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Musker SD, Pirie MD, Nürk NM. Pollinator shifts despite hybridisation in the Cape's hyperdiverse heathers (Erica, Ericaceae). Mol Ecol 2024:e17505. [PMID: 39188071 DOI: 10.1111/mec.17505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/23/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024]
Abstract
Interrogating the ecological and geographic factors that influence population divergence dynamics can reveal why some groups of organisms diversify more prolifically than others. One such group is the heathers (Erica, Ericaceae), the largest plant genus in the Cape Floristic Region. We study Erica abietina, a highly variable species complex with four subspecies differing in geographic range, habitat and pollination syndrome. We test for population differentiation, hybridisation, introgression and pollinator-driven divergence using genotyping-by-sequencing on samples across the entire distribution. We find five variably distinct genetic groups, with one subspecies comprising two independent lineages that are geographically isolated and occur on different soil types. Phylogenetic analysis suggests two independent shifts between bird and insect pollination, with accompanying genetic divergence. However, for one pair of populations with different pollinators, we uncover several individuals of hybrid origin at a site of sympatry. These results suggest that floral differentiation driven by divergent selection acts in concert with geographic isolation to maintain reproductive isolation and promote speciation. Our investigations reveal a highly dynamic system whose diversity has been shaped by a variety of interacting forces. We suggest that such a system could be a model for much of the diversification of the Cape flora.
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Affiliation(s)
- Seth D Musker
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | | | - Nicolai M Nürk
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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Pirie MD, Bellstedt DU, Bouman RW, Fagúndez J, Gehrke B, Kandziora M, Le Maitre NC, Musker SD, Newman E, Nürk NM, Oliver EGH, Pipins S, van der Niet T, Forest F. Spatial decoupling of taxon richness, phylogenetic diversity and threat status in the megagenus Erica (Ericaceae). PHYTOKEYS 2024; 244:127-150. [PMID: 39027483 PMCID: PMC11255470 DOI: 10.3897/phytokeys.244.124565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024]
Abstract
Estimates of the number of vascular plant species currently under threat of extinction are shockingly high, with the highest extinction rates reported for narrow-range, woody plants, especially in biodiversity hotspots with Mediterranean and tropical climates. The large genus Erica is a prime example, as a large proportion of its 851 species, all shrubs or small trees, are endemic to the Cape Floristic Region (CFR) of South Africa. Almost two hundred are known to be threatened and a further hundred are 'Data Deficient'. We need to target conservation efforts and research to fill the most problematic knowledge gaps. This can be especially challenging in large genera, such as Erica, with numerous threatened species that are closely related. One approach involves combining knowledge of phylogenetic diversity with that of IUCN threat status to identify the most Evolutionarily Distinct and Globally Endangered (EDGE) species. We present an expanded and improved phylogenetic hypothesis for Erica (representing 65% of described species diversity) and combine this with available threat and distribution data to identify species and geographic areas that could be targeted for conservation effort to maximise preservation of phylogenetic diversity (PD). The resulting 39 EDGE taxa include 35 from the CFR. A further 32 high PD, data deficient taxa are mostly from outside the CFR, reflecting the low proportion of assessed taxa outside South Africa. The most taxon-rich areas are found in the south-western CFR. They are not the most phylogenetically diverse, but do include the most threatened PD. These results can be cross-referenced to existing living and seed-banked ex situ collections and used to target new and updated threat assessments and conservation action.
