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Campbell LI, Nwezeobi J, van Brunschot SL, Kaweesi T, Seal SE, Swamy RAR, Namuddu A, Maslen GL, Mugerwa H, Armean IM, Haggerty L, Martin FJ, Malka O, Santos-Garcia D, Juravel K, Morin S, Stephens ME, Muhindira PV, Kersey PJ, Maruthi MN, Omongo CA, Navas-Castillo J, Fiallo-Olivé E, Mohammed IU, Wang HL, Onyeka J, Alicai T, Colvin J. Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors. BMC Genomics 2023; 24:408. [PMID: 37468834 DOI: 10.1186/s12864-023-09474-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The group of > 40 cryptic whitefly species called Bemisia tabaci sensu lato are amongst the world's worst agricultural pests and plant-virus vectors. Outbreaks of B. tabaci s.l. and the associated plant-virus diseases continue to contribute to global food insecurity and social instability, particularly in sub-Saharan Africa and Asia. Published B. tabaci s.l. genomes have limited use for studying African cassava B. tabaci SSA1 species, due to the high genetic divergences between them. Genomic annotations presented here were performed using the 'Ensembl gene annotation system', to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification. RESULTS We present here six new B. tabaci s.l. genomes from Africa and Asia, and two re-annotated previously published genomes, to provide evolutionary insights into these globally distributed pests. Genome sizes ranged between 616-658 Mb and exhibited some of the highest coverage of transposable elements reported within Arthropoda. Many fewer total protein coding genes (PCG) were recovered compared to the previously published B. tabaci s.l. genomes and structural annotations generated via the uniform methodology strongly supported a repertoire of between 12.8-13.2 × 103 PCG. An integrative systematics approach incorporating phylogenomic analysis of nuclear and mitochondrial markers supported a monophyletic Aleyrodidae and the basal positioning of B. tabaci Uganda-1 to the sub-Saharan group of species. Reciprocal cross-mating data and the co-cladogenesis pattern of the primary obligate endosymbiont 'Candidatus Portiera aleyrodidarum' from 11 Bemisia genomes further supported the phylogenetic reconstruction to show that African cassava B. tabaci populations consist of just three biological species. We include comparative analyses of gene families related to detoxification, sugar metabolism, vector competency and evaluate the presence and function of horizontally transferred genes, essential for understanding the evolution and unique biology of constituent B. tabaci. s.l species. CONCLUSIONS These genomic resources have provided new and critical insights into the genetics underlying B. tabaci s.l. biology. They also provide a rich foundation for post-genomic research, including the selection of candidate gene-targets for innovative whitefly and virus-control strategies.
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Affiliation(s)
- Lahcen I Campbell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Joachim Nwezeobi
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK.
| | - Sharon L van Brunschot
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- CSIRO Health and Biosecurity, Dutton Park, QLD, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Tadeo Kaweesi
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- Rwebitaba Zonal Agricultural Research and Development Institute, Fort Portal, Uganda
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
| | - Rekha A R Swamy
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
| | - Annet Namuddu
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- National Crops Resources Research Institute, Kampala, Uganda
| | - Gareth L Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Imperial College London, South Kensington, London, UK
| | - Habibu Mugerwa
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- Department of Entomology, University of Georgia, Griffin, GA, USA
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Osnat Malka
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos-Garcia
- CNRS, Laboratory of Biometry and Evolutionary Biology UMR 5558, University of Lyon, Villeurbanne, France
- Center for Biology and Management of Populations, INRAe UMR1062, Montferrier-sur-Lez, France
| | - Ksenia Juravel
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Paul Visendi Muhindira
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Royal Botanic Gardens, Kew, London, UK
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
| | | | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical Y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Málaga, Algarrobo-Costa, Spain
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical Y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Málaga, Algarrobo-Costa, Spain
| | | | - Hua-Ling Wang
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Joseph Onyeka
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
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Boykin LM, Sseruwagi P, Alicai T, Ateka E, Mohammed IU, Stanton JAL, Kayuki C, Mark D, Fute T, Erasto J, Bachwenkizi H, Muga B, Mumo N, Mwangi J, Abidrabo P, Okao-Okuja G, Omuut G, Akol J, Apio HB, Osingada F, Kehoe MA, Eccles D, Savill A, Lamb S, Kinene T, Rawle CB, Muralidhar A, Mayall K, Tairo F, Ndunguru J. Tree Lab: Portable genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa. Genes (Basel) 2019; 10:genes10090632. [PMID: 31438604 PMCID: PMC6769854 DOI: 10.3390/genes10090632] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 02/01/2023] Open
Abstract
In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall-degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This closed system delivers purified DNA with no cross-contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into nucleotide base called data locally in real-time, removing the need for high-specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and setup. To evaluate and validate capability of the system for unbiased pathogen identification by real-time sequencing in a farmer’s field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or destroy cassava crops. Eight hundred (800) million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint to its production. Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus-resistant or replacement planting. This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, Internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis, including sample collection, processing and provisional sequencing results was complete in under 3 h. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.
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Affiliation(s)
- Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia.
