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Park H, Kim HS, Abassi S, Bui QTN, Ki JS. Two novel glutathione S-transferase (GST) genes in the toxic marine dinoflagellate Alexandrium pacificum and their transcriptional responses to environmental contaminants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169983. [PMID: 38215848 DOI: 10.1016/j.scitotenv.2024.169983] [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: 06/06/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/14/2024]
Abstract
The present study identified two novel glutathione S-transferase (GST) genes from the toxic dinoflagellate Alexandrium pacificum and examined their molecular characteristics and transcriptional responses to algicides and environmental contaminants. Bioinformatic analysis revealed that both ApGSTs are cytosolic, belonging to the chi-like class (ApGST1) and an undefined class (ApGST2). The overall expression of ApGSTs showed similar patterns depending on the exposed contaminants, while they were differently regulated by polychlorinated biphenyl (PCB). Copper treatments (CuCl2 and CuSO4) did not significantly induce the expression of ApGSTs. The highest up-regulations of ApGST1 and ApGST2 were under 6-h treatments of 0.10 and 0.50 mg L-1 NaOCl. Interestingly, only ApGST1 increased significantly after 0.10, 0.50, and 1.00 mg L-1 of PCB exposure (6 h). Intracellular reactive oxygen species (ROS) increased considerably under NaOCl; however, it was not significantly higher in the PCB-treated cells. GST activity was increased by NaOCl and PCB treatments, but only PCB caused apoptosis. These results suggest that GSTs are involved in the first line of phase II detoxification, protecting dinoflagellate cells against oxidative damage.
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Affiliation(s)
- Hyunjun Park
- Department of Life Science, Sangmyung University, Seoul, South Korea
| | - Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul, South Korea
| | - Sofia Abassi
- Department of Life Science, Sangmyung University, Seoul, South Korea
| | - Quynh Thi Nhu Bui
- Department of Life Science, Sangmyung University, Seoul, South Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul, South Korea; Department of Biotechnology, Sangmyung University, Seoul, South Korea.
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Zapata-Alvarez A, Bedoya-Vergara C, Porras-Barrientos LD, Rojas-Mora JM, Rodríguez-Cabal HA, Gil-Garzon MA, Martinez-Alvarez OL, Ocampo-Arango CM, Ardila-Castañeda MP, Monsalve-F ZI. Molecular, biochemical, and sensorial characterization of cocoa ( Theobroma cacao L.) beans: A methodological pathway for the identification of new regional materials with outstanding profiles. Heliyon 2024; 10:e24544. [PMID: 38322871 PMCID: PMC10844050 DOI: 10.1016/j.heliyon.2024.e24544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/11/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
Cocoa is an economically important product in Colombia. On-farm germplasm evaluations enable the selection of superior genotypes for propagation and distribution across the country. This study examined 12 cocoa samples from Antioquia along with five reference materials, employing 96 single nucleotide polymorphism (SNP) markers. Furthermore, these genetic findings were correlated with physical, chemical, and sensory attributes. Primary coordinate analysis revealed that the majority of samples were hybrids derived from five original germplasm pools, including Criollo, Amelonado, and three Upper Amazon Forastero cocoas. The integral profile of the 12 selected materials was classified into Modern Criollo (Rodriguez-Medina et al., 2019) [3], Forasteros (Rodriguez-Medina et al., 2019) [3], and Trinitarios (Borja Fajardo et al., 2022) [6]. Three key factors were identified to best account for the sample classification: type of variety, functional properties, and quality.
