uniformed Services University of the Health Sciences (USUHS)
- Department of Defense (DoD)
- Coast Guard, Washington, DC
- School of Aerospace Medicine, Dayton, OH
- William Beaumont Army Medical Center, El Paso, TX
- Womack Army Medical Center, Fort Bragg
- Henry M. Jackson Foundation, Inc., Bethesda, MD
- Carl R. Darnall Army Medical Center
- United States Air Force
- Tripler Army Medical Center, Honolulu, HI
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Affiliation(s)
- Bethany L Dearlove
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, United States
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
| | - Anthony C Fries
- The Applied Technology and Genomics (PHT) Division, US Air Force School of Aerospace Medicine, 2510 5th St, Dayton, OH 45433, United States
| | - Nusrat J Epsi
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Stephanie A Richard
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Anuradha Ganesan
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Division of Infectious Diseases, Walter Reed National Military Medical Center, 8901 Rockville Pike, Bethesda, MD 20889, United States
| | - Nikhil Huprikar
- Division of Infectious Diseases, Walter Reed National Military Medical Center, 8901 Rockville Pike, Bethesda, MD 20889, United States
| | - David A Lindholm
- Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Division of Infectious Diseases, Brooke Army Medical Center, 3551 Roger Brooke Drive, San Antonio, TX 78234, United States
| | - Katrin Mende
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Division of Infectious Diseases, Brooke Army Medical Center, 3551 Roger Brooke Drive, San Antonio, TX 78234, United States
| | - Rhonda E Colombo
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Division of Infectious Diseases, Madigan Army Medical Center, 9040 Jackson Avenue, Tacoma, WA 98431, United States
| | - Christopher Colombo
- Division of Infectious Diseases, Madigan Army Medical Center, 9040 Jackson Avenue, Tacoma, WA 98431, United States
| | - Hongjun Bai
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, United States
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
| | - Derek T Larson
- Division of Infectious Diseases, Alexander T. Augusta Military Medical Center, 9300 DeWitt Loop, Fort Belvoir, VA 22060, United States
| | - Evan C Ewers
- Division of Infectious Diseases, Alexander T. Augusta Military Medical Center, 9300 DeWitt Loop, Fort Belvoir, VA 22060, United States
| | - Tahaniyat Lalani
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Division of Infectious Diseases, Naval Medical Center Portsmouth, 620 John Paul Jones Circle, Portsmouth, VA 23708, United States
| | - Alfred G Smith
- Division of Infectious Diseases, Naval Medical Center Portsmouth, 620 John Paul Jones Circle, Portsmouth, VA 23708, United States
| | - Catherine M Berjohn
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
- Infectious Diseases and Internal Medicine, Naval Medical Center San Diego, 34800 Bob Wilson Drive, San Diego, CA 92134, United States
| | - Ryan C Maves
- Sections of Infectious Diseases and Critical Care Medicine, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, United States
| | - Milissa U Jones
- Department of Pediatrics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - David Saunders
- Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Carlos J Maldonado
- Department of Clinical Investigation, Womack Army Medical Center, 2817 Rock Merritt Avenue, Fort Liberty, NC, United States
| | - Rupal M Mody
- Division of Infectious Diseases, William Beaumont Army Medical Center, 18511 Highlander Medics Street, El Paso, TX 79918, United States
| | - Samantha E Bazan
- Department of Primary Care, Carl R. Darnall Army Medical Center, 590 Medical Center Road, Fort Cavazos, TX 76544, United States
| | - David R Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Timothy Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Mark P Simons
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Brian K Agan
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Simon D Pollett
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, United States
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, United States
- Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, United States
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Takadate Y, Mine J, Tsunekuni R, Sakuma S, Kumagai A, Nishiura H, Miyazawa K, Uchida Y. Genetic diversity of H5N1 and H5N2 high pathogenicity avian influenza viruses isolated from poultry in Japan during the winter of 2022-2023. Virus Res 2024; 347:199425. [PMID: 38906223 PMCID: PMC11250885 DOI: 10.1016/j.virusres.2024.199425] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
High pathogenicity avian influenza viruses (HPAIVs) of the H5N1 and H5N2 subtypes were responsible for 84 HPAI outbreaks on poultry premises in Japan during October 2022-April 2023. The number of outbreaks during the winter of 2022-2023 is the largest ever reported in Japan. In this study, we performed phylogenetic analyses using the full genetic sequences of HPAIVs isolated in Japan during 2022-2023 and those obtained from a public database to identify their genetic origin. Based on the hemagglutinin genes, these HPAIVs were classified into the G2 group of clade 2.3.4.4b, whose ancestors were H5 HPAIVs that circulated in Europe in late 2020, and were then further divided into three subgroups (G2b, G2d, and G2c). Approximately one-third of these viruses were classified into the G2b and G2d groups, which also included H5N1 HPAIVs detected in Japan during 2021-2022. In contrast, the remaining two-thirds were classified into the G2c group, which originated from H5N1 HPAIVs isolated in Asian countries and Russia during the winter of 2021-2022. Unlike the G2b and G2d viruses, the G2c viruses were first detected in Japan in the fall of 2022. Importantly, G2c viruses caused the largest number of outbreaks throughout Japan over the longest period during the season. Phylogenetic analyses using eight segment genes revealed that G2b, G2d, and G2c viruses were divided into 2, 4, and 11 genotypes, respectively, because they have various internal genes closely related to those of avian influenza viruses detected in wild birds in recent years in Asia, Russia, and North America, respectively. These results suggest that HPAIVs were disseminated among migratory birds, which may have generated numerous reassortant viruses with various gene constellations, resulting in a considerable number of outbreaks during the winter of 2022-2023.
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Affiliation(s)
- Yoshihiro Takadate
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Junki Mine
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Ryota Tsunekuni
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Saki Sakuma
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Asuka Kumagai
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Hayate Nishiura
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Kohtaro Miyazawa
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan
| | - Yuko Uchida
- Emerging Virus Group, Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305856, Japan.
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Deng PT, Liu WH, Ge ZW, Zhang P. Three new ramarioid species of Phaeoclavulina (Gomphaceae, Gomphales) from China. MycoKeys 2024; 108:1-14. [PMID: 39220354 PMCID: PMC11358615 DOI: 10.3897/mycokeys.108.128716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Three new species of Phaeoclavulina from China are described: Phaeoclavulinabicolor, P.echinoflava, and P.jilinensis. Recognition of the new species is supported by morphological and molecular evidence. Phylogenetic analyses of concatenated ITS1-5.8S-ITS2 and nuclear large subunit sequences support the establishment of the new species and their placement within the Phaeoclavulina clade. A key to the known Phaeoclavulina species in China is provided.
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Affiliation(s)
- Peng-Tao Deng
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Wen-Hao Liu
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Zai-Wei Ge
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Ping Zhang
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
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36
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Tang Y, Zhou X, Zhu M, He B, Jiang C, Ding G. The complete chloroplast genome of Camellia flava (Pitard) Sealy, a golden camellia of Vietnam. Mitochondrial DNA B Resour 2024; 9:1117-1121. [PMID: 39175482 PMCID: PMC11340231 DOI: 10.1080/23802359.2024.2392741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/10/2024] [Indexed: 08/24/2024] Open
Abstract
Camellia flava (Pit.) Sealy 1949 is a rare and precious species with golden flowers, which hold important ornamental and breeding values. In this study, the complete chloroplast genome of C. flava is reported for the first time. The chloroplast genome exhibits a typical quadripartite structure with a total length of 156,670 bp and a GC content of 37.32%, including a large single-copy region (86,250 bp), a small single-copy region (18,292 bp), and a pair of inverted repeat regions (26,064 bp). A total of 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. The phylogenetic analysis revealed a close relationship between C. flava and C. tamdaoensis. The chloroplast genome sequence of C. flava serves as a valuable resource for further breeding research and genetic phylogenetic studies.
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Affiliation(s)
- Yunxia Tang
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingwen Zhou
- College of Architecture and Planning, Fujian University of Technology
| | - Mengyao Zhu
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - BingBing He
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Changjie Jiang
- Golden Camellia Park of Nanning, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guochang Ding
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
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Wang X, Wang L, Kong J, Kong N. The complete chloroplast genome of Lindernia crustacea (L.) F. Muell 1882 (Linderniaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:1048-1052. [PMID: 39139658 PMCID: PMC11321110 DOI: 10.1080/23802359.2024.2391087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Lindernia crustacea (L.) F. Muell 1882, a species in the Linderniaceae family, holds traditional medicinal value in China. To investigate its genetic diversity, we assembled, annotated, and characterized the first complete chloroplast genome of L. crustacea using Illumina sequencing data and various bioinformatics tools. The genome is 153,647 bp in length, with a GC content of 37.6%. It exhibits a typical quadripartite structure, consisting of a large single-copy region (LSC) of 85,411 bp, a small single-copy region (SSC) of 18,724 bp, and two inverted repeat sequences (IRa and IRb) of 25,816 bp each. The genome was predicted to contain 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenomic analysis indicated that L. crustacea is closely related to L. stricta. These findings provide a foundation for further research on the evolution and potential medicinal applications of the Linderniaceae family.
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Affiliation(s)
- Xinhua Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Jiaojiao Kong
- Personnel Office, Heze Medical College, Heze, Shandong Province, P. R. China
| | - Na Kong
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
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Thomé PC, Wolinska J, Van Den Wyngaert S, Reñé A, Ilicic D, Agha R, Grossart HP, Garcés E, Monaghan MT, Strassert JFH. Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum. Mol Phylogenet Evol 2024; 197:108103. [PMID: 38754710 DOI: 10.1016/j.ympev.2024.108103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/01/2023] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.
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Affiliation(s)
- Pauline C Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Silke Van Den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Department of Biology, University of Turku, Turku, Finland
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Doris Ilicic
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Ramsy Agha
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
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Unneberg P, Larsson M, Olsson A, Wallerman O, Petri A, Bunikis I, Vinnere Pettersson O, Papetti C, Gislason A, Glenner H, Cartes JE, Blanco-Bercial L, Eriksen E, Meyer B, Wallberg A. Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins. Nat Commun 2024; 15:6297. [PMID: 39090106 PMCID: PMC11294593 DOI: 10.1038/s41467-024-50239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/15/2024] [Indexed: 08/04/2024] Open
Abstract
Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.
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Affiliation(s)
- Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Anna Petri
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
| | | | - Astthor Gislason
- Marine and Freshwater Research Institute, Pelagic Division, Reykjavik, Iceland
| | - Henrik Glenner
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Center for Macroecology, Evolution and Climate Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joan E Cartes
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
| | | | | | - Bettina Meyer
- Section Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carlvon Ossietzky University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden.
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Jiang T, He J, Li J, Zhao L, Niu H, Bu Y. Analysis of the complete mitochondrial genome sequence of Hipposideros pratti. Mitochondrial DNA B Resour 2024; 9:902-906. [PMID: 39055531 PMCID: PMC11271134 DOI: 10.1080/23802359.2024.2381806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
In order to explore the characteristics of the mitochondrial genome sequence of Pratt's leaf-nosed bat (Hipposideros pratti Thomas 1891) and understand their phylogenetic status in Chiroptera, this study determined the mitochondrial genome sequences of H. pratti from five regions in China using high-throughput sequencing technology, sequence assembly, and genome annotation. The results showed that these sequences contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region, all exhibiting a significant AT bias. Based on the phylogenetic tree constructed using 13 protein-coding genes from 15 Chiroptera species, the study found that H. pratti from the five regions clustered together, and then clustered with H. lylei into a single clade. Meanwhile, H. pratti from Jiangxi, Fujian, and Guangdong regions of China showed closer genetic relationships, while H. pratti from Yunnan and Henan regions of China exhibited closer genetic relationships. This study not only supplemented the mitochondrial genome database of H. pratti but also laid a foundation for genetic variation, molecular classification, and evolutionary studies of H. pratti.
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Affiliation(s)
- Tiantian Jiang
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jingying He
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jing Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Liming Zhao
- Henan Fisheries Technology Extension Center, Zhengzhou, Henan, China
| | - Hongxing Niu
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Yanzhen Bu
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
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Fu YT, Xun Y, Peng YY, Zhang Y, Wu X. The complete mitochondrial genome of the rodent flea Nosopsyllus laeviceps: genome description, comparative analysis, and phylogenetic implications. Parasit Vectors 2024; 17:253. [PMID: 38863074 PMCID: PMC11165799 DOI: 10.1186/s13071-024-06329-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Fleas are one of the most common and pervasive ectoparasites worldwide, comprising at least 2500 valid species. They are vectors of several disease-causing agents, such as Yersinia pestis. Despite their significance, however, the molecular genetics, biology, and phylogenetics of fleas remain poorly understood. METHODS We sequenced, assembled, and annotated the complete mitochondrial (mt) genome of the rodent flea Nosopsyllus laeviceps using next-generation sequencing technology. Then we combined the new mitogenome generated here with mt genomic data available for 23 other flea species to perform comparative mitogenomics, nucleotide diversity, and evolutionary rate analysis. Subsequently, the phylogenetic relationship within the order Siphonaptera was explored using the Bayesian inference (BI) and maximum likelihood (ML) methods based on concentrated data for 13 mt protein-coding genes. RESULTS The complete mt genome of the rodent flea N. laeviceps was 16,533 base pairs (bp) in a circular DNA molecule, containing 37 typical genes (13 protein-coding genes, 22 transfer RNA [tRNA] genes, and two ribosomal RNA [rRNA] genes) with one large non-coding region (NCR). Comparative analysis among the order Siphonaptera showed a stable gene order with no gene arrangement, and high AT content (76.71-83.21%) with an apparent negative AT and GC skew except in three fleas Aviostivalius klossi bispiniformis, Leptopsylla segnis, and Neopsylla specialis. Moreover, we found robust evidence that the cytochrome c oxidase subunit 1 (cox1) gene was the most conserved protein-coding gene (Pi = 0.15, non-synonymous/synonymous [Ka/Ks] ratio = 0.13) of fleas. Phylogenomic analysis conducted using two methods revealed different topologies, but both results strongly indicated that (i) the families Ceratophyllidae and Leptopsyllidae were paraphyletic and were the closest to each other, and (ii) the family Ctenophthalmidae was paraphyletic. CONCLUSIONS In this study, we obtained a high-quality mt genome of the rodent flea N. laeviceps and performed comparative mitogenomics and phylogeny of the order Siphonaptera using the mt database. The results will enrich the mt genome data for fleas, lay a foundation for the phylogenetic analysis of fleas, and promote the evolutionary analysis of Siphonaptera.
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Affiliation(s)
- Yi-Tian Fu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Ying Xun
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yan-Yan Peng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yu Zhang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, 410013, Hunan, China.
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Sultana M, Tayyab M, Parveen S, Hussain M, Shafique L. Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:843-864. [PMID: 38587724 DOI: 10.1007/s10695-024-01337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.
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Affiliation(s)
- Mehwish Sultana
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Wildlife & Fisheries, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
- Department of Zoology, Wildlife & Fisheries, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan.
| | - Muhammad Hussain
- Department of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Laiba Shafique
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, 535011, People's Republic of China.
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Tsang CTT, Hui TKL, Chung NM, Yuen WT, Tsang LM. Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification. Mol Ecol 2024; 33:e17377. [PMID: 38713089 DOI: 10.1111/mec.17377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024]
Abstract
The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.