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Affiliation(s)
- Michael D. Pirie
- University Museum, University of Bergen, Postboks 7800, N-5020 Bergen, Norway
| | - Dirk U. Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Roderick W. Bouman
- Hortus botanicus Leiden, Leiden University, P.O. Box 9500, 2300 RA, Leiden, Netherlands
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, Netherlands
| | - Jaime Fagúndez
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA Leiden, Netherlands
| | - Berit Gehrke
- University Museum, University of Bergen, Postboks 7800, N-5020 Bergen, Norway
| | - Martha Kandziora
- Universidade da Coruña, BIOCOST research group, Centro Interdisciplinar de Química e Bioloxía (CICA), Rúa As Carballeiras, 15071, A Coruña, Spain
- Universidade da Coruña, Departamento de Bioloxía, Facultade de Ciencias, 15071, A Coruña, Spain
| | - Nicholas C. Le Maitre
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Seth D. Musker
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Ethan Newman
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
| | - Nicolai M. Nürk
- Department of Genetics, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - E. G. H. Oliver
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
| | - Sebastian Pipins
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Timotheus van der Niet
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
| | - Félix Forest
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa
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Ablazov A, Felemban A, Braguy J, Kuijer HNJ, Al-Babili S. A Fast and Cost-Effective Genotyping Method for CRISPR-Cas9-Generated Mutant Rice Lines. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112189. [PMID: 37299168 DOI: 10.3390/plants12112189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
With increasing throughput in both the generation and phenotyping of mutant lines in plants, it is important to have an efficient and reliable genotyping method. Traditional workflows, still commonly used in many labs, have time-consuming and expensive steps, such as DNA purification, cloning and growing E. coli cultures. We propose an alternative workflow where these steps are bypassed, using Phire polymerase on fresh plant tissue, and ExoProStar treatment as preparation for sequencing. We generated CRISPR-Cas9 mutants for ZAS (ZAXINONE SYNTHASE) in rice with two guide RNAs. Using both a traditional workflow and our proposed workflow, we genotyped nine T1 plants. To interpret the sequencing output, which is often complex in CRISPR-generated mutants, we used free online automatic analysis systems and compared the results. Our proposed workflow produces results of the same quality as the old workflow, but in 1 day instead of 3 days and about 35 times cheaper. This workflow also consists of fewer steps and reduces the risk of cross contamination and mistakes. Furthermore, the automated sequence analysis packages are mostly accurate and could easily be used for bulk analysis. Based on these advantages, we encourage academic and commercial labs conducting genotyping to consider switching over to our proposed workflow.
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Affiliation(s)
- Abdugaffor Ablazov
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Abrar Felemban
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Justine Braguy
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Hendrik N J Kuijer
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Krishnan N, Kumari S, Kumar R, Pandey KK, Singh J. Loop-mediated isothermal amplification assay for quicker detection of tomato leaf curl Joydebpur virus infection in chilli. J Virol Methods 2022; 302:114474. [PMID: 35077721 DOI: 10.1016/j.jviromet.2022.114474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/21/2021] [Accepted: 01/20/2022] [Indexed: 11/26/2022]
Abstract
Chilli leaf curl disease caused by whitefly transmitted begomoviruses is an important constraint to chilli (Capsicum anuum L.) cultivation in India. Tomato leaf curl Joydebpur virus (ToLCJoV) was characterized and identified as incitant of leaf curl disease through rolling circle amplification (RCA) and PCR assay from the symptomatic samples collected from Uttar Pradesh, India. Although PCR assay provides the gold standard in diagnostics, this method consumes more time and requires convenient portable instruments. Therefore, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of ToLCJoV by targeting the AC1 and AC2 region. Detection has been achieved through a laddered pattern of amplification in agarose gel electrophoresis. The assay has detected ToLCJoV in a total DNA concentration of 1 × 10-1 ng indicating 200-fold higher sensitivity than that of the PCR. Further, the replacement of total DNA with leaf extracts using the grinding buffer and GES buffer coupled with LAMP assay also detected the presence of ToLCJoV in the infected chilli samples. With this assay, ToLCJoV can be detected in less than 2 h without DNA extraction. Besides, this assay will be highly useful in discriminating the leaf curl disease etiology by ToLCJoV from other begomoviruses and insects (thrips and mites). To the best of our knowledge, this is the first report of a LAMP assay for the detection of ToLCJoV.
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Affiliation(s)
- Nagendran Krishnan
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India.
| | - Shweta Kumari
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | - Rajesh Kumar
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | | | - Jagdish Singh
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
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Matsuo K. Evaluation of methods for plant genomic DNA sequence analysis without DNA and PCR product purification. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111023. [PMID: 34620428 DOI: 10.1016/j.plantsci.2021.111023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Genome-editing technologies are widely used to characterize gene functions and improve the features of agricultural plants. Although sequence analysis of gene editing target DNA is the most reliable method of screening gene-edited plants, the current DNA sequence analysis methods are time consuming and labor intensive because they include genomic DNA and polymerase chain reaction (PCR) product purification. In this study, seven methods were performed for sequence analysis of plant genomic DNA with and/or without genomic DNA and PCR product purification. Consequently, good-quality sequencing chromatograms were obtained using all methods. Results showed that the partial genomic DNA sequence of Nicotiana benthamiana and Arabidopsis thaliana could be sufficiently analyzed without plant genomic DNA and PCR product purification. Furthermore, screening of gene-edited N. benthamiana was successful using the present methods. Therefore, the tested methods could reduce the time, simplify the workflow of plant gene analysis, and help in screening gene-edited plants.