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Affiliation(s)
- Andrea Zapata-Alvarez
- University of Antioquia, Faculty of Exact and Natural Sciences, Institute of Biology, Agrobiotechnology Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
| | - Carolina Bedoya-Vergara
- La Sallista University Corporation, Caldas, Antioquia, Colombia, Food Engineering Research Group, GRIAL, Carrera 51 N°.118 sur 57, Caldas, Antioquia, Colombia
| | - Luis D. Porras-Barrientos
- University of Antioquia, Faculty of Pharmaceutical and Food Sciences, Sensory Science Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
| | - Jessica M. Rojas-Mora
- Metropolitan Technological Institute, Faculty of Exact and Applied Sciences, Medellín, Colombia
| | - Héctor A. Rodríguez-Cabal
- University of Antioquia, Faculty of Exact and Natural Sciences, Institute of Biology, Agrobiotechnology Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
| | - Maritza A. Gil-Garzon
- La Sallista University Corporation, Caldas, Antioquia, Colombia, Food Engineering Research Group, GRIAL, Carrera 51 N°.118 sur 57, Caldas, Antioquia, Colombia
- Metropolitan Technological Institute, Faculty of Exact and Applied Sciences, Medellín, Colombia
| | - Olga L. Martinez-Alvarez
- University of Antioquia, Faculty of Pharmaceutical and Food Sciences, Sensory Science Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
| | - Carlos M. Ocampo-Arango
- University of Antioquia, Faculty of Pharmaceutical and Food Sciences, Sensory Science Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
| | - Maurem P. Ardila-Castañeda
- University of Antioquia, Faculty of Pharmaceutical and Food Sciences, Sensory Science Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
| | - Zulma I. Monsalve-F
- University of Antioquia, Faculty of Exact and Natural Sciences, Institute of Biology, Agrobiotechnology Research Group, Calle 67 N°. 53 - 108, A.A 1226, Medellín, Colombia
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Dutta M, Sharma P, Raturi V, Bhargava B, Zinta G. SarCTAB: an efficient and cost-effective DNA isolation protocol from geophytes. 3 Biotech 2024; 14:36. [PMID: 38221992 PMCID: PMC10784239 DOI: 10.1007/s13205-023-03874-8] [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: 03/14/2023] [Accepted: 12/04/2023] [Indexed: 01/16/2024] Open
Abstract
Geophytes are herbaceous plants that grow anew from underground buds and are excellent models to study storage organ formation. However, molecular studies involving geophytes are constrained due to the presence of a wide spectrum of polysaccharides and polyphenols that contaminate the genomic DNA. At present, several protocols exist for the extraction of genomic DNA from different plant species; however, isolating high-quality DNA from geophytes is challenging. Such challenges are further complexed by longer incubation time and multiple precipitation steps involved in existing DNA isolation methods. To overcome such problems, we aimed to establish a DNA extraction method (SarCTAB) which is an economical, quick, and sustainable way of DNA isolation from geophytes. We improved the traditional CTAB method by optimizing key ingredients such as sarcosine, β-mercaptoethanol, and high molar concentration of sodium chloride (NaCl), which resulted in high concentration and good-quality DNA with lesser polysaccharides, proteins, and polyphenols. This method was evaluated to extract DNA from storage organs of six different geophytes. The SarCTAB method provides an average yield of 1755 ng/µl of high-quality DNA from 100 mg of underground storage tissues with an average standard purity of 1.86 (260/280) and 1.42 (260/230). The isolated genomic DNA performed well with Inter-simple sequence repeat (ISSR) amplification, restriction digestion with EcoRI, and PCR amplification of plant barcode genes viz. matK and rbcL. Also, the cost involved in DNA isolation was low when compared to that with commercially available kits. Overall, SarCTAB method works effectively to isolate high-quality genomic DNA in a cost-effective manner from the underground storage tissues of geophytes, and can be applied for next-generation sequencing, DNA barcoding, and whole genome bisulfite sequencing.
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Affiliation(s)
- Madhushree Dutta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Paras Sharma
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh 176061 India
| | - Vidhi Raturi
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Bhavya Bhargava
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh 176061 India
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh 176061 India
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
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Krishnan S, Sasi S, Kodakkattumannil P, Al Senaani S, Lekshmi G, Kottackal M, Amiri KMA. Cationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species. Anal Biochem 2024; 684:115372. [PMID: 37940013 DOI: 10.1016/j.ab.2023.115372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Because of the heterogeneity among seedlings of outbreeding species, the use of seedling tissues as a source of DNA is unsuitable for the genomic characterization of elite germplasms. High-quality DNA, free of RNA, proteins, polysaccharides, secondary metabolites, and shearing, is mandatory for downstream molecular biology applications, especially for next-generation genome sequencing and pangenome analysis aiming to capture the complete genetic diversity within a species. The study aimed to accomplish an efficient protocol for the extraction of high-quality DNA suitable for diverse plant species/tissues. We describe a reliable, and consistent protocol suitable for the extraction of DNA from 42 difficult-to-extract plant species belonging to 33 angiosperm (monocot and dicot) families, including tissues such as seeds, roots, endosperm, and flower/fruit tissues. The protocol was first optimized for the outbreeding recalcitrant trees viz., Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera, which are rich in proteins, polysaccharides, and secondary metabolites, and the quality of the extracted DNA was confirmed by downstream applications. Nine procedures were attempted to extract high-quality, impurities-free DNA from these three plant species. Extraction of the ethanol-precipitated DNA from cetyltrimethylammonium bromide (CTAB) protocol using sodium dodecyl sulfate (SDS) buffer, i.e., the extraction using a cationic (CTAB) detergent followed by an anionic (SDS) detergent was the key for high yield and high purity (1.75-1.85 against A260/280 and an A260/230 ratio of >2) DNA. A vice versa extraction procedure, i.e., SDS buffer followed by CTAB buffer, and also CTAB buffer followed by CTAB, did not yield good-quality DNA. PCR (using different primers) and restriction endonuclease digestion of the DNA extracted from these three plants validated the protocol. The accomplishment of the genome of P. cineraria using the DNA extracted using the modified protocol confirmed its applicability to genomic studies. The optimized protocol successful in extracting high-quality DNA from diverse plant species/tissues extends its applicability and is useful for accomplishing genome sequences of elite germplasm of recalcitrant plant species with quality reads.
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Affiliation(s)
- Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Preshobha Kodakkattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Salima Al Senaani
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates.
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates; Department of Biology, College of Science, United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
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Paasela T, Lim KJ, Pavicic M, Harju A, Venäläinen M, Paulin L, Auvinen P, Kärkkäinen K, Teeri TH. Transcriptomic Analysis Reveals Novel Regulators of the Scots Pine Stilbene Pathway. PLANT & CELL PHYSIOLOGY 2023; 64:1204-1219. [PMID: 37674261 PMCID: PMC10579783 DOI: 10.1093/pcp/pcad089] [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: 02/28/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Stilbenes accumulate in Scots pine heartwood where they have important roles in protecting wood from decaying fungi. They are also part of active defense responses, and their production is induced by different (a)biotic stressors. The specific transcriptional regulators as well as the enzyme responsible for activating the stilbene precursor cinnamate in the pathway are still unknown. UV-C radiation was the first discovered artificial stress activator of the pathway. Here, we describe a large-scale transcriptomic analysis of pine needles in response to UV-C and treatment with translational inhibitors, both activating the transcription of stilbene pathway genes. We used the data to identify putative candidates for the missing CoA ligase and for pathway regulators. We further showed that the pathway is transcriptionally activated by phosphatase inhibitor, ethylene and jasmonate treatments, as in grapevine, and that the stilbene synthase promoter retains its inducibility in some of the tested conditions in Arabidopsis, a species that normally does not synthesize stilbenes. Shared features between gymnosperm and angiosperm regulation and partially retained inducibility in Arabidopsis suggest that pathway regulation occurs not only via ancient stress-response pathway(s) but also via species-specific regulators. Understanding which genes control the biosynthesis of stilbenes in Scots pine aids breeding of more resistant trees.
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Affiliation(s)
| | - Kean-Jin Lim
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, Helsinki 00014, Finland
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an District, Hangzhou, Zhejiang 311300, China
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Biosciences Division, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Anni Harju
- Production Systems Unit, Natural Resources Institute Finland (Luke), Vipusenkuja 5, Savonlinna 57200, Finland
| | - Martti Venäläinen
- Production Systems Unit, Natural Resources Institute Finland (Luke), Vipusenkuja 5, Savonlinna 57200, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Katri Kärkkäinen
- Production Systems Unit, Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, Oulu 90570, Finland
| | - Teemu H Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, Helsinki 00014, Finland
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Lv Y, Xie M, Zhou S, Wen B, Sui S, Li M, Ma J. CpCAF1 from Chimonanthus praecox Promotes Flowering and Low-Temperature Tolerance When Expressed in Arabidopsis thaliana. Int J Mol Sci 2023; 24:12945. [PMID: 37629126 PMCID: PMC10455127 DOI: 10.3390/ijms241612945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
CCR4-associated factor I (CAF1) is a deadenylase that plays a critical role in the initial step of mRNA degradation in most eukaryotic cells, and in plant growth and development. Knowledge of CAF1 proteins in woody plants remains limited. Wintersweet (Chimonanthus praecox) is a highly ornamental woody plant. In this study, CpCAF1 was isolated from wintersweet. CpCAF1 belongs to the DEDDh (Asp-Glu-Asp-Asp-His) subfamily of the DEDD (Asp-Glu-Asp-Asp) nuclease family. The amino acid sequence showed highest similarity to the homologous gene of Arabidopsis thaliana. In transgenic Arabidopsis overexpressing CpCAF1, the timing of bolting, formation of the first rosette, and other growth stages were earlier than those of the wild-type plants. Root, lateral branch, rosette leaf, and silique growth were positively correlated with CpCAF1 expression. FLOWERING LOCUS T (FT) and SUPPRESSOROF OVEREXPRESSION OF CO 1 (SOC1) gene expression was higher while EARLY FLOWERING3 (ELF3) and FLOWERING LOCUS C (FLC) gene expression of transgenic Arabidopsis was lower than the wild type grown for 4 weeks. Plant growth and flowering occurrences were earlier in transgenic Arabidopsis overexpressing CpCAF1 than in the wild-type plants. The abundance of the CpCAF1 transcript grew steadily, and significantly exceeded the initial level under 4 °C in wintersweet after initially decreasing. After low-temperature exposure, transgenic Arabidopsis had higher proline content and stronger superoxide dismutase activity than the wild type, and the malondialdehyde level in transgenic Arabidopsis was decreased significantly by 12 h and then increased in low temperature, whereas it was directly increased in the wild type. A higher potassium ion flux in the root was detected in transgenic plants than in the wild type with potassium deficiency. The CpCAF1 promoter was a constitutive promoter that contained multiple cis-acting regulatory elements. The DRE, LTR, and MYB elements, which play important roles in response to low temperature, were identified in the CpCAF1 promoter. These findings indicate that CpCAF1 is involved in flowering and low-temperature tolerance in wintersweet, and provide a basis for future genetic and breeding research on wintersweet.
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Affiliation(s)
| | | | | | | | | | | | - Jing Ma
- Chongqing Engineering Research Centre for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China; (Y.L.); (M.X.); (S.Z.); (B.W.); (S.S.); (M.L.)
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7
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Carey SJ, Becklund LE, Fabre PP, Schenk JJ. Optimizing the lysis step in CTAB DNA extractions of silica-dried and herbarium leaf tissues. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11522. [PMID: 37342163 PMCID: PMC10278933 DOI: 10.1002/aps3.11522] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/11/2023] [Indexed: 06/22/2023]
Abstract
Premise The use of cetyltrimethylammonium bromide (CTAB) is an effective and inexpensive method of extracting DNA from plants. The CTAB protocol is frequently modified to optimize DNA extractions, but experimental approaches rarely perturb a single variable at a time to systematically infer their effect on DNA quantity and quality. Methods and Results We investigated how chemical additives, incubation temperature, and lysis duration affected DNA quantity and quality. Altering those parameters influenced DNA concentrations and fragment lengths, but only extractant purity was significantly affected. CTAB and CTAB plus polyvinylpyrrolidone buffers produced the highest DNA quality and quantity. Extractions from silica gel-preserved tissues had significantly higher DNA yield, longer DNA fragments, and purer extractants compared to herbarium-preserved tissues. Conclusions We recommend DNA extractions of silica gel-preserved tissues that include a shorter and cooler lysis step, which results in purer extractions compared to a longer and hotter lysis step, while preventing fragmentation and reducing time.
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Affiliation(s)
- S. James Carey
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701‐2979USA
| | - L. Ellie Becklund
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701‐2979USA
| | - Paige P. Fabre
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701‐2979USA
| | - John J. Schenk
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701‐2979USA
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8
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Schenk JJ, Becklund LE, Carey SJ, Fabre PP. What is the "modified" CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11517. [PMID: 37342162 PMCID: PMC10278931 DOI: 10.1002/aps3.11517] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/22/2023]
Abstract
Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies.
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Affiliation(s)
- John J. Schenk
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
| | - L. Ellie Becklund
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
| | - S. James Carey
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
| | - Paige P. Fabre
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
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Skolotneva ES, Kosman E, Kelbin VN, Morozova EV, Laprina YV, Baranova OA, Kolomiets TM, Kiseleva MI, Sergeeva EM, Salina EA. SSR Variability of Stem Rust Pathogen on Spring Bread Wheat in Russia. PLANT DISEASE 2023; 107:493-499. [PMID: 36265157 DOI: 10.1094/pdis-10-22-2373-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, which used to be a harmful disease of winter wheat in the southern part of Russia, has been largely affecting the yield of spring bread wheat in the territories of the temperate climate zone since 2009. In total, 222 P. graminis f. sp. tritici isolates were obtained from samples of susceptible cultivars of spring bread wheat in Central and Volga regions and Omsk and Novosibirsk provinces in 2019. Genotyping of the isolates was carried out at 16 simple-sequence repeat (SSR) loci. Number of alleles, proportion of heterozygotes, and deviation from Hardy-Weinberg equilibrium were determined at each SSR locus. Based on genetic variability of SSR genotypes, it was shown that the P. graminis f. sp. tritici population is subdivided into two large clusters in the territory of the Russian temperate climate zone: the "European" population (the Central region) and the "Asian" one (the Volga region and two main wheat provinces of Western Siberia). Both of the P. graminis f. sp. tritici populations are characterized by a mixed mode of reproduction (sexual and clonal) but different sources of inoculum seem to shape a genotype structure within them. A group of P. graminis f. sp. tritici genotypes with high variability, the inbreeding coefficient closed to zero, and low observed heterozygosity was revealed among samples from Omsk. Moreover, two singular SSR genotypes identified among the Asian samples of P. graminis f. sp. tritici isolates should attract special attention in the monitoring of stem rust in order to disclose unexpected rapid changes of the pathogen in the corresponding regions and to prevent disease outbreak.
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Affiliation(s)
- Ekaterina S Skolotneva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Evsey Kosman
- Institute for Cereal Crops Research, School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vasiliy N Kelbin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Eugenia V Morozova
- Branch of Institute of Cytology and Genetics SB RAS, Siberian Research Institute of Plant Industry and Breeding, Krasnoobsk 630501, Russia
| | - Yulia V Laprina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga A Baranova
- All-Russian Institute of Plant Protection, St. Petersburg-Pushkin 196608, Russia
| | | | - Marina I Kiseleva
- All-Russian Research Institute of Phytopathology, Moscow 143050, Russia
| | - Ekaterina M Sergeeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Zhang H, Wafula EK, Eilers J, Harkess A, Ralph PE, Timilsena PR, dePamphilis CW, Waite JM, Honaas LA. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes. FRONTIERS IN PLANT SCIENCE 2022; 13:975942. [PMID: 36452099 PMCID: PMC9702816 DOI: 10.3389/fpls.2022.975942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/21/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.
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Affiliation(s)
- Huiting Zhang
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Eric K. Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jon Eilers
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Alex E. Harkess
- College of Agriculture, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Paula E. Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Claude W. dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jessica M. Waite
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Loren A. Honaas
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
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11
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Liu J, Jiang J, Guo X, Qian L, Xu J, Che Z, Chen G, Liu S. Sensitivity and Resistance Risk Assessment of Fusarium graminearum from Wheat to Prothioconazole. PLANT DISEASE 2022; 106:2097-2104. [PMID: 35171639 DOI: 10.1094/pdis-12-21-2684-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fusarium head blight (FHB), caused mainly by Fusarium graminearum, is one of the most devastating diseases of wheat. Prothioconazole is a broad-spectrum demethylation inhibitor fungicide with excellent efficacy against FHB. In this study, 235 strains of F. graminearum collected from different regions of Henan Province of China in 2016, 2017, and 2018 were randomly selected. The sensitivity of F. graminearum to prothioconazole was determined by the mycelial growth inhibition method. The results showed that the half maximal effective concentration (EC50) values of F. graminearum to prothioconazole ranged from 0.4742 to 3.4403 μg/ml, and the average EC50 value was 1.7758 ± 0.6667 μg/ml. The sensitivity frequency distribution presented a consequent unimodal curve, and thus the average EC50 value can be established as the baseline sensitivity of F. graminearum to prothioconazole. Ten strains of prothioconazole-resistant mutants were obtained by fungicide taming, and the resistance factor of the mutants ranged from 5.71 to 12.32. The genetic stability assay showed that resistance can be inherited stably for 10 generations. All mutants displayed different degrees of defects in vegetative growth, conidia formation, and pathogenicity compared with the parental strain. These results indicated that F. graminearum has a low risk of resistance to prothioconazole. Cross-resistance assay showed that no cross-resistance was found between prothioconazole and carbendazim, tebuconazole, phenamacril, and pydiflumetofen. Among all mutants, sequence analysis showed that no mutation site was found in cyp51A and cyp51B. Real-time PCR assays showed that the expression levels of cyp51A and cyp51B of the mutants were significantly increased after prothioconazole treatment for 24 h. In summary, our study provided a theoretical basis for the resistance risk assessment of F. graminearum to prothioconazole and scientific application of prothioconazole in controlling FHB.
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Affiliation(s)
- Jinliang Liu
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Jia Jiang
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Xuhao Guo
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Le Qian
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Jianqiang Xu
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Zhiping Che
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Genqiang Chen
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Shengming Liu
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
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12
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Ge C, Wentzel E, D'Souza N, Chen K, Oliver RP, Ellwood SR. Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad-spectrum resistance. THE PLANT GENOME 2021; 14:e20129. [PMID: 34392613 DOI: 10.1002/tpg2.20129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew isa major disease of barley (Hordeum vulgare L.) for which breeders have traditionally relied on dominant, pathogen race-specific resistance genes for genetic control. Directional selection pressures in extensive monocultures invariably result in such genes being overcome as the pathogen mutates to evade recognition. This has led to a widespread reliance on fungicides and a single broad-spectrum recessive resistance provided by the mlo gene. The range of resistance genes and alleles found in wild crop relatives and landraces has been reduced in agricultural cultivars through an erosion of genetic diversity during domestication and selective breeding. Three novel major-effect adult plant resistance (APR) genes from landraces, designated Resistance to Blumeria graminis f. sp. hordei (Rbgh1 to Rbgh3), were identified in the terminal regions of barley chromosomes 5HL, 7HS, and 1HS, respectively. The phenotype of the new APR genes showed neither pronounced penetration resistance, nor the spontaneous necrosis and mesophyll cell death typical of mlo resistance, nor a whole epidermal cell hypersensitive response, typical of race-specific resistance. Instead, resistance was localized to the site of attempted penetration in an epidermal cell and was associated with cell wall appositions and cytosolic vesicle-like bodies, and lacked strong induction of reactive oxygen species. The APR genes exhibited differences in vesicle-like body sizes, their distribution, and the extent of localized 3,3-diaminobenzidine staining in individual doubled haploid lines. The results revealed a set of unique basal penