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Barnes TA, Ellis S, Chen J, Plimpton SJ, Nash JA. Plugin-based interoperability and ecosystem management for the MolSSI Driver Interface Project. J Chem Phys 2024; 160:214114. [PMID: 38832733 DOI: 10.1063/5.0214279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
The MolSSI Driver Interface (MDI) Project is an effort to simplify and standardize the process of enabling tight interoperability between independently developed code bases and is supported by numerous software packages across the domain of chemical physics. It enables a wide variety of use cases, including quantum mechanics/molecular mechanics, advanced sampling, path integral molecular dynamics, machine learning, ab initio molecular dynamics, etc. We describe two major developments within the MDI Project that provide novel solutions to key interoperability challenges. The first of these is the development of the MDI Plugin System, which allows MDI-supporting libraries to be used as highly modular plugins, with MDI enforcing a standardized application programming interface across plugins. Codes can use these plugins without linking against them during their build process, and end-users can select which plugin(s) they wish to use at runtime. The MDI Plugin System features a sophisticated callback system that allows codes to interact with plugins on a highly granular level and represents a significant advancement toward increased modularity among scientific codes. The second major development is MDI Mechanic, an ecosystem management tool that utilizes Docker containerization to simplify the process of developing, validating, maintaining, and deploying MDI-supporting codes. Additionally, MDI Mechanic provides a framework for launching MDI simulations in which each interoperating code is executed within a separate computational environment. This eliminates the need to compile multiple production codes within a single computational environment, reducing opportunities for dependency conflicts and lowering the barrier to entry for users of MDI-enabled codes.
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Affiliation(s)
- T A Barnes
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - S Ellis
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - J Chen
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - S J Plimpton
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - J A Nash
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
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2
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Klesser R, Blick T, Fritze MA, Marten A, Hemauer M, Kastner L, Höfer H, Jäger G, Husemann M. Ice cage: new records and cryptic, isolated lineages in wingless snow flies (Diptera, Limoniidae: Chionea spp.) in German lower mountain ranges. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:15. [PMID: 38478046 PMCID: PMC10937758 DOI: 10.1007/s00114-024-01900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
In Earth's history warm and cold periods have alternated. Especially, during the Pleistocene, the alternation between these different climatic conditions has led to frequent range expansions and retractions of many species: while thermophilic species dispersed during warm periods, cold adapted species retracted to cold refugia and vice versa. After the last Pleistocene cycle many cold adapted taxa found refuges in relict habitats in mountain ranges. One example for such a cold adapted relict is the flightless snow fly Chionea araneoides (Dalman, 1816). It can be found in lower mountain ranges of Central Europe exclusively in stone runs and stony accumulations which provide cold microclimates. Imagines develop only in winter. They have strongly restricted ranges and hence experienced strong isolation predicting that local populations may show local adaptation and hence also genetic differentiation. We investigated this for several middle mountain ranges of Germany using the COI barcoding gene. Our analyses revealed two distinct lineages, one in the Bavarian Forest and a second one in all other more northern locations up to Scandinavia. These lineages likely go back to post-Pleistocene isolation and should be studied in more detail in the future, also to confirm the taxonomic status of both lineages. Further, we confirmed former records of the species for Germany and report new records for the federal states of Saxony, Lower Saxony, Saxony-Anhalt and Thuringia. Finally, we provide the first evidence of two types of males for the species, a small and a larger male type.
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Affiliation(s)
- Robert Klesser
- Leibniz Institut zur Analyse des Biodiversitätswandels, ztm, Zoologisches Museum Hamburg Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
- Naturkundemuseum Leipzig, Lortzingstraße 3, D-04105, Leipzig, Germany.
| | - Theo Blick
- Private researcher, Heidloh 8, D-95503, Hummeltal, Germany
| | - Michael-Andreas Fritze
- Arbeitsgruppe für Tierökologie und Planung GmbH, Johann-Strauß-Str. 22, 70794, Filderstadt, Germany
| | - Andreas Marten
- Harz National Park, Lindenallee 35, D-38855, Wernigerode, Germany
| | - Michael Hemauer
- Private researcher, Wallbergstraße 20, D-81539, Munich, Germany
| | - Laura Kastner
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| | - Hubert Höfer
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| | - Gero Jäger
- Private researcher, Fuldatalstraße 55, D-34125, Kassel, Germany
| | - Martin Husemann
- Leibniz Institut zur Analyse des Biodiversitätswandels, ztm, Zoologisches Museum Hamburg Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
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Yang L, Zhou G. Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations. BMC PLANT BIOLOGY 2023; 23:450. [PMID: 37749488 PMCID: PMC10521563 DOI: 10.1186/s12870-023-04471-w] [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: 08/20/2022] [Accepted: 09/17/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Climate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles. METHODS In this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera. RESULTS The genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding. CONCLUSION Our study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Guoying Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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Campbell AM, Hauton C, Baker-Austin C, van Aerle R, Martinez-Urtaza J. An integrated eco-evolutionary framework to predict population-level responses of climate-sensitive pathogens. Curr Opin Biotechnol 2023; 80:102898. [PMID: 36739640 DOI: 10.1016/j.copbio.2023.102898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023]
Abstract
It is critical to gain insight into how climate change impacts evolutionary responses within climate-sensitive pathogen populations, such as increased resilience, opportunistic responses and the emergence of dominant variants from highly variable genomic backgrounds and subsequent global dispersal. This review proposes a framework to support such analysis, by combining genomic evolutionary analysis with climate time-series data in a novel spatiotemporal dataframe for use within machine learning applications, to understand past and future evolutionary pathogen responses to climate change. Recommendations are presented to increase the feasibility of interdisciplinary applications, including the importance of robust spatiotemporal metadata accompanying genome submission to databases. Such workflows will inform accessible public health tools and early-warning systems, to aid decision-making and mitigate future human health threats.
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Affiliation(s)
- Amy M Campbell
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, UK; Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, UK
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK; Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain.
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Kumar R, Yadav G, Kuddus M, Ashraf GM, Singh R. Unlocking the microbial studies through computational approaches: how far have we reached? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:48929-48947. [PMID: 36920617 PMCID: PMC10016191 DOI: 10.1007/s11356-023-26220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/24/2023] [Indexed: 04/16/2023]
Abstract
The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.
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Affiliation(s)
- Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Garima Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah , 27272, United Arab Emirates
| | - Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India.
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Mendoza AR, Margaria P, Nagata T, Winter S, Blawid R. Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent. Virus Genes 2022; 58:294-307. [PMID: 35538384 DOI: 10.1007/s11262-022-01903-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bulbifera, D. subhastata, and D. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only in D. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled from HTS and one by Sanger sequencing to group the sequences in a clade phylogenetically distinct from YMV from other origins. Temporal phylogenetic analyses estimated the mean evolutionary rate for the CP gene of YMV as 1.76 × 10-3 substitutions per site per year, and the time to the most recent common ancestor as 168.68 years (95% Highest Posterior Density, HPD: 48.56-363.28 years), with a most likely geographic origin in the African continent. The data presented in this study contribute to reveal key aspects of the probable epidemiological history of YMV in Brazil.
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Affiliation(s)
- Alejandro Risco Mendoza
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil. .,Department of Plant Pathology, Agronomy Faculty, Universidad Nacional Agraria La Molina, Lima, Peru.
| | - Paolo Margaria
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Tatsuya Nagata
- Department of Cell Biology, Laboratory of Electron Microscopy and Virology, University of Brasília, Distrito Federal, Brasília, Brazil
| | - Stephan Winter
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Rosana Blawid
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil
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7
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Le CTM, Okane I, Ono Y, Tsuda Y, Yamaoka Y. Incidence of Coffee Leaf Rust in Vietnam, Possible Original Sources and Subsequent Pathways of Migration. FRONTIERS IN PLANT SCIENCE 2022; 13:872877. [PMID: 35449887 PMCID: PMC9016365 DOI: 10.3389/fpls.2022.872877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/08/2022] [Indexed: 05/30/2023]
Abstract
This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix, to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863-869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam.