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Affiliation(s)
- Kouki Matsuo
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan.
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Chandrakanth N, Makwana P, Satish L, Rabha M, Sivaprasad V. Molecular approaches for detection of pebrine disease in sericulture. J Microbiol Methods 2021. [DOI: 10.1016/bs.mim.2021.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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Beaver-Kanuya E, Harper SJ. Development of RT-qPCR assays for the detection of three latent viruses of pome. J Virol Methods 2020; 278:113836. [PMID: 32087190 DOI: 10.1016/j.jviromet.2020.113836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/30/2020] [Accepted: 02/08/2020] [Indexed: 10/25/2022]
Abstract
Latent fruit tree viruses present economic threat to the industry and nurseries as diseases they cause not only reduce fruit quality and production yield, but can also be spread inadvertently through propagation due to the lack of viral symptoms on an infected mother plant. As a result, these viruses require appropriate detection tools for effective management. In this study we developed RT-qPCR assays for the detection of three latent viruses of pome, apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), and apple mosaic virus (ApMV), using the alignment of representative sequences from the NCBI database. The optimized assays were shown to be specific by successfully amplifying the target from positive controls without showing any detectable amplification in negative and non-target controls, and revealed high sensitivity by reliably detecting as low as 101 copies per reaction. The results also demonstrated that both the choice of extraction method and the reagents used for RT-qPCRcould play a critical role in virus detection outcome. These assays were both reliable and robust compared to the extant RT-PCR methods, and they could be a viable tool for making informed management decisions.
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Affiliation(s)
- E Beaver-Kanuya
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States.
| | - S J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States
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Le Maitre NC, Pirie MD, Bellstedt DU. An approach to determining anthocyanin synthesis enzyme gene expression in an evolutionary context: an example from Erica plukenetii. ANNALS OF BOTANY 2019; 124:121-130. [PMID: 31008513 PMCID: PMC6676384 DOI: 10.1093/aob/mcz046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 03/24/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Floral colour in angiosperms can be controlled by variations in the expression of the genes of the anthocyanin pathway. Floral colour shifts influence pollinator specificity. Multiple shifts in floral colour occurred in the diversification of the genus Erica (Ericaceae), from plesiomorphic pink to, for example, red or white flowers. Variation in anthocyanin gene expression and its effects on floral colour in the red-, pink- and white-flowered Erica plukenetii species complex was investigated. METHODS Next generation sequencing, reverse transcriptase PCR and real-time reverse transcriptase quantitative PCR were used to quantify anthocyanin gene expression. KEY RESULTS Non-homologous mutations causing loss of expression of single genes were found, indicating that the cause was likely to be mutations in transcription factor binding sites upstream of the 5'-untranslated region of the genes, and this was confirmed by sequencing. CONCLUSIONS Independent evolution and subsequent loss of expression of anthocyanin genes may have influenced diversification in the E. plukenetii species complex. The approach developed here should find more general application in studies on the role of floral colour shifts in diversification.
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Affiliation(s)
- N C Le Maitre
- Biochemistry Department, Stellenbosch University, Private Bag X1, Matieland, South Africa
- University of the Free State, Bloemfontein, South Africa
| | - M D Pirie
- Johannes Gutenberg-Universität, Mainz, Mainz, Germany
- University Museum, University of Bergen, Postboks, Bergen, Norway
| | - D U Bellstedt
- Biochemistry Department, Stellenbosch University, Private Bag X1, Matieland, South Africa
- For correspondence. E-mail
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Žiarovská J, Zeleňáková L, Kačániová M, Cusimamani EF. A thaumatin-like genomic sequence identification in Vitis vinifera l., stormy wines and musts based on direct pcr. POTRAVINARSTVO 2018. [DOI: 10.5219/892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Direct polymerase chain reaction method was use to amplify a thaumatin-like sequence of Vitis vinifera L. in grapes as well as in stormy wines and musts. Thaumatin-like proteins (TLPs) of Vitis vinifera possess beside its function in abiotic and biotic stress response another one - they are able to cause protein haze in wine unless removed prior to bottling. Direct PCR is an approach where omission of DNA extraction is typical prior the amplification of the target site of plant genome. Crude extract or small pieces of plant tissues are used in the analysis directly without steps of extraction and purification of gDNA. The biological material that was used in analysis was collected during August - October 2017 in local stores and winery Sabo and comprises from cultivars Iršai, Muškát, Savignon Blanc, Svätovavrinecké, Dornfelder and Pálava. Direct PCR was performed by a cutted piece of grape tissue and a dilution buffer was use in 1:2 for stormy wine or must, respectively. Direct amplification of thaumatin-like protein sequence of Vitis vinifera was performed along with the control reactions with the primers for conserved region of plant chloroplast. Possitive amplification of thaumatin-like allergen sequence resulted in 570 bp amplicon. The most abundant amplicons were amplified in stormy wines, followed by musts and the amplicons from grapes were weaker when comparing them to others. The amplicon specificity checking of obtained PCR product of thaumatin-like allergen was performed by restriction cleavage by Psi I and resulted in restriction amplicons of the 80 bp, 81 bp, 94 bp and 315 bp in length. Confirmation of the amplicon specificity by restriction cleavage support the potential of direct PCR to become a reproducible method that will be fully applicable in routine analysis of not only plant genomes in the future, but it was demonstrated, that it works in liquids, too.
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Kadlec M, Bellstedt DU, Le Maitre NC, Pirie MD. Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"? PeerJ 2017; 5:e3569. [PMID: 28761782 PMCID: PMC5530999 DOI: 10.7717/peerj.3569] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/22/2017] [Indexed: 12/05/2022] Open
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for "one size fits all" universal markers, we should improve and make more accessible the tools necessary for developing "made to measure" ones.
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Affiliation(s)
- Malvina Kadlec
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk U. Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | | | - Michael D. Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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11
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Kadlec M, Bellstedt DU, Le Maitre NC, Pirie MD. Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"? PeerJ 2017. [PMID: 28761782 DOI: 10.7717/peerj3569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for "one size fits all" universal markers, we should improve and make more accessible the tools necessary for developing "made to measure" ones.
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Affiliation(s)
- Malvina Kadlec
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Nicholas C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Michael D Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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12
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Direct LAMP Assay without Prior DNA Purification for Sex Determination of Papaya. Int J Mol Sci 2016; 17:ijms17101630. [PMID: 27669237 PMCID: PMC5085663 DOI: 10.3390/ijms17101630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/15/2016] [Accepted: 09/20/2016] [Indexed: 11/17/2022] Open
Abstract
Papaya (Carica papaya L.) is an economically important tropical fruit tree with hermaphrodite, male and female sex types. Hermaphroditic plants are the major type used for papaya production because their fruits have more commercial advantages than those of female plants. Sex determination of the seedlings, or during the early growth stages, is very important for the papaya seedling industry. Thus far, the only method for determining the sex type of a papaya at the seedling stage has been DNA analysis. In this study, a molecular technique—based on DNA analysis—was developed for detecting male-hermaphrodite-specific markers to examine the papaya’s sex type. This method is based on the loop-mediated isothermal amplification (LAMP) and does not require prior DNA purification. The results show that the method is an easy, efficient, and inexpensive way to determine a papaya’s sex. This is the first report on the LAMP assay, using intact plant materials-without DNA purification-as samples for the analysis of sex determination of papaya. We found that using high-efficiency DNA polymerase was essential for successful DNA amplification, using trace intact plant material as a template DNA source.
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Pirie MD, Oliver EGH, Mugrabi de Kuppler A, Gehrke B, Le Maitre NC, Kandziora M, Bellstedt DU. The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region. BMC Evol Biol 2016; 16:190. [PMID: 27639849 PMCID: PMC5027107 DOI: 10.1186/s12862-016-0764-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/08/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The disproportionate species richness of the world's biodiversity hotspots could be explained by low extinction (the evolutionary "museum") and/or high speciation (the "hot-bed") models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the genus Erica L. We generate a novel phylogenetic hypothesis informed by nuclear and plastid DNA sequences of c. 60 % of the c. 800 Erica species (of which 690 are endemic to the CFR), and use this to estimate clade ages (using RELTIME; BEAST), net diversification rates (GEIGER), and shifts in rates of diversification in different areas (BAMM; MuSSE). RESULTS The diversity of Erica species in the CFR is the result of a single radiation within the last c. 15 million years. Compared to ancestral lineages in the Palearctic, the rate of speciation accelerated across Africa and Madagascar, with a further burst of speciation within the CFR that also exceeds the net diversification rates of other Cape clades. CONCLUSIONS Erica exemplifies the "hotbed" model of assemblage through recent speciation, implying that with the advent of the modern Cape a multitude of new niches opened and were successively occupied through local species diversification.
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Affiliation(s)
- M D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.
| | - E G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - A Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - B Gehrke
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
| | - N C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - M Kandziora
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
| | - D U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Ossa CG, Larridon I, Peralta G, Asselman P, Pérez F. Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae). Mol Biol Rep 2016; 43:1315-1320. [PMID: 27631640 DOI: 10.1007/s11033-016-4069-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
The aim of this study was to develop microsatellite markers as a tool to study population structure, genetic diversity and effective population size of Echinopsis chiloensis, an endemic cactus from arid and semiarid regions of Central Chile. We developed 12 polymorphic microsatellite markers for E. chiloensis using next-generation sequencing and tested them in 60 individuals from six sites, covering all the latitudinal range of this species. The number of alleles per locus ranged from 3 to 8, while the observed (Ho) and expected (He) heterozygosity ranged from 0.0 to 0.80 and from 0.10 to 0.76, respectively. We also detected significant differences between sites, with FST values ranging from 0.05 to 0.29. Microsatellite markers will enable us to estimate genetic diversity and population structure of E. chiloensis in future ecological and phylogeographic studies.
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Affiliation(s)
- Carmen G Ossa
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile. .,Institute of Ecology and Biodiversity (IEB), Casilla 653, Santiago, Chile.
| | - Isabel Larridon
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.,Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Gioconda Peralta
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Pieter Asselman
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Fernanda Pérez
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Casilla 653, Santiago, Chile
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15
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Lauterbach M, van der Merwe PDW, Keßler L, Pirie MD, Bellstedt DU, Kadereit G. Evolution of leaf anatomy in arid environments – A case study in southern African Tetraena and Roepera (Zygophyllaceae). Mol Phylogenet Evol 2016; 97:129-144. [DOI: 10.1016/j.ympev.2016.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 12/28/2022]
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Li SL, Vasemägi A, Ramula S. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader. ANNALS OF BOTANY 2016; 117:187-194. [PMID: 26420202 PMCID: PMC4701146 DOI: 10.1093/aob/mcv145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND AIMS Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. METHODS Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. KEY RESULTS It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. CONCLUSIONS The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity.
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Affiliation(s)
- Shou-Li Li
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA,
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia and
| | - Satu Ramula
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Aronia Coastal Zone Research Team, Åbo Akademi University and Novia University of Applied Sciences, Raseborgsvägen 9, 10600 Ekenäs, Finland
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Mugrabi de Kuppler AL, Fagúndez J, Bellstedt DU, Oliver EGH, Léon J, Pirie MD. Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae). Mol Phylogenet Evol 2015; 88:121-31. [PMID: 25888972 DOI: 10.1016/j.ympev.2015.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/02/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022]
Abstract
Whilst most of the immense species richness of heathers (Calluna, Daboecia and Erica: Ericeae; Ericaceae) is endemic to Africa, particularly the Cape Floristic Region, the oldest lineages are found in the Northern Hemisphere. We present phylogenetic hypotheses for the major clades of Ericeae represented by multiple accessions of all northern Erica species and placeholder taxa for the large nested African/Madagascan clade. We identified consistent, strongly supported conflict between gene trees inferred from ITS and chloroplast DNA sequences with regard to the position of Erica lusitanica. We used coalescent simulations to test whether this conflict could be explained by coalescent stochasticity, as opposed to reticulation (e.g. hybridisation), given estimates of clade ages, generation time and effective population sizes (Ne). A standard approach, comparing overall differences between real and simulated trees, could not clearly reject coalescence. However, additional simulations showed that at the (higher) Ne necessary to explain conflict in E. lusitanica, further topological conflict would also be expected. Ancient hybridisation between ancestors of northern species is therefore a plausible scenario to explain the origin of E. lusitanica, and its morphological similarities to E. arborea. Assuming either process influences the results of species tree and further evolutionary inference. The coalescence scenario is equivocal with regard the standing hypothesis of stepping stone dispersal of Erica from Europe into Africa; whereas reticulate evolution in E. lusitanica would imply that the colonisation of Tropical East Africa by E. arborea instead occurred independently of dispersals within the rest of the African/Madagascan clade.
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Affiliation(s)
- A L Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - J Fagúndez
- Department of Plant and Animal Biology and Ecology, University of A Coruña, Faculty of Science, 15001 A Coruña, Spain
| | - D U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - E G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - J Léon
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - M D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa; Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, Germany.
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18
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Hughes PW, Jaworski AF, Davis CS, Aitken SM, Simons AM. Development of polymorphic microsatellite markers for Indian tobacco, Lobelia inflata (Campanulaceae)(1.). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1300096. [PMID: 25202618 PMCID: PMC4103137 DOI: 10.3732/apps.1300096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/03/2014] [Indexed: 05/26/2023]
Abstract
PREMISE OF THE STUDY Nuclear microsatellite markers were developed for Lobelia inflata (Campanulaceae), an obligately self-fertilizing plant species, for use in the study of temporal fluctuation in allele frequency and of the genetic structure within and among populations. • METHODS AND RESULTS We developed 28 primer pairs for L. inflata, all of which amplify CT dinucleotide repeats. We evaluated amplification of these loci in 53 L. inflata individuals at three sites in eastern North America and found that 24 loci showed microsatellite polymorphism. We also found that 16 loci amplified successfully in L. cardinalis, and 11 amplified successfully in L. siphilitica. • CONCLUSIONS These primers will be useful for assessing allelic diversity within and among populations of L. inflata, and show potential for use in congeneric species.
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Affiliation(s)
- P. William Hughes
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
| | - Allison F. Jaworski
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
| | - Corey S. Davis
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9 Alberta, Canada
| | - Susan M. Aitken
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
| | - Andrew M. Simons
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
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Tamari F, Hinkley CS, Ramprashad N. A comparison of DNA extraction methods using Petunia hybrida tissues. J Biomol Tech 2014; 24:113-8. [PMID: 23997658 DOI: 10.7171/jbt.13-2403-001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Extraction of DNA from plant tissue is often problematic, as many plants contain high levels of secondary metabolites that can interfere with downstream applications, such as the PCR. Removal of these secondary metabolites usually requires further purification of the DNA using organic solvents or other toxic substances. In this study, we have compared two methods of DNA purification: the cetyltrimethylammonium bromide (CTAB) method that uses the ionic detergent hexadecyltrimethylammonium bromide and chloroform-isoamyl alcohol and the Edwards method that uses the anionic detergent SDS and isopropyl alcohol. Our results show that the Edwards method works better than the CTAB method for extracting DNA from tissues of Petunia hybrida. For six of the eight tissues, the Edwards method yielded more DNA than the CTAB method. In four of the tissues, this difference was statistically significant, and the Edwards method yielded 27-80% more DNA than the CTAB method. Among the different tissues tested, we found that buds, 4 days before anthesis, had the highest DNA concentrations and that buds and reproductive tissue, in general, yielded higher DNA concentrations than other tissues. In addition, DNA extracted using the Edwards method was more consistently PCR-amplified than that of CTAB-extracted DNA. Based on these results, we recommend using the Edwards method to extract DNA from plant tissues and to use buds and reproductive structures for highest DNA yields.
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Affiliation(s)
- Farshad Tamari
- Department of Biological Sciences, Kingsborough Community College, Brooklyn, New York 11235, USA.