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Elijah Ateka
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Ibrahim Umar Mohammed
- Department of Crop Science, Faculty of Agriculture, Kebbi State University of Science and Technology, Aliero P.O. Box 1144, Nigeria
| | - Jo-Ann L Stanton
- Department of Anatomy, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Charles Kayuki
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Deogratius Mark
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Tarcisius Fute
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Joel Erasto
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Hilda Bachwenkizi
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Brenda Muga
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Naomi Mumo
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Jenniffer Mwangi
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Phillip Abidrabo
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Geoffrey Okao-Okuja
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Geresemu Omuut
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Jacinta Akol
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Hellen B Apio
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Francis Osingada
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Monica A Kehoe
- Department of Primary Industries and Regional Development Diagnostic Laboratory Services, Plant Pathology, South Perth, WA 6151, Australia
| | - David Eccles
- Malaghan Institute of Medical Research, P.O. Box 7060, Newtown, Wellington 6242, New Zealand
| | - Anders Savill
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Stephen Lamb
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Tonny Kinene
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Christopher B Rawle
- Department of Anatomy, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | | | - Kirsty Mayall
- MicroGEM Ltd., 9 Melody Ln, Ruakura, Hamilton 3216, New Zealand
| | - Fred Tairo
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
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Mohammed IU, Deeni Y, Hapca SM, McLaughlin K, Spiers AJ. Predicting the minimum liquid surface tension activity of pseudomonads expressing biosurfactants. Lett Appl Microbiol 2014; 60:37-43. [PMID: 25256441 DOI: 10.1111/lam.12331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/12/2014] [Accepted: 09/19/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Bacteria produce a variety of biosurfactants capable of significantly reducing liquid (aqueous) surface tension (γ) with a range of biological roles and biotechnological uses. To determine the lowest achievable surface tension (γMin ), we tested a diverse collection of Pseudomonas-like isolates from contaminated soil and activated sludge and identified those expressing biosurfactants by drop-collapse assay. Liquid surface tension-reducing ability was quantitatively determined by tensiometry, with 57 isolates found to significantly lower culture supernatant surface tensions to 24·5-49·1 mN m(-1) . Differences in biosurfactant behaviour determined by foaming, emulsion and oil-displacement assays were also observed amongst isolates producing surface tensions of 25-27 mN m(-1) , suggesting that a range of structurally diverse biosurfactants were being expressed. Individual distribution identification (IDI) analysis was used to identify the theoretical probability distribution that best fitted the surface tension data, which predicted a γMin of 24·24 mN m(-1) . This was in agreement with predictions based on earlier work of published mixed bacterial spp. data, suggesting a fundamental limit to the ability of bacterial biosurfactants to reduce surface tensions in aqueous systems. This implies a biological restriction on the synthesis and export of these agents or a physical-chemical restriction on their functioning once produced. SIGNIFICANCE AND IMPACT OF THE STUDY Numerous surveys of biosurfactant-producing bacteria have been conducted, but only recently has an attempt been made to predict the minimum liquid surface tension these surface-active agents can achieve. Here, we determine a theoretical minimum of 24 mN m(-1) by statistical analysis of tensiometry data, suggesting a fundamental limit for biosurfactant activity in bacterial cultures incubated under standard growth conditions. This raises a challenge to our understanding of biosurfactant expression, secretion and function, as well as being of interest to biotechnology where they are used in an increasingly wide range of applications.
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Affiliation(s)
- I U Mohammed
- SIMBIOS Centre & School of Science, Engineering and Technology, Abertay University, Dundee, UK
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Abarshi MM, Mohammed IU, Jeremiah SC, Legg JP, Kumar PL, Hillocks RJ, Maruthi MN. Multiplex RT-PCR assays for the simultaneous detection of both RNA and DNA viruses infecting cassava and the common occurrence of mixed infections by two cassava brown streak viruses in East Africa. J Virol Methods 2011; 179:176-84. [PMID: 22080852 DOI: 10.1016/j.jviromet.2011.10.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 10/20/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022]
Abstract
Uniplex and multiplex reverse transcription-polymerase chain reaction (RT-PCR) protocols were developed for the detection of cassava brown streak viruses (CBSVs) in single and mixed infections with cassava mosaic begomoviruses (CMBs) in a tropical crop plant, cassava (Manihot esculenta). CMBs contain ssDNA as their genome (genus Begomovirus, family Geminiviridae) while CBSVs are made up of positive sense ssRNA (genus Ipomovirus, family Potyviridae), and they cause the economically important cassava mosaic and cassava brown streak diseases, respectively, in sub-Saharan Africa. Diagnostic methodologies have long been available for CMBs but they are limited for CBSVs especially in mixed infections. In this study, the two CBSVs, Cassava brown streak virus (CBSV) and Cassava brown streak Uganda virus (CBSUV) occurring singly or in mixed infection with CMBs, African cassava mosaic virus and East African cassava mosaic virus were detected in a single RT-PCR using both previously described and newly designed virus-specific primers. These protocols were highly efficient for detecting CBSVs compared to the existing methods and have great potential to minimize sample handling and contamination. As well as improving the diagnosis of cassava viruses, the development of multiplex RT-PCR protocols have revealed the common occurrence of mixed infections by CBSV and CBSUV in cassava fields of Tanzania and Kenya, which was contrary to the common belief until recently that these two viruses have existed separately. These protocols have implications for diagnosis and epidemiological studies on cassava virus diseases in Eastern Africa.
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Affiliation(s)
- M M Abarshi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, United Kingdom
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Abarshi MM, Mohammed IU, Wasswa P, Hillocks RJ, Holt J, Legg JP, Seal SE, Maruthi MN. Optimization of diagnostic RT-PCR protocols and sampling procedures for the reliable and cost-effective detection of Cassava brown streak virus. J Virol Methods 2009; 163:353-9. [PMID: 19879299 DOI: 10.1016/j.jviromet.2009.10.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 10/19/2009] [Accepted: 10/22/2009] [Indexed: 12/01/2022]
Abstract
Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10x cheaper (0.53 pounds sterling=US$0.80 per sample) than the RNeasy method (5.91 pounds sterling=US$8.86 per sample). A two-step RT-PCR (1.34 pounds sterling=US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (4.48 pounds sterling=US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100-400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7-1.7%, respectively. CBSV was detected at 10(-4)-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV.
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Affiliation(s)
- M M Abarshi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, United Kingdom
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