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Affiliation(s)
- Cham Thi Mai Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Division of Microbial Technology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Izumi Okane
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshitaka Ono
- College of Education, Ibaraki University, Mito, Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Ueda, Japan
| | - Yuichi Yamaoka
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Ge D, Feijó A, Wen Z, Lissovsky A, Zhang D, Cheng J, Yan C, Mu D, Wu X, Xia L, Yang Q. Ancient introgression underlying the unusual mito‐nuclear discordance and coat phenotypic variation in the Moupin pika. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology Chinese Academy of Sciences Sichuan China
| | - Danping Mu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology Xinjiang University Urumqi China
| | - Xinlai Wu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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Li R, Lin M, Guo S, Yang S, Han X, Ren M, Song Y, Du L, You Y, Zhan J, Huang W. A fundamental landscape of fungal biogeographical patterns across the main Chinese wine-producing regions and the dominating shaping factors. Food Res Int 2021; 150:110736. [PMID: 34865755 DOI: 10.1016/j.foodres.2021.110736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/02/2021] [Accepted: 09/30/2021] [Indexed: 01/20/2023]
Abstract
The microbial terroir plays an indispensable role in the formation of regional wine characteristics. A fundamental landscape of the fungal biogeographical patterns across Chinese wine-producing regions was obtained by characterizing the fungal communities in spontaneous fermentation. After confirming the established national microbial terroir, the fungal heterogeneity was evaluated at different geographical levels. The result showed that the variation between the wineries was more evident than at a regional level. Moreover, the microbial comparability from various regions with similar climates or wineries within the same regions was revealed. Further discriminant analysis determined the specific fungal biomarkers in different regions, while the associated reverse identification model displayed reliable accuracy (>70%). Correlation analysis illustrated the primary role of the geoclimatic factors (>41%) in shaping the fungal geographical patterns, and the relationship between the microbiome and spontaneous fermentation performance. In addition to expanding the knowledge regarding wine microbes, these findings provided a new benchmark for harnessing the microbial terroir to enhance regional wine expression.
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Affiliation(s)
- Ruilong Li
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Mengyuan Lin
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Sijiang Guo
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Siyu Yang
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoyu Han
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Mengmeng Ren
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yinghui Song
- Penglai Grape and Wine Industry Development Service Center, Yantai 265600, China
| | - Le Du
- Wuhan Donghu Big Data Trading Center Co. Ltd., Wuhan 430200, China
| | - Yilin You
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jicheng Zhan
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Weidong Huang
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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Ellepola G, Herath J, Manamendra-Arachchi K, Wijayathilaka N, Senevirathne G, Pethiyagoda R, Meegaskumbura M. Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae). PLoS One 2021; 16:e0258594. [PMID: 34665841 PMCID: PMC8525734 DOI: 10.1371/journal.pone.0258594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.
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Affiliation(s)
- Gajaba Ellepola
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
- Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Jayampathi Herath
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
| | | | - Nayana Wijayathilaka
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Gayani Senevirathne
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Rohan Pethiyagoda
- Ichthyology Section, Australian Museum, Sydney, New South Wales, Australia
| | - Madhava Meegaskumbura
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
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Magalhães KX, da Silva RDF, Sawakuchi AO, Gonçalves AP, Gomes GFE, Muriel-Cunha J, Sabaj MH, de Sousa LM. Phylogeography of Baryancistrus xanthellus (Siluriformes: Loricariidae), a rheophilic catfish endemic to the Xingu River basin in eastern Amazonia. PLoS One 2021; 16:e0256677. [PMID: 34449827 PMCID: PMC8396747 DOI: 10.1371/journal.pone.0256677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Baryancistrus xanthellus (Loricariidae) is an endemic fish species from the Xingu River basin with its life history in the shallow rapid waters flowing over bedrock substrates. In order to investigate the genetic diversity and demographic history of B. xanthellus we analyzed sequence data for one mitochondrial gene (Cyt b) and introns 1 and 5 of nuclear genes Prolactin (Prl) and Ribosomal Protein L3 (RPL3). The analyses contain 358 specimens of B. xanthellus from 39 localities distributed throughout its range. The number of genetically diverged groups was estimated using Bayesian inference on Cyt b haplotypes. Haplotype networks, AMOVA and pairwise fixation index was used to evaluate population structure and gene flow. Historical demography was inferred through neutrality tests and the Extended Bayesian Skyline Plot (EBSP) method. Five longitudinally distributed Cyt b haplogroups for B. xanthellus were identified in the Xingu River and its major tributaries, the Bacajá and Iriri. The demographic analysis suggests that rapids habitats have expanded in the Iriri and Lower Xingu rivers since 200 ka (thousand years) ago. This expansion is possibly related to an increase in water discharge as a consequence of higher rainfall across eastern Amazonia. Conversely, this climate shift also would have promoted zones of sediment trapping and reduction of rocky habitats in the Xingu River channel upstream of the Iriri River mouth. Populations of B. xanthellus showed strong genetic structure along the free-flowing river channels of the Xingu and its major tributaries, the Bacajá and Iriri. The recent impoundment of the Middle Xingu channel for the Belo Monte hydroelectric dam may isolate populations at the downstream limit of the species distribution. Therefore, future conservation plans must consider the genetic diversity of B. xanthellus throughout its range.
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Affiliation(s)
- Keila Xavier Magalhães
- Laboratório de Ictiologia de Altamira, Universidade Federal do Pará, Altamira, Pará, Brazil
| | | | | | - Alany Pedrosa Gonçalves
- Instituto Nacional de Pesquisa da Amazônia, INPA, Programa de Pós-Graduação em Biologia de Água Doce e Pesca Interior, Manaus, Amazonas, Brazil
| | | | - Janice Muriel-Cunha
- Instituto de Estudos Costeiros, Campus Bragança, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Mark H. Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA, United States of America
| | - Leandro Melo de Sousa
- Laboratório de Ictiologia de Altamira, Universidade Federal do Pará, Altamira, Pará, Brazil
- * E-mail:
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12
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Xu S, He C, Song S, Li C. Spatiotemporal dynamics of marine microbial communities following a Phaeocystis bloom: biogeography and co-occurrence patterns. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:294-308. [PMID: 33527743 DOI: 10.1111/1758-2229.12929] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Marine microbes play important roles in the development of phytoplankton blooms. The diversity and composition of free living (FL) and particle attached (PA) microbial communities have been well studied, while little is known about their geographic and co-occurrence patterns, especially during the subsiding process of Phaeocystis globosa blooms. Herein, the beta-diversity of FL and PA microbial communities in both the surface and bottom layers of different habitats were comprehensively examined during succession of a P. globosa bloom event. The results showed that microbial communities from bloom and non-bloom sites exhibited distinct community compositions. Among the different sampling sites, the community similarities decreased with spatial distance, in which the FL communities' similarity in bottom waters was more influenced by spatial variation. The variation of microbial communities was mostly attributed to environmental selection, spatial distance, and the abundance of P. globosa successively. The co-occurrence networks of microbial communities in bloom and non-bloom waters differed in terms of structure and composition, and the bloom network had more links and closer relationships between genera than the non-bloom network. The correlation among genera and modules suggested that the bloom microbes were likely driven by high environmental selection and low competitive effect between each other.
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Affiliation(s)
- Sha Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuqun Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Caiwen Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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13
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Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits. BMC Ecol Evol 2021; 21:45. [PMID: 33731021 PMCID: PMC7968296 DOI: 10.1186/s12862-021-01776-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
Background Natural model systems are indispensable for exploring adaptations in response to environmental pressures. Sinocyclocheilus of China, the most diverse cavefish clade in the world (75 species), provide unique opportunities to understand recurrent evolution of stereotypic traits (such as eye loss and sensory expansion) in the context of a deep and diverse phylogenetic group. However, they remain poorly understood in terms of their morphological evolution. Therefore, we explore key patterns of morphological evolution, habitat utilization and geographic distribution in these fishes. Results We constructed phylogenies and categorized 49 species based on eye-related condition (Blind, Micro-eyed, and Normal-eyed), habitat types (Troglobitic—cave-restricted; Troglophilic—cave-associated; Surface—outside caves) and existence of horns. Geometric-morphometric analyses show Normal-eyed morphs with fusiform shapes segregating from Blind/Micro-eyed deeper bodied morphs along the first principal-component axis; second axis accounts for shape complexity related to horns. The body shapes showed a significant association with eye-related condition and horn, but not habitat types. Ancestral reconstructions suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to their ancestral Normal-eyed morphs; Sinocyclocheilus are also pre-adapted for cave dwelling. Our geophylogeny shows an east-to-west diversification spanning Pliocene and Pleistocene, with early-diversifying Troglobitic species dominating subterranean habitats of karstic plains whereas predominantly Surface forms inhabit hills to the west. Evolutionary rates analyses suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 5–20 fold increase in rate of eye regression, possibly explained by limited resource availability. Body size and eye size have undergone reversals, but not horns, a trait entailing considerable time to form. Conclusions Sinocyclocheilus occupied cave habitats in response to drying associated with aridification of China during late Miocene and the Pliocene. The prominent cave-adaptations (eye-regression, horn-evolution) occur in clades associated with the extensive subterranean cave system in Guangxi and Guizhou provinces. Integration of morphology, phylogeny, rate analyses, molecular-dating and distribution show not only several remarkable patterns of evolution, but also interesting exceptions to these patterns signifying the diversification of Sinocyclocheilus as an invaluable model system to explore evolutionary novelty. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01776-y.