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Affiliation(s)
- Chandlar Tsz To Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tom Kwok Lun Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nga Man Chung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing Tan Yuen
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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Kochanova E, Mayor T, Väinölä R. Cryptic diversity and speciation in an endemic copepod crustacean Harpacticella inopinata within Lake Baikal. Ecol Evol 2024; 14:e11471. [PMID: 38826165 PMCID: PMC11140236 DOI: 10.1002/ece3.11471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/04/2024] Open
Abstract
Ancient lakes are hotspots of species diversity, posing challenges and opportunities for exploration of the dynamics of endemic diversification. Lake Baikal in Siberia, the oldest lake in the world, hosts a particularly rich crustacean fauna, including the largest known species flock of harpacticoid copepods with some 70 species. Here, we focused on exploring the diversity and evolution within a single nominal species, Harpacticella inopinata Sars, 1908, using molecular markers (mitochondrial COI, nuclear ITS1 and 28S rRNA) and a set of qualitative and quantitative morphological traits. Five major mitochondrial lineages were recognized, with model-corrected COI distances of 0.20-0.37. A concordant pattern was seen in the nuclear data set, and qualitative morphological traits also distinguish a part of the lineages. All this suggests the presence of several hitherto unrecognized cryptic taxa within the baikalian H. inopinata, with long independent histories. The abundances, distributions and inferred demographic histories were different among taxa. Two taxa, H. inopinata CE and H. inopinata CW, were widespread on the eastern and western coasts, respectively, and were largely allopatric. Patterns in mitochondrial variation, that is, shallow star-like haplotype networks, suggest these taxa have spread through the lake relatively recently. Three other taxa, H. inopinata RE, RW and RW2, instead were rare and had more localized distributions on either coast, but showed deeper intraspecies genealogies, suggesting older regional presence. The rare taxa were often found in sympatry with the others and occasionally introgressed by mtDNA from the common ones. The mitochondrial divergence between and within the H. inopinata lineages is still unexpectedly deep, suggesting an unusually high molecular rate. The recognition of true systematic diversity in the evaluation and management of ecosystems is important in hotspots, as it is everywhere else, while the translation of the diversity into a formal taxonomy remains a challenge.
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Affiliation(s)
- Elena Kochanova
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Tatyana Mayor
- Laboratory of IchthyologyLimnological Institute SB RASIrkutskRussia
| | - Risto Väinölä
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
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Sinaiko G, Cao Y, Dietrich CH. Phylogenomics of the leafhopper genus Neoaliturus Distant, 1918 (Hemiptera: Cicadellidae: Deltocephalinae) reveals genetically divergent lineages in the invasive beet leafhopper. Mol Phylogenet Evol 2024; 195:108071. [PMID: 38579933 DOI: 10.1016/j.ympev.2024.108071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Phylogenomic analysis based on nucleotide sequences of 398 nuclear gene loci for 67 representatives of the leafhopper genus Neoaliturus yielded well-resolved estimates of relationships among species of the genus. Subgenus Neoaliturus (Neoaliturus) is consistently paraphyletic with respect to Neoaliturus (Circulifer). The analysis revealed the presence of at least ten genetically divergent clades among specimens consistent with the previous morphology-based definition of the leafhopper genus "Circulifer" which includes three previously recognized "species complexes." Specimens of the American beet leafhopper, N. tenellus (Baker), collected from the southwestern USA consistently group with one of these clades, comprising specimens from the eastern Mediterranean. Some of the remaining lineages are consistent with ecological differences previously observed among eastern Mediterranean populations and suggest that N. tenellus, as previously defined, comprises multiple monophyletic species, distinguishable by slight morphological differences.
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Affiliation(s)
- Guy Sinaiko
- School of Zoology, Tel-Aviv University, Tel-Aviv 6997801, Israel.
| | - Yanghui Cao
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
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Rosling A, Eshghi Sahraei S, Kalsoom Khan F, Desirò A, Bryson AE, Mondo SJ, Grigoriev IV, Bonito G, Sánchez-García M. Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics 2024; 25:529. [PMID: 38811885 PMCID: PMC11134847 DOI: 10.1186/s12864-024-10391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. RESULTS In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. CONCLUSION Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.
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Affiliation(s)
- Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | | | | | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Abigail E Bryson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Stephen J Mondo
- Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
- Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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47
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Li H, Ma C, Wang L. The complete plastome of Acalypha australis (Euphorbiaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:636-640. [PMID: 38770147 PMCID: PMC11104693 DOI: 10.1080/23802359.2023.2294891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/10/2023] [Indexed: 05/22/2024] Open
Abstract
Acalypha australis L. 1753 is a potherb popular among Asian populations and is a traditional herbal medicine. In the current study, the overall genetic diversity of A. australis still needs to be better. Here, we assembled and characterized the complete plastome of A. australis. The plastome is 168,885 bp in length with a large single-copy (LSC) of 94,576 bp, a small single-copy (SSC) of 19,715 bp, and two copies of inverted repeat region (IRs) of 27,297 bp each. The overall GC content is 34.9%. The plastome contains 127 genes, including 83 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenomic analysis of the representative species of Euphorbiaceae showed that A. australis and A. hispida formed a monophyletic sister clade. The results of this study will support further research on the evolution and conservation of the Euphorbiaceae species; they will benefit pharmaceutical applications and ornamentation of the medicinal plant A. australis.
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Affiliation(s)
- Hongqin Li
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Changhao Ma
- Inspection Department Three, Shandong Center for Food and Drug Evaluation and Inspection, Jinan, Shandong Province, P. R. China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
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48
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Warwick-Dugdale J, Tian F, Michelsen ML, Cronin DR, Moore K, Farbos A, Chittick L, Bell A, Zayed AA, Buchholz HH, Bolanos LM, Parsons RJ, Allen MJ, Sullivan MB, Temperton B. Long-read powered viral metagenomics in the oligotrophic Sargasso Sea. Nat Commun 2024; 15:4089. [PMID: 38744831 PMCID: PMC11094077 DOI: 10.1038/s41467-024-48300-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.
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Affiliation(s)
- Joanna Warwick-Dugdale
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
- Plymouth Marine Laboratory, Plymouth, Devon, PL1 3DH, UK.
| | - Funing Tian
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | | | - Dylan R Cronin
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Karen Moore
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Audrey Farbos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Lauren Chittick
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Ashley Bell
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Ahmed A Zayed
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Holger H Buchholz
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Luis M Bolanos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Rachel J Parsons
- Bermuda Institute of Ocean Sciences, St.George's, GE, 01, Bermuda
- School of Ocean Futures, Arizona State University, Tempe, AZ, US
| | - Michael J Allen
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Matthew B Sullivan
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
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Wang X, Zhao W, Cui S, Su B, Huang Y, Chen H. Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers. Animals (Basel) 2024; 14:1454. [PMID: 38791671 PMCID: PMC11117285 DOI: 10.3390/ani14101454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of Dendrocerus (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of Dendrocerus and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of D. bellus and D. anisodontus were 15,445 bp and 15,373 bp, respectively, with the trnG of D. bellus missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (D. bellus) and 82.4% (D. anisodontus). Using Ceraphron sp. (Ceraphronidae) as reference, the Ka/Ks values of NAD4L and NAD6 in D. anisodontus were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with Ceraphon sp. gene order, nine operations were identified in D. anisodontus, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the COX1 genes in Megaspilidae and a 60% rate of success was achieved in the genus Dendrocerus.
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Affiliation(s)
- Xu Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100000, China;
| | - Wenjing Zhao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
| | - Shanshan Cui
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
| | - Baoshan Su
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China;
| | - Yixin Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100000, China;
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China;
| | - Huayan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Chinese Academy of Sciences, Guangzhou 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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50
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Fan X, Yuan K, Zheng Y. The complete chloroplast genome and phylogenetic analysis of Cyperus brevifolius (Rottb.) Hassk. 1844 (Cyperaceae). Mitochondrial DNA B Resour 2024; 9:621-624. [PMID: 38737394 PMCID: PMC11086023 DOI: 10.1080/23802359.2024.2349769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
The medicinal plant Cyperus brevifolius (Rottb.) Hassk. 1844 has a long history of use in traditional Chinese medicine. In this study, we determined and systematically analyzed the complete chloroplast (cp) genome of C. brevifolius. The genome is 183,717 bp in length with a GC content of 33.24%. It comprises four distinct regions: a large-single copy (LSC) region of 101,190 bp, a small-single copy (SSC) region of 10,366 bp, and two inverted repeat (IR) regions of 36,079 bp each. A total of 137 genes are present in the genome including 89 protein-coding genes, 40 tRNA genes, and eight rRNA genes. Phylogenetic analysis reveals that C. brevifolius belongs to the Cyperus genus. This newly sequenced cp genome provides valuable insights for future genetic and genomic studies on Cyperus.
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Affiliation(s)
- Xia Fan
- College of Biology and Agriculture Resources, Huanggang Normal University, Huanggang, China
| | - Kai Yuan
- College of Biology and Agriculture Resources, Huanggang Normal University, Huanggang, China
| | - Yongliang Zheng
- College of Biology and Agriculture Resources, Huanggang Normal University, Huanggang, China
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