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Van der Niet T, Pirie MD, Shuttleworth A, Johnson SD, Midgley JJ. Do pollinator distributions underlie the evolution of pollination ecotypes in the Cape shrub Erica plukenetii? ANNALS OF BOTANY 2014; 113:301-15. [PMID: 24071499 PMCID: PMC3890384 DOI: 10.1093/aob/mct193] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS According to the Grant-Stebbins model of pollinator-driven divergence, plants that disperse beyond the range of their specialized pollinator may adapt to a new pollination system. Although this model provides a compelling explanation for pollination ecotype formation, few studies have directly tested its validity in nature. Here we investigate the distribution and pollination biology of several subspecies of the shrub Erica plukenetii from the Cape Floristic Region in South Africa. We analyse these data in a phylogenetic context and combine these results with information on pollinator ranges to test whether the evolution of pollination ecotypes is consistent with the Grant-Stebbins model. METHODS AND KEY RESULTS Pollinator observations showed that the most common form of E. plukenetii with intermediate corolla length is pollinated by short-billed Orange-breasted sunbirds. Populations at the northern fringe of the distribution are characterized by long corollas, and are mainly pollinated by long-billed Malachite sunbirds. A population with short corollas in the centre of the range was mainly pollinated by insects, particularly short-tongued noctuid moths. Bird exclusion in this population did not have an effect on fruit set, while insect exclusion reduced fruit set. An analysis of floral scent across the range, using coupled gas chromatography-mass spectrometry, showed that the scent bouquets of flowers from moth-pollinated populations are characterized by a larger number of scent compounds and higher emission rates than those in bird-pollinated populations. This was also reflected in clear separation of moth- and bird-pollinated populations in a two-dimensional phenotype space based on non-metric multidimensional scaling analysis of scent data. Phylogenetic analyses of chloroplast and nuclear DNA sequences strongly supported monophyly of E. plukenetii, but not of all the subspecies. Reconstruction of ancestral character states suggests two shifts from traits associated with short-billed Orange-breasted sunbird pollination: one towards traits associated with moth pollination, and one towards traits associated with pollination by long-billed Malachite sunbirds. The latter shift coincided with the colonization of Namaqualand in which Orange-breasted sunbirds are absent. CONCLUSIONS Erica plukenetii is characterized by three pollination ecotypes, but only the evolutionary transition from short- to long-billed sunbird pollination can be clearly explained by the Grant-Stebbins model. Corolla length is a key character for both ecotype transitions, while floral scent emission was important for the transition from bird to moth pollination.
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Affiliation(s)
- Timotheüs Van der Niet
- Naturalis Biodiversity Center, PO Box 9514, 2300 RA, Leiden, The Netherlands
- Leiden University, PO Box 9514, 2300 RA, Leiden, The Netherlands
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
- For correspondence. E-mail
| | - Michael D. Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, D-55099 Mainz, Germany
| | - Adam Shuttleworth
- School of Life Sciences, University of KwaZulu Natal, P/Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
| | - Steven D. Johnson
- School of Life Sciences, University of KwaZulu Natal, P/Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
| | - Jeremy J. Midgley
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
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Biswas C, Dey P, Satpathy S. A method of direct PCR without DNA extraction for rapid detection of begomoviruses infecting jute and mesta. Lett Appl Microbiol 2013; 58:350-5. [PMID: 24261838 DOI: 10.1111/lam.12196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/16/2013] [Accepted: 11/17/2013] [Indexed: 11/30/2022]
Affiliation(s)
- C. Biswas
- Crop Protection Division; Central Research Institute for Jute and Allied Fibres (CRIJAF); Barrackpore Kolkata West Bengal India
| | - P. Dey
- Crop Protection Division; Central Research Institute for Jute and Allied Fibres (CRIJAF); Barrackpore Kolkata West Bengal India
| | - S. Satpathy
- Crop Protection Division; Central Research Institute for Jute and Allied Fibres (CRIJAF); Barrackpore Kolkata West Bengal India
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Visser JC, Bellstedt DU, Pirie MD. The recent recombinant evolution of a major crop pathogen, potato virus Y. PLoS One 2012; 7:e50631. [PMID: 23226339 PMCID: PMC3511492 DOI: 10.1371/journal.pone.0050631] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/23/2012] [Indexed: 11/19/2022] Open
Abstract
Potato virus Y (PVY) is a major agricultural disease that reduces crop yields worldwide. Different strains of PVY are associated with differing degrees of pathogenicity, of which the most common and economically important are known to be recombinant. We need to know the evolutionary origins of pathogens to prevent further escalations of diseases, but putatively reticulate genealogies are challenging to reconstruct with standard phylogenetic approaches. Currently available phylogenetic hypotheses for PVY are either limited to non-recombinant strains, represent only parts of the genome, and/or incorrectly assume a strictly bifurcating phylogenetic tree. Despite attempts to date potyviruses in general, no attempt has been made to date the origins of pathogenic PVY. We test whether diversification of the major strains of PVY and recombination between them occurred within the time frame of the domestication and modern cultivation of potatoes. In so doing, we demonstrate a novel extension of a phylogenetic approach for reconstructing reticulate evolutionary scenarios. We infer a well resolved phylogeny of 44 whole genome sequences of PVY viruses, representative of all known strains, using recombination detection and phylogenetic inference techniques. Using Bayesian molecular dating we show that the parental strains of PVY diverged around the time potatoes were first introduced to Europe, that recombination between them only occurred in the last century, and that the multiple recombination events that led to highly pathogenic PVY(NTN) occurred within the last 50 years. Disease causing agents are often transported across the globe by humans, with disastrous effects for us, our livestock and crops. Our analytical approach is particularly pertinent for the often small recombinant genomes involved (e.g. HIV/influenza A). In the case of PVY, increased transport of diseased material is likely to blame for uniting the parents of recombinant pathogenic strains: this process needs to be minimised to prevent further such occurrences.
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Affiliation(s)
| | - Dirk Uwe Bellstedt
- Department of Biochemistry, The University of Stellenbosch, Stellenbosch, South Africa
| | - Michael David Pirie
- Department of Biochemistry, The University of Stellenbosch, Stellenbosch, South Africa
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Zhang JH, Yang R, Wang TY, Dong WH, Wang F, Wang L. A simple and practical method that prepares high molecular weight DNA ladders. Mol Med Rep 2012; 6:1211-3. [PMID: 22948498 DOI: 10.3892/mmr.2012.1061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/24/2012] [Indexed: 11/06/2022] Open
Abstract
The purpose of the current study was to report a simple and practical method to prepare high molecular weight (mw) DNA ladders. The method involves 1,000-4,000-base pairs (bp) DNA fragments being amplified by polymerase chain reaction (PCR), using λ DNA as a template. The constructed plasmids are digested by restriction endonucleases to produce 5-, 6-, 8- and 10-kb DNA fragments, followed by purification and precipitation with ethanol, and mixed proportionally. The 1,000-4,000-bp DNA fragments were successfully generated by PCR and 5-, 6-, 8- and 10-kb DNA fragments were obtained through the digestion of the plasmids. The bands of the prepared high mw DNA ladder were clear and may aid future molecular biology studies.
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Affiliation(s)
- Jun-He Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
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Pirie MD, Oliver EGH, Bellstedt DU. A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology. Mol Phylogenet Evol 2011; 61:593-601. [PMID: 21722743 DOI: 10.1016/j.ympev.2011.06.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 11/26/2022]
Abstract
Erica L. is the largest of the 'Cape' clades that together comprise around half of the disproportionately high species richness of the Cape Floristic Region (CFR) of South Africa. Around 840 species of Erica are currently recognised, C.680 of which are found in the CFR, the rest distributed across the rest of Southern Africa, the highlands of Tropical Africa and Madagascar, and Europe. Erica is taxonomically well documented, but very little is known about species-level relationships. We present the first densely sampled phylogenetic analysis of Erica, using nuclear ribosomal DNA sequences (internal transcribed spacers; ITS) of c. 45% of the species from across the full geographic range of the genus, both Calluna and Daboecia (Ericeae; monotypic genera and putative sister groups of Erica), and further Ericoideae outgroups. Our results show both morphological and geographic coherence of some clades, but numerous shifts in floral macro-morphology as represented by variation in individual morphological characters and pollination syndromes. European Ericeae is a paraphyletic grade subtending a monophyletic African/Malagasy Erica. Given the limited resolution of this single gene tree, more data are needed for further conclusions. Clades are identified that will serve as an effective guide for targeted sampling from multiple linkage groups.
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Affiliation(s)
- Michael D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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