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Klesser R, Husemann M, Schmitt T, Sousa P, Moussi A, Habel JC. Molecular biogeography of the Mediterranean Buthus species complex (Scorpiones: Buthidae) at its southern Palaearctic margin. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Neogene orogenesis and climatic cycles strongly influenced inter- and intraspecific differentiation and variability of taxa. In this study, we focused on the southern margin of the western Palaearctic, known to be a geographically complex region. We performed mitochondrial DNA analyses of Buthus scorpions from the Moroccan Atlas Mountains, from the Hoggar Mountains in Algeria and from Tunisia, Iberia and Israel. Molecular species delimitation suggests the existence of ≥ 24 molecular operational taxonomic units. The data confirm complex differentiation patterns across the Atlas Mountains of Morocco, but structures in Iberia, Algeria and Tunisia have considerably lower complexity. This identifies the Atlas Mountain region as the most important differentiation centre of Buthus scorpions. Samples from the Hoggar Mountains (southern Algeria) cluster with those from the southernmost parts of Morocco in the middle and upper parts of the Draa Valley. This reinforces a recent connection of these regions. Samples from Israel are genetically similar to individuals from eastern Algeria and Tunisia. This suggests a widespread group across major parts of North Africa. Divergence time estimates indicate that differentiation in the genus began during the late Miocene, a period characterized by strong tectonic activities in this region. Further differentiation could be linked to subsequent climatic changes that have occurred since the end of the Miocene, with an increasing aridification of the Moroccan area. This also produced many microrefugia in the mountains of the area during the Pleistocene climatic fluctuations.
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Affiliation(s)
- Robert Klesser
- Department of Invertebrates, Natural History Museum Leipzig, Leipzig, Germany
- Department of Entomology, Centrum für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Martin Husemann
- Department of Entomology, Centrum für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, Müncheberg, Germany
- Zoology, Institute of Biology, Faculty Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Pedro Sousa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Abdelhamid Moussi
- Laboratory Valorization and Conservation of Natural Resources, University of Biskra, Algeria
| | - Jan Christian Habel
- Evolutionary Zoology, Department of Biosciences, University of Salzburg, Salzburg, Austria
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15
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Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere ID, Asante-Poku A, Asare P, Sánchez-Busó L, Gehre F, Sanoussi CN, Antonio M, Affolabi D, Fyfe J, Beckert P, Niemann S, Alabi AS, Grobusch MP, Kobbe R, Parkhill J, Beisel C, Fenner L, Böttger EC, Meehan CJ, Harris SR, de Jong BC, Yeboah-Manu D, Brites D. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom 2021; 7:000477. [PMID: 33555243 PMCID: PMC8208692 DOI: 10.1099/mgen.0.000477] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
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Affiliation(s)
- Mireia Coscolla
- ISysBio, University of Valencia-FISABIO Joint Unit, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Florian Gehre
- Infectious Disease Epidemiology Department, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- Health Department, East African Community (EAC), Arusha, Tanzania
| | - C. N’Dira Sanoussi
- Laboratoire de Référence des Mycobactéries, Ministry of Health, Cotonou, Bénin
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Martin Antonio
- London School of Hygiene and Tropical Medicine, London, UK
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries, Ministry of Health, Cotonou, Bénin
| | - Janet Fyfe
- Mycobacterium Reference Laboratory, Victoria Infectious Diseases Reference Laboratory, Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research, Borstel, Germany
| | - Abraham S. Alabi
- Centre de Recherches Médicales en Lambaréné (Cermel), Lambaréné, Gabon
| | - Martin P. Grobusch
- Centre de Recherches Médicales en Lambaréné (Cermel), Lambaréné, Gabon
- Institut für Tropenmedizin, Deutsches Zentrum fuer Infektionsforschung, University of Tübingen, Tübingen, Germany
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, The Netherlands
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Germany
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Erik C. Böttger
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Conor J. Meehan
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Simon R. Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Microbiotica Limited, Bioinnovation Centre, Wellcome Genome Campus, Cambridge, CB10 1DR, UK
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Zhou J, Cavagnaro TR, De Bei R, Nelson TM, Stephen JR, Metcalfe A, Gilliham M, Breen J, Collins C, López CMR. Wine Terroir and the Soil Bacteria: An Amplicon Sequencing-Based Assessment of the Barossa Valley and Its Sub-Regions. Front Microbiol 2021; 11:597944. [PMID: 33488543 PMCID: PMC7817890 DOI: 10.3389/fmicb.2020.597944] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/04/2020] [Indexed: 02/01/2023] Open
Abstract
A wines' terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.
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Affiliation(s)
- Jia Zhou
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Timothy R. Cavagnaro
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Roberta De Bei
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Tiffanie M. Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - John R. Stephen
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
- ARC Industrial Transformation Training Centre for Innovative Wine Production, Waite Research Institute, Adelaide, SA, Australia
| | - James Breen
- Bioinformatics Hub, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Cassandra Collins
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
- ARC Industrial Transformation Training Centre for Innovative Wine Production, Waite Research Institute, Adelaide, SA, Australia
| | - Carlos M. Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
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Vélez JM, Morris RM, Vilgalys R, Labbé J, Schadt CW. Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives. PLoS One 2021; 16:e0231367. [PMID: 33406078 PMCID: PMC7787446 DOI: 10.1371/journal.pone.0231367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.
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Affiliation(s)
- Jessica M. Vélez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States of America
| | - Reese M. Morris
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Rytas Vilgalys
- Biology Department, Duke University, Raleigh, NC, United States of America
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States of America
- Dept of Microbiology, University of Tennessee, Knoxville, TN, United States of America
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18
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Morales-Rodríguez C, Sferrazza I, Aleandri MP, Dalla Valle M, Speranza S, Contarini M, Vannini A. The fungal community associated with the ambrosia beetle Xylosandrus compactus invading the mediterranean maquis in central Italy reveals high biodiversity and suggests environmental acquisitions. Fungal Biol 2020; 125:12-24. [PMID: 33317772 DOI: 10.1016/j.funbio.2020.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
In summer 2016 a severe infestation of the alien ambrosia beetle Xylosandrus compactus was recorded from the Mediterranean maquis in the Circeo National Park in Central Italy. Trees and shrubs were infested and displayed wilting and necrosis of terminal branches caused by the combined impact of the insect and associated pathogenic fungi. A preliminary screening carried out on captured adults resulted in the isolation of a discrete number of fungal taxa with different life strategies, ranging from true mutualist (e.g. Ambrosiella xylebori) to plant pathogens (Fusarium spp.). In the present study, high-throughput sequencing was applied to determine the total diversity and functionality of the fungal community associated with X. compactus adults collected in the galleries of three Mediterranean woody hosts, Quercus ilex, Laurus nobilis, and Ceratonia siliqua. The effect of season and host in determining the composition of the associated fungal community was investigated. A total of 206 OTUs composed the fungal community associated with X. compactus. Eighteen OTUs were shared among the three hosts, including A. xylebori and members of the Fusarium solani complex. All but two were previously associated with beetles. Sixty-nine out of 206 OTUs were resolved to species level, identifying 60 different fungal species, 22 of which already reported in the literature as associated with beetles or other insects. Functional guild assigned most of the fungal species to saprotrophs and plant pathogens. Effects of seasonality and host on fungal community assemblage were highlighted suggesting the acquisition by the insect of new fungal taxa during the invasion process. The consequences of enriched fungal community on the risk of the insurgence of novel threatful insect-fungus association are discussed considering direct and indirect effects on the invaded habitat.
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Affiliation(s)
- Carmen Morales-Rodríguez
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Ivano Sferrazza
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Maria Pia Aleandri
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Matteo Dalla Valle
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Stefano Speranza
- Department of Agriculture and Forest Science (DAFNE) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Mario Contarini
- Department of Agriculture and Forest Science (DAFNE) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Andrea Vannini
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy.
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Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology. Sci Rep 2020; 10:15657. [PMID: 32973260 PMCID: PMC7519111 DOI: 10.1038/s41598-020-72369-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/09/2020] [Indexed: 11/17/2022] Open
Abstract
Albacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resource requires a robust understanding of the species’ biology and of the pattern of connectivity among oceanic regions, yet Indian Ocean albacore population dynamics remain poorly understood and its level of connectivity with the Atlantic Ocean population is uncertain. We analysed morphometrics and genetics of albacore (n = 1,874) in the southwest Indian (SWIO) and southeast Atlantic (SEAO) Oceans to investigate the connectivity and population structure. Furthermore, we examined the species’ dispersal potential by modelling particle drift through major oceanographic features. Males appear larger than females, except in South African waters, yet the length–weight relationship only showed significant male–female difference in one region (east of Madagascar and Reunion waters). The present study produced a genetic differentiation between the southeast Atlantic and southwest Indian Oceans, supporting their demographic independence. The particle drift models suggested dispersal potential of early life stages from SWIO to SEAO and adult or sub-adult migration from SEAO to SWIO.
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Donne C, Neiman M, Woodell JD, Haase M, Verhaegen G. A layover in Europe: Reconstructing the invasion route of asexual lineages of a New Zealand snail to North America. Mol Ecol 2020; 29:3446-3465. [PMID: 32741004 DOI: 10.1111/mec.15569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022]
Abstract
Non-native invasive species are threatening ecosystems and biodiversity worldwide. High genetic variation is thought to be a critical factor for invasion success. Accordingly, the global invasion of a few clonal lineages of the gastropod Potamopyrgus antipodarum is thus both puzzling and has the potential to help illuminate why some invasions succeed while others fail. Here, we used SNP markers and a geographically broad sampling scheme (N = 1617) including native New Zealand populations and invasive North American and European populations to provide the first widescale population genetic assessment of the relationships between and among native and invasive P. antipodarum. We used a combination of traditional and Bayesian molecular analyses to demonstrate that New Zealand populations harbour very high diversity relative to the invasive populations and are the source of the two main European genetic lineages. One of these two European lineages was in turn the source of at least one of the two main North American genetic clusters of invasive P. antipodarum, located in Lake Ontario. The other widespread North American group had a more complex origin that included the other European lineage and two New Zealand clusters. Altogether, our analyses suggest that just a small handful of clonal lineages of P. antipodarum were responsible for invasion across continents. Our findings provide critical information for prevention of additional invasions and control of existing invasive populations and are of broader relevance towards understanding the establishment and evolution of asexual populations and the forces driving biological invasion.
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Affiliation(s)
- Carina Donne
- Department of Biology, Department of Gender, Women's, and Sexuality Studies, The University of Iowa, Iowa, USA
| | - Maurine Neiman
- Department of Biology, Department of Gender, Women's, and Sexuality Studies, The University of Iowa, Iowa, USA
| | - James D Woodell
- Department of Biology, Department of Gender, Women's, and Sexuality Studies, The University of Iowa, Iowa, USA
| | - Martin Haase
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Gerlien Verhaegen
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.,Advanced Science-Technology Research (ASTER) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science Technology (JAMSTEC), Yokosuka, Japan
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21
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Crisan A, Gardy JL, Munzner T. A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT. Bioinformatics 2020; 35:1668-1676. [PMID: 30256887 PMCID: PMC6513170 DOI: 10.1093/bioinformatics/bty832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/27/2018] [Accepted: 09/24/2018] [Indexed: 11/28/2022] Open
Abstract
Motivation Data visualization is an important tool for exploring and communicating findings from genomic and healthcare datasets. Yet, without a systematic way of organizing and describing the design space of data visualizations, researchers may not be aware of the breadth of possible visualization design choices or how to distinguish between good and bad options. Results We have developed a method that systematically surveys data visualizations using the analysis of both text and images. Our method supports the construction of a visualization design space that is explorable along two axes: why the visualization was created and how it was constructed. We applied our method to a corpus of scientific research articles from infectious disease genomic epidemiology and derived a Genomic Epidemiology Visualization Typology (GEViT) that describes how visualizations were created from a series of chart types, combinations and enhancements. We have also implemented an online gallery that allows others to explore our resulting design space of visualizations. Our results have important implications for visualization design and for researchers intending to develop or use data visualization tools. Finally, the method that we introduce is extensible to constructing visualizations design spaces across other research areas. Availability and implementation Our browsable gallery is available at http://gevit.net and all project code can be found at https://github.com/amcrisan/gevitAnalysisRelease. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anamaria Crisan
- Department of Computer Science, University of British Columbia, Vancouver, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada.,British Columbia Centre for Disease Control, Vancouver, Canada
| | - Tamara Munzner
- Department of Computer Science, University of British Columbia, Vancouver, Canada
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22
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Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects. Sci Rep 2020; 10:7547. [PMID: 32372020 PMCID: PMC7200715 DOI: 10.1038/s41598-020-64570-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/16/2020] [Indexed: 12/19/2022] Open
Abstract
The animal gut microbiota evolves quickly towards a complex community and plays crucial roles in its host’s health and development. Factors such as host genetics and environmental changes are regarded as important for controlling the dynamics of animal gut microbiota. Migratory animals are an important group for studying how these factors influence gut microbiota because they experience strong environmental perturbations during migration. The commercially important grey mullet, Mugil cephalus, is a cosmopolitan species complex that display reproductive migration behaviour. There are three cryptic species of M. cephalus fish distributed across the Northwest Pacific, and their spawning sites overlap in the Taiwan Strait. This extraordinary natural occurrence makes the grey mullet an ideal model organism for exploring the nature of wild animal-gut microbiota relationships and interactions. This study investigates the diversity and structure of the gut microbial community in three cryptic M. cephalus species using 16S rRNA amplicon sequencing. Gut microbial compositions from adult and juvenile fish samples were analysed. Our results indicate that gut microbial communities within the grey mullet share a core microbiome dominated by Proteobacteria, Firmicutes and Actinobacteria. However, the structures of gut microbial communities were more distinct between adult mullet groups than they were between juvenile ones. Intriguingly, we found that adult fish that migrate to different geographical tracts harbour gut microbiota similar to historical records of seawater microflora, along their respective migration routes. This observation provides new insights into the interaction between aquatic animal gut microbial communities and the environments along their hosts’ migratory routes, and thus warrants future study.
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23
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Mason VC, Helgen KM, Murphy WJ. Comparative Phylogeography of Forest-Dependent Mammals Reveals Paleo-Forest Corridors throughout Sundaland. J Hered 2020; 110:158-172. [PMID: 30247638 DOI: 10.1093/jhered/esy046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life-history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors and their influence on observed biogeographic patterns. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins, but not in greater mouse deer. This deep east-west split within Borneo has not been commonly described in mammals. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos, and suggests that forests present during the middle Pliocene within the Sunda Shelf were more evergreen and contiguous, while forests were more fragmented, transient, seasonal, or with lower density canopies in the Pleistocene.
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Affiliation(s)
- Victor C Mason
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX.,Victor C. Mason is now at Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, Länggassstrasse, Bern, Switzerland
| | - Kristofer M Helgen
- School of Biological Sciences, Environment Institute, and Centre for Applied Conservation Science, University of Adelaide, Adelaide, SA, Australia
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
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24
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Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems. Sci Rep 2020; 10:6012. [PMID: 32265458 PMCID: PMC7138807 DOI: 10.1038/s41598-020-62919-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 03/09/2020] [Indexed: 11/25/2022] Open
Abstract
Unraveling the key drivers of bacterial community assembly in agricultural soils is pivotal for soil nutrient management and crop productivity. Presently, the drivers of microbial community structure remain unexplored in maize cropping systems under complex and variable environmental scenarios across large spatial scales. In this study, we conducted high-throughput 16S rRNA gene sequencing and network analysis to identify the major environmental factors driving bacterial community diversity and co-occurrence patterns in 21 maize field soils across China. The results show that mean annual precipitation and soil pH are the major environmental factors that shape soil bacterial communities in maize soils. The similarities of bacterial communities significantly decreased with increasing geographic distance between different sites. The differences in spatial turnover rates across bacterial phyla indicate the distinct dispersal capabilities of bacterial groups, and some abundant phyla exhibited high dispersal capabilities. Aeromicrobium, Friedmanniella, Saccharothrix, Lamia, Rhodococcus, Skermanella, and Pedobacter were identified as keystone taxa. Based on the node-level and network-level topological features, members of the core microbiome were more frequently found in the center of the ecosystem network compared with other taxa. This study highlights the major environmental factors driving bacterial community assembly in agro-ecosystems and the central ecological role of the core microbiome in maintaining the web of complex bacterial interactions.
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25
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Vujić A, Šašić Zorić L, Ačanski J, Likov L, Radenković S, Djan M, Milić D, Šebić A, Ranković M, Khaghaninia S. Hide-and-seek with hoverflies: Merodon aureus – a species, a complex or a subgroup? Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
In order to disentangle the currently confused interpretations and nomenclature of Merodon aureus and M. aeneus, we have reviewed all existing type material and species names known to us as assigned synonyms of these taxa. We resolve M. aeneus as being a junior synonym of M. aureus. We designate a lectotype for M. aureus and a neotype for M. aeneus. Additionally, we provide evidence that M. aureus, together with two newly discovered taxa (M. calidus sp. nov. and M. ortus sp. nov.), represent a complex of cryptic species named the M. aureus species complex. This complex, together with the M. unicolor species complex and the species M. pumilus, is part of the M. aureus subgroup. The M. unicolor species complex comprises two cryptic species: M. unicolor and M. albidus sp. nov. The new species are described by applying an integrative taxonomic approach using several data types (COI and 28S rRNA genes, geometric morphometry of the wings, ecological and distributional data). Based on the COI gene sequence analysis and distributional data, the pupa previously described as an immature stage of the species M. aureus is redefined as an immature stage of the new species M. calidus. Speciation within the M. aureus subgroup is discussed in the context of the phylogeographic history in the studied region.
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Affiliation(s)
- Ante Vujić
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Ljiljana Šašić Zorić
- University of Novi Sad, BioSense Institute, Dr Zorana Đinđića 1, 21000 Novi Sad, Serbia
| | - Jelena Ačanski
- University of Novi Sad, BioSense Institute, Dr Zorana Đinđića 1, 21000 Novi Sad, Serbia
| | - Laura Likov
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Snežana Radenković
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Mihajla Djan
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Dubravka Milić
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Anja Šebić
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Milica Ranković
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Samad Khaghaninia
- University of Tabriz, Faculty of Agriculture, Department of Plant Protection, Tabriz, Iran
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26
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Vujić A, Likov L, Radenković S, Tubić NK, Djan M, Šebić A, Pérez-Bañón C, Barkalov A, Hayat R, Rojo S, Andrić A, Ståhls G. Revision of the Merodon serrulatus group (Diptera, Syrphidae). Zookeys 2020; 909:79-158. [PMID: 32089636 PMCID: PMC7015954 DOI: 10.3897/zookeys.909.46838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/11/2019] [Indexed: 11/12/2022] Open
Abstract
The phytophagous hoverfly genus Merodon Meigen, 1803 (Diptera, Syrphidae), which comprises more than 160 species distributed in Palaearctic and Afrotropical regions, can be differentiated into multiple groups of species that harbor high levels of hidden diversity. In this work, the serrulatus species group of Merodon is revised, providing an illustrated key to species, a detailed discussion on the taxonomic characters and a morphological diagnosis, including also the first data about the preimaginal morphology of this species group. The study includes characteristics of the 13 species of the M. serrulatus group, along with the available distributional data. Moreover, descriptions are provided for seven new species, namely M. defectus Vujić, Likov & Radenković sp. nov., M. disjunctus Vujić, Likov & Radenković sp. nov., M. medium Vujić, Likov & Radenković sp. nov., M. nigrocapillatus Vujić, Likov & Radenković sp. nov., M. nigropunctum Vujić, Likov & Radenković sp. nov., M. opacus Vujić, Likov & Radenković sp. nov., and M. trianguloculus Vujić, Likov & Radenković sp. nov. In addition, the taxa M. serrulatus (Wiedemann in Meigen, 1822), M. bequaerti Hurkmans, 1993, M. hirsutus Sack, 1913, M. kawamurae Matsumura, 1916, M. sacki (Paramonov, 1936) and M. sophron Hurkmans, 1993 are redefined and redescribed. Following a detailed study of the type material sourced from different entomological collections, the status of all available taxa related to M. serrulatus is revised and a new synonymy is proposed: M. tener Sack, 1913 syn. nov. (junior synonym of M. serrulatus). The identity of M. trizonus (Szilády, 1940) could not be assessed as the type specimens are lost. Thus, the name M. trizonus is considered as nomen dubium. The monophyly and composition of this species group are assessed through Maximum Parsimony and Maximum Likelihood analyses of the mitochondrial COI and nuclear 28S rRNA gene sequences.
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Affiliation(s)
- Ante Vujić
- University of Novi Sad, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad, Serbia
| | - Laura Likov
- University of Novi Sad, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad, Serbia
| | - Snežana Radenković
- University of Novi Sad, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad, Serbia
| | - Nataša Kočiš Tubić
- University of Novi Sad, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad, Serbia
| | - Mihajla Djan
- University of Novi Sad, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad, Serbia
| | - Anja Šebić
- University of Novi Sad, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad, Serbia
| | - Celeste Pérez-Bañón
- Department of Environmental Sciences and Natural Resources, Faculty of Sciences III, Campus of San Vicente, University of Alicante, Spain
| | - Anatolij Barkalov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Rüstem Hayat
- Department of Plant Protection, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Santos Rojo
- Department of Environmental Sciences and Natural Resources, Faculty of Sciences III, Campus of San Vicente, University of Alicante, Spain
| | - Andrijana Andrić
- University of Novi Sad, BioSense Institute, Dr Zorana Đinđića 1, Novi Sad, Serbia
| | - Gunilla Ståhls
- Zoology Unit, Finnish Museum of Natural History Luomus, University of Helsinki, Finland
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27
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Vujić A, Radenković S, Likov L, Andrić A, Janković M, Ačanski J, Popov G, de Courcy Williams M, Šašić Zorić L, Djan M. Conflict and congruence between morphological and molecular data: revision of the Merodon constans group (Diptera : Syrphidae). INVERTEBR SYST 2020. [DOI: 10.1071/is19047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We revise the Merodon constans species group of the genus Merodon Meigen, 1803 (Diptera: Syrphidae), provide morphological diagnosesand descriptions, as well as an illustrated key and a discussion on the different taxonomic characters used. In total, 15 species were studied, their geographic distributions are presented on maps, and nine new species are described. Two species are redefined and neotypes are designated, lectotypes are designated for five species, and onespeciesis reinstated as valid. Following a detailed study of type material in different entomological collections, the status of several species is revised and three new synonymies are proposed. The M. constans species group was resolved as being monophyletic within the M. albifrons lineage based on molecular analyses using COI and 28S rRNA gene sequences. Three species morphologically similar to M. constans (Rossi, 1794) but occurring outside its distributional rangewere supported as being valid and distinct species on the basis of molecular data, but they were not distinguishable based on morphological characters. By contrast, continental populations of M. analis Meigen, 1822 could not be separated from Mediterranean M. constans based on differences in COI or 28S rRNA genes. The same molecular markers could not discriminate between two other species pairs. We conclude that these molecular markers only partially resolve species within the M. constans group. Geometric morphometry of wing shape successfully separated M. analis and M. constans, as well as M. spineus Vujić, Šašić Zorić & Likov, sp. nov. in both species and population analyses.
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28
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Morales-Rodriguez C, Sferrazza I, Aleandri M, Dalla Valle M, Mazzetto T, Speranza S, Contarini M, Vannini A. Fungal community associated with adults of the chestnut gall wasp Dryocosmus kuriphilus after emergence from galls: Taxonomy and functional ecology. Fungal Biol 2019; 123:905-912. [PMID: 31733733 DOI: 10.1016/j.funbio.2019.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/18/2019] [Accepted: 09/24/2019] [Indexed: 01/16/2023]
Abstract
The diversity of the fungal community associated with adults of Dryocosmus kuriphilus following emergence was examined using HTS analysis. Ascomycota dominated the fungal core-biome community. The functional guilds of the 90 taxa forming the core-biome were assessed, demonstrating three main groups: saprotrophs, plant pathogens and entomopathogens. Twenty-nine OTUs out of 90 were resolved to species level identifying 26 different fungal species. Among these species, many were cosmopolitan or previously recorded in Europe. Ten taxa were previously recorded on chestnut, including some recognized plant pathogens associated with foliage and green tissues such as Epicoccum nigrum, Gnomoniopsis castanea, Colletotrichum acutatum, Stromatoseptoria castaneicola, Ramularia endophylla. Beauveria bassiana; within the core microbiome, Fusarium larvarum represented the most abundant entomopathogenic species. Some of these species are known to impact directly or indirectly the vitality of the insects in the galls. The chestnut blight pathogen, Cryphonectria parasitica, was never found associated with D. kuriphilus. Based on the present study, an active role for D. kuriphilus as a vector of chestnut fungal endophyte/pathogens cannot be demonstrated but neither ruled out.
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Affiliation(s)
- Carmen Morales-Rodriguez
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Ivano Sferrazza
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - MariaPia Aleandri
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Matteo Dalla Valle
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Tommaso Mazzetto
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Stefano Speranza
- Department of Agriculture and Forest Science (DAFNE) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Mario Contarini
- Department of Agriculture and Forest Science (DAFNE) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Andrea Vannini
- Department for Innovation in Biological, Agro-food and Forestry Systems (DIBAF) - University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy.
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29
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Stapleton PJ, Eshaghi A, Seo CY, Wilson S, Harris T, Deeks SL, Bolotin S, Goneau LW, Gubbay JB, Patel SN. Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada. Sci Rep 2019; 9:12615. [PMID: 31471545 PMCID: PMC6717193 DOI: 10.1038/s41598-019-47740-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/18/2019] [Indexed: 01/30/2023] Open
Abstract
In 2017 Ontario experienced the largest mumps outbreak in the province in 8 years, at a time when multiple outbreaks were occurring across North America. Of 259 reported cases, 143 occurred in Toronto, primarily among young adults. Routine genotyping of the small hydrophobic gene indicated that the outbreak was due to mumps virus genotype G. We performed a retrospective study of whole genome sequencing of 26 mumps virus isolates from early in the outbreak, using a tiling amplicon method. Results indicated that two of the cases were genetically divergent, with the remaining 24 cases belonging to two major clades and one minor clade. Phylogeographic analysis confirmed circulation of virus from each clade between Toronto and other regions in Ontario. Comparison with other genotype G strains from North America suggested that the presence of co-circulating major clades may have been due to separate importation events from outbreaks in the United States. A transmission network analysis performed with the software program TransPhylo was compared with previously collected epidemiological data. The transmission tree correlated with known epidemiological links between nine patients and identified new potential clusters with no known epidemiological links.
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Affiliation(s)
- P J Stapleton
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, ON, Canada
| | - A Eshaghi
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, ON, Canada
| | - C Y Seo
- Communicable Diseases, Emergency Preparedness and Response, Public Health Ontario, Toronto, ON, Canada
| | - S Wilson
- Communicable Diseases, Emergency Preparedness and Response, Public Health Ontario, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T Harris
- Communicable Diseases, Emergency Preparedness and Response, Public Health Ontario, Toronto, ON, Canada
| | - S L Deeks
- Communicable Diseases, Emergency Preparedness and Response, Public Health Ontario, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - S Bolotin
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Applied Immunisation Research and Evaluation, Public Health Ontario, Toronto, ON, Canada
| | - L W Goneau
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, ON, Canada
| | - J B Gubbay
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, ON, Canada
| | - S N Patel
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, ON, Canada.
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30
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Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species. G3-GENES GENOMES GENETICS 2019; 9:2325-2336. [PMID: 31097479 PMCID: PMC6643897 DOI: 10.1534/g3.119.400220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other perennials, except for G. tomentella, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Most genic sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced a very similar evolution as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.
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31
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Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol 2019; 79:96-115. [PMID: 30621881 PMCID: PMC6492263 DOI: 10.1016/j.fm.2018.11.005] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 01/06/2023]
Abstract
Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.
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Affiliation(s)
- Balamurugan Jagadeesan
- Nestlé Research, Nestec Ltd, Route du Jorat 57, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland.
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, MS-CO-3, 1600 Clifton Road, 30329-4027, Atlanta, USA
| | - Marc W Allard
- US Food and Drug Administration, 5001 Campus Drive, College Park, MD, 02740, USA
| | - Sébastien Leuillet
- Institut Mérieux, Mérieux NutriSciences, 3 route de la Chatterie, 44800, Saint Herblain, France
| | - Anett Winkler
- Cargill Deutschland GmbH, Cerestarstr. 2, 47809, Krefeld, Germany
| | - Yinghua Xiao
- Arla Innovation Center, Agro Food Park 19, 8200, Aarhus, Denmark
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France
| | - Jos Van Der Vossen
- The Netherlands Organisation for Applied Scientific Research, TNO, Utrechtseweg 48, 3704 HE, Zeist, NL, the Netherlands
| | - Silin Tang
- Mars Global Food Safety Center, Yanqi Economic Development Zone, 101407, Beijing, China
| | - Mitsuru Katase
- Fuji Oil Co., Ltd., Sumiyoshi-cho 1, Izumisano Osaka, 598-8540, Japan
| | - Peter McClure
- Mondelēz International, Linden 3, Bournville Lane, B30 2LU, Birmingham, United Kingdom
| | - Bon Kimura
- Tokyo University of Marine Science & Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Lay Ching Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - John Chapman
- Unilever Research & Development, Postbus, 114, 3130 AC, Vlaardingen, the Netherlands
| | - Kathie Grant
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom.
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Li F, van Kleunen M, Li J, Liu X, Gao K, Zhu J, Zhao X, Zhao C, Li J. Patterns of genetic variation reflect multiple introductions and pre-admixture sources of common ragweed (Ambrosia artemisiifolia) in China. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01966-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Mycobacterium ulcerans Population Genomics To Inform on the Spread of Buruli Ulcer across Central Africa. mSphere 2019; 4:4/1/e00472-18. [PMID: 30728280 PMCID: PMC6365612 DOI: 10.1128/msphere.00472-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue caused by infection with the pathogen Mycobacterium ulcerans Many critical issues for disease control, such as understanding the mode of transmission and identifying source reservoirs of M. ulcerans, are still largely unknown. Here, we used genomics to reconstruct in detail the evolutionary trajectory and dynamics of M. ulcerans populations at a central African scale and at smaller geographical village scales. Whole-genome sequencing (WGS) data were analyzed from 179 M. ulcerans strains isolated from all Buruli ulcer foci in the Democratic Republic of the Congo, The Republic of Congo, and Angola that have ever yielded positive M. ulcerans cultures. We used both temporal associations and the study of the mycobacterial demographic history to estimate the contribution of humans as a reservoir in Buruli ulcer transmission. Our phylogeographic analysis revealed one almost exclusively predominant sublineage of M. ulcerans that arose in Central Africa and proliferated in its different regions of endemicity during the Age of Discovery. We observed how the best sampled endemic hot spot, the Songololo territory, became an area of endemicity while the region was being colonized by Belgium (1880s). We furthermore identified temporal parallels between the observed past population fluxes of M. ulcerans from the Songololo territory and the timing of health policy changes toward control of the Buruli ulcer epidemic in that region. These findings suggest that an intervention based on detecting and treating human cases in an area of endemicity might be sufficient to break disease transmission chains, irrespective of other reservoirs of the bacterium.IMPORTANCE Buruli ulcer is a destructive skin and soft tissue infection caused by Mycobacterium ulcerans The disease is characterized by progressive skin ulceration, which can lead to permanent disfigurement and long-term disability. Currently, the major hurdles facing disease control are incomplete understandings of both the mode of transmission and environmental reservoirs of M. ulcerans As decades of spasmodic environmental sampling surveys have not brought us much closer to overcoming these hurdles, the Buruli ulcer research community has recently switched to using comparative genomics. The significance of our research is in how we used both temporal associations and the study of the mycobacterial demographic history to estimate the contribution of humans as a reservoir in Buruli ulcer transmission. Our approach shows that it might be possible to use bacterial population genomics to assess the impact of health interventions, providing valuable feedback for managers of disease control programs in areas where health surveillance infrastructure is poor.
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Kočiš Tubić N, Ståhls G, Ačanski J, Djan M, Obreht Vidaković D, Hayat R, Khaghaninia S, Vujić A, Radenković S. An integrative approach in the assessment of species delimitation and structure of the Merodon nanus species group (Diptera: Syrphidae). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0381-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Ecomorphology of a generalist freshwater gastropod: complex relations of shell morphology, habitat, and fecundity. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0377-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Pie MR, Faircloth BC, Ribeiro LF, Bornschein MR, Mccormack JE. Phylogenomics of montane frogs of the Brazilian Atlantic Forest is consistent with isolation in sky islands followed by climatic stability. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Mater Natura – Instituto de Estudos Ambientais, Curitiba, Paraná, Brazil
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Luiz F Ribeiro
- Mater Natura – Instituto de Estudos Ambientais, Curitiba, Paraná, Brazil
- Escola de Ciências da Vida, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Marcos R Bornschein
- Mater Natura – Instituto de Estudos Ambientais, Curitiba, Paraná, Brazil
- Instituto de Biociências, Universidade Estadual Paulista, São Vicente, São Paulo, Brazil
| | - John E Mccormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA
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Geospatial Analysis and the Internet of Things. ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION 2018. [DOI: 10.3390/ijgi7070269] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Vujić A, Radenković S, Likov L. Revision of the Palaearctic species of the Merodon desuturinus group (Diptera, Syrphidae). Zookeys 2018:105-138. [PMID: 30008578 PMCID: PMC6043631 DOI: 10.3897/zookeys.771.20481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 05/14/2018] [Indexed: 11/15/2022] Open
Abstract
This revision of material belonging to the Merodondesuturinus group from the Palaearctic Region resulted in the delimitation of four species: Merodoncabanerensis Marcos-García, Vujić & Mengual, 2007; Merodondesuturinus Vujić, Šimić & Radenković, 1995; Merodonneolydicus Vujić, nom. n.; and Merodonmurorum Fabricius, 1794. Merodonmurorum is redescribed. A neotype for Merodonauripilus Meigen, 1830 is designated, which is a new junior synonym of Merodonmurorum. The related Afrotropical species Merodoncuthbertsoni Curran, 1939 is re-evaluated and compared to its sibling Palaearctic taxon Merodondesuturinus. An identification key for the Merodondesuturinus group is provided.
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Affiliation(s)
- Ante Vujić
- Department of Biology and Ecology, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Snežana Radenković
- Department of Biology and Ecology, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Laura Likov
- Department of Biology and Ecology, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
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Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG. PMERGE: Computational filtering of paralogous sequences from RAD-seq data. Ecol Evol 2018; 8:7002-7013. [PMID: 30073062 PMCID: PMC6065343 DOI: 10.1002/ece3.4219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/01/2023] Open
Abstract
Restriction-site associated DNA sequencing (RAD-seq) can identify and score thousands of genetic markers from a group of samples for population-genetics studies. One challenge of de novo RAD-seq analysis is to distinguish paralogous sequence variants (PSVs) from true single-nucleotide polymorphisms (SNPs) associated with orthologous loci. In the absence of a reference genome, it is difficult to differentiate true SNPs from PSVs, and their impact on downstream analysis remains unclear. Here, we introduce a network-based approach, PMERGE that connects fragments based on their DNA sequence similarity to identify probable PSVs. Applying our method to de novo RAD-seq data from 150 Atlantic salmon (Salmo salar) samples collected from 15 locations across the Southern Newfoundland coast allowed the identification of 87% of total PSVs identified through alignment to the Atlantic salmon genome. Removal of these paralogs altered the inferred population structure, highlighting the potential impact of filtering in RAD-seq analysis. PMERGE is also applied to a green crab (Carcinus maenas) data set consisting of 242 samples from 11 different locations and was successfully able to identify and remove the majority of paralogous loci (62%). The PMERGE software can be run as part of the widely used Stacks analysis package.
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Affiliation(s)
| | - Paul Bentzen
- Marine Gene Probe LaboratoryDepartment of BiologyDalhousie UniversityHalifaxNSCanada
| | - Ian R. Bradbury
- Salmonids SectionScience BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
| | - Robert G. Beiko
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
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Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D, Kilian A, Kamphuis LG, Singh KB, Berger JD, Hane JK, Edwards D, Erskine W, Nelson MN. Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:887-901. [PMID: 29353413 PMCID: PMC5852200 DOI: 10.1007/s00122-017-3045-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE This first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East-West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables. Most grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Bhavna Hurgobin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | | | - Lars G. Kamphuis
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Jens D. Berger
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - James K. Hane
- CCDM Bioinformatics, Centre for Crop Disease Management, Curtin University, Bentley, WA 6102 Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Matthew N. Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
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Carriço JA, Rossi M, Moran-Gilad J, Van Domselaar G, Ramirez M. A primer on microbial bioinformatics for nonbioinformaticians. Clin Microbiol Infect 2018; 24:342-349. [PMID: 29309933 DOI: 10.1016/j.cmi.2017.12.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/13/2017] [Accepted: 12/22/2017] [Indexed: 01/19/2023]
Abstract
BACKGROUND Presently, the bottleneck in the deployment of high-throughput sequencing technology is the ability to analyse the increasing amount of data produced in a fit-for-purpose manner. The field of microbial bioinformatics is thriving and quickly adapting to technological changes, which creates difficulties for nonbioinformaticians in following the complexity and increasingly obscure jargon of this field. AIMS This review is directed towards nonbioinformaticians who wish to gain understanding of the overall microbial bioinformatic processes, from raw data obtained from sequencers to final outputs. SOURCES The software and analytical strategies reviewed are based on the personal experience of the authors. CONTENT The bioinformatic processes of transforming raw reads to actionable information in a clinical and epidemiologic context is explained. We review the advantages and limitations of two major strategies currently applied: read mapping, which is the comparison with a predefined reference genome, and de novo assembly, which is the unguided assembly of the raw data. Finally, we discuss the main analytical methodologies and the most frequently used freely available software and its application in the context of bacterial infectious disease management. IMPLICATIONS High-throughput sequencing technologies are overhauling outbreak investigation and epidemiologic surveillance while creating new challenges due to the amount and complexity of data generated. The continuously evolving field of microbial bioinformatics is required for stakeholders to fully harness the power of these new technologies.
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Affiliation(s)
- J A Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
| | - M Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - J Moran-Gilad
- Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Public Health Services, Ministry of Health, Jerusalem, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - G Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB, R3E 3R2, Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - M Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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Sathkumara HD, Merritt AJ, Corea EM, Krishnananthasivam S, Natesan M, Inglis TJJ, De Silva AD. Clinical, Bacteriologic, and Geographic Stratification of Melioidosis Emerges from the Sri Lankan National Surveillance Program. Am J Trop Med Hyg 2018; 98:607-615. [PMID: 29313474 PMCID: PMC5929190 DOI: 10.4269/ajtmh.17-0441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Melioidosis, a potentially fatal tropical infection, is said to be underdiagnosed in low-income countries. An increase in melioidosis cases in Sri Lanka allowed us to analyze the relationship among clinical outcome, bacteriology, epidemiology, and geography in the first 108 laboratory-confirmed cases of melioidosis from a nationwide surveillance program. The additional 76 cases of laboratory-confirmed melioidosis confirmed further associations between Burkholderia pseudomallei multilocus sequence typing (MLST) and infection phenotype; ST1137/unifocal bacteremic infection (χ2 = 3.86, P < 0.05), ST1136/multifocal infection without bacteremia (χ2 = 15.8, P < 0.001), and ST1132/unifocal nonbacteremic infection (χ2 = 6.34, P = 0.02). ST1137 infections were predominantly seen in the Western Province, whereas ST1132, 1135, and 1136 infections predominated in the Northwestern Province. Early participating centers in the surveillance program had a lower melioidosis-associated mortality than later participants (χ2 = 3.99, P < 0.05). The based upon related sequence types (eBURST) algorithm, a MLST clustering method that infers founding genotypes and patterns of descent for related isolates and clonal complexes in an unrooted tree, showed uneven distribution of sequence types (STs). There was spatial clustering of the commonest STs (ST1132, 1136, and 1137) in the Western, Northwestern, and Central provinces. The recent increase in melioidosis in Sri Lanka uncovered by laboratory-enhanced surveillance is likely to be the result of a combination of improved laboratory detection, increased clinician awareness, recruitment of clinical centers, and small outbreaks. Further development of the surveillance program into a national genotyping-supported melioidosis registry will improve melioidosis diagnosis, treatment, and prevention where underdiagnosis and mortality rates remain high.
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Affiliation(s)
| | - Adam J Merritt
- Faculty of Health Sciences and Medicine, Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,PathWest Laboratory Medicine, QE2 Medical Centre, Nedlands, Western Australia, Australia
| | - Enoka M Corea
- Department of Microbiology, University of Colombo, Colombo, Sri Lanka
| | | | - Mohan Natesan
- Division of Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Timothy J J Inglis
- PathWest Laboratory Medicine, QE2 Medical Centre, Nedlands, Western Australia, Australia.,Faculty of Health Sciences and Medicine, School of Medicine, University of Western Australia, Perth, Western Australia, Australia.,Faculty of Health Sciences and Medicine, Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Aruna Dharshan De Silva
- Division of Vaccine Discovery, La Jolla Institute of Allergy and Immunology, La Jolla, California.,Department of Paraclinical Sciences, Faculty of Medicine, Kotelawala Defense University, Ratmalana, Sri Lanka.,Genetech Research Institute, Colombo, Sri Lanka
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Genetic Variation in Quercus acutissima Carruth., in Traditional Japanese Rural Forests and Agricultural Landscapes, Revealed by Chloroplast Microsatellite Markers. FORESTS 2017. [DOI: 10.3390/f8110451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ismail NA, Adilah-Amrannudin N, Hamsidi M, Ismail R, Dom NC, Ahmad AH, Mastuki MF, Camalxaman SN. The Genetic Diversity, Haplotype Analysis, and Phylogenetic Relationship of Aedes albopictus (Diptera: Culicidae) Based on the Cytochrome Oxidase 1 Marker: A Malaysian Scenario. JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:1573-1581. [PMID: 28981849 DOI: 10.1093/jme/tjx126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Indexed: 05/23/2023]
Abstract
The global expansion of Ae. albopictus from its native range in Southeast Asia has been implicated in the recent emergence of dengue endemicity in Malaysia. Genetic variability studies of Ae. albopictus are currently lacking in the Malaysian setting, yet are crucial to enhancing the existing vector control strategies. The study was conducted to establish the genetic variability of maternally inherited mitochondrial DNA encoding for cytochrome oxidase subunit 1 (CO1) gene in Ae. albopictus. Twelve localities were selected in the Subang Jaya district based on temporal indices utilizing 120 mosquito samples. Genetic polymorphism and phylogenetic analysis were conducted to unveil the genetic variability and geographic origins of Ae. albopictus. The haplotype network was mapped to determine the genealogical relationship of sequences among groups of population in the Asian region. Comparison of Malaysian CO1 sequences with sequences derived from five Asian countries revealed genetically distinct Ae. albopictus populations. Phylogenetic analysis revealed that all sequences from other Asian countries descended from the same genetic lineage as the Malaysian sequences. Noteworthy, our study highlights the discovery of 20 novel haplotypes within the Malaysian population which to date had not been reported. These findings could help determine the genetic variation of this invasive species, which in turn could possibly improve the current dengue vector surveillance strategies, locally and regionally.
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Affiliation(s)
- Nurul-Ain Ismail
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
| | - Nurul Adilah-Amrannudin
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
| | - Mayamin Hamsidi
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
| | - Rodziah Ismail
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
| | - Nazri Che Dom
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
| | - Abu Hassan Ahmad
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
| | - Mohd Fahmi Mastuki
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
| | - Siti Nazrina Camalxaman
- Faculty of Health Sciences, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia
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Gao Y, Yin S, Wu L, Dai D, Wang H, Liu C, Tang L. Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq. Sci Rep 2017; 7:14183. [PMID: 29079830 PMCID: PMC5660214 DOI: 10.1038/s41598-017-14738-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/13/2017] [Indexed: 11/08/2022] Open
Abstract
Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, 655011, China
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Lifang Wu
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Dongqin Dai
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, 655011, China
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Haibo Wang
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, 655011, China
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Chao Liu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, 655011, China
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Lizhou Tang
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, 655011, China.
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China.
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A Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks. Appl Environ Microbiol 2017; 83:AEM.01482-17. [PMID: 28821546 DOI: 10.1128/aem.01482-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/11/2017] [Indexed: 01/12/2023] Open
Abstract
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure, with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based on L. pneumophila core genome single nucleotide polymorphism (SNP) comparisons eliminates ambiguity for defining outbreak clusters and accurately predicts exposure sources for clinical cases. We illustrate the performance of our method by genome comparisons of 234 L. pneumophila isolates obtained from patients and cooling towers in Melbourne, Australia, between 1994 and 2014. This collection included one of the largest reported Legionnaires' disease outbreaks, which involved 125 cases at an aquarium. Using only sequence data from L. pneumophila cooling tower isolates and including all core genome variation, we built a multivariate model using discriminant analysis of principal components (DAPC) to find cooling tower-specific genomic signatures and then used it to predict the origin of clinical isolates. Model assignments were 93% congruent with epidemiological data, including the aquarium Legionnaires' disease outbreak and three other unrelated outbreak investigations. We applied the same approach to a recently described investigation of Legionnaires' disease within a UK hospital and observed a model predictive ability of 86%. We have developed a promising means to breach L. pneumophila genetic diversity extremes and provide objective source attribution data for outbreak investigations.IMPORTANCE Microbial outbreak investigations are moving to a paradigm where whole-genome sequencing and phylogenetic trees are used to support epidemiological investigations. It is critical that outbreak source predictions are accurate, particularly for pathogens, like Legionella pneumophila, which can spread widely and rapidly via cooling system aerosols, causing Legionnaires' disease. Here, by studying hundreds of Legionella pneumophila genomes collected over 21 years around a major Australian city, we uncovered limitations with the phylogenetic approach that could lead to a misidentification of outbreak sources. We implement instead a statistical learning technique that eliminates the ambiguity of inferring disease transmission from phylogenies. Our approach takes geolocation information and core genome variation from environmental L. pneumophila isolates to build statistical models that predict with high confidence the environmental source of clinical L. pneumophila during disease outbreaks. We show the versatility of the technique by applying it to unrelated Legionnaires' disease outbreaks in Australia and the UK.
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Vujić A, Nedeljković Z, Hayat R, Demirözer O, Mengual X, Kazerani F. New data on the genusChrysotoxumMeigen (Diptera: Syrphidae) from North-East Turkey, Armenia, Azerbaijan and Iran including descriptions of three new species. ZOOLOGY IN THE MIDDLE EAST 2017. [DOI: 10.1080/09397140.2017.1349241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ante Vujić
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Zorica Nedeljković
- BioSense Institute-Research Institute for Information Technologies in Biosystems, Novi Sad, Serbia
| | | | - Ozan Demirözer
- Department of Plant Protection, Faculty of Agriculture, Süleyman Demirel University, Isparta, Turkey
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut für Biodiversität der Tiere, Bonn, Germany
| | - Farzaneh Kazerani
- Research Institute of Forests and Rangelands, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
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48
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Kaestli M, Skillington A, Kennedy K, Majid M, Williams D, McGuinness K, Munksgaard N, Gibb K. Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization. Front Microbiol 2017; 8:1313. [PMID: 28751882 PMCID: PMC5507994 DOI: 10.3389/fmicb.2017.01313] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 12/02/2022] Open
Abstract
Darwin Harbour in northern Australia is an estuary in the wet-dry tropics subject to increasing urbanization with localized water quality degradation due to increased nutrient loads from urban runoff and treated sewage effluent. Tropical estuaries are poorly studied compared to temperate systems and little is known about the microbial community-level response to nutrients. We aimed to examine the spatial and temporal patterns of the bacterial community and its association with abiotic factors. Since Darwin Harbour is macrotidal with strong seasonal patterns and mixing, we sought to determine if a human impact signal was discernible in the microbiota despite the strong hydrodynamic forces. Adopting a single impact–double reference design, we investigated the bacterial community using next-generation sequencing of the 16S rRNA gene from water and sediment from reference creeks and creeks affected by effluent and urban runoff. Samples were collected over two years during neap and spring tides, in the dry and wet seasons. Temporal drivers, namely seasons and tides had the strongest relationship to the water microbiota, reflecting the macrotidal nature of the estuary and its location in the wet-dry tropics. The neap-tide water microbiota provided the clearest spatial resolution while the sediment microbiota reflected current and past water conditions. Differences in patterns of the microbiota between different parts of the harbor reflected the harbor's complex hydrodynamics and bathymetry. Despite these variations, a microbial signature was discernible relating to specific effluent sources and urban runoff, and the composite of nutrient levels accounted for the major part of the explained variation in the microbiota followed by salinity. Our results confirm an overall good water quality but they also reflect the extent of some hypereutrophic areas. Our results show that the microbiota is a sensitive indicator to assess ecosystem health even in this dynamic and complex ecosystem.
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Affiliation(s)
- Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | - Anna Skillington
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | | | - Matthew Majid
- Aquatic Health Unit, Department of Environment and Natural Resources, Northern Territory GovernmentDarwin, NT, Australia
| | - David Williams
- Australian Institute of Marine ScienceDarwin, NT, Australia
| | - Keith McGuinness
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | - Niels Munksgaard
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
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49
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Qiu J, Zhou Y, Mao L, Ye C, Wang W, Zhang J, Yu Y, Fu F, Wang Y, Qian F, Qi T, Wu S, Sultana MH, Cao YN, Wang Y, Timko MP, Ge S, Fan L, Lu Y. Genomic variation associated with local adaptation of weedy rice during de-domestication. Nat Commun 2017; 8:15323. [PMID: 28537247 PMCID: PMC5477509 DOI: 10.1038/ncomms15323] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiu et al. re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.
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Affiliation(s)
- Jie Qiu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongjun Zhou
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Lingfeng Mao
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Ye
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weidi Wang
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianping Zhang
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yongyi Yu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Fu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunfei Wang
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Feijian Qian
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Ting Qi
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sanling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longjiang Fan
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongliang Lu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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50
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Taboada EN, Graham MR, Carriço JA, Van Domselaar G. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol 2017; 8:909. [PMID: 28588568 PMCID: PMC5440521 DOI: 10.3389/fmicb.2017.00909] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/04/2017] [Indexed: 11/24/2022] Open
Abstract
Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.
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Affiliation(s)
- Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Biological Sciences, University of Lethbridge, LethbridgeAB, Canada
| | - Morag R Graham
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
| | - João A Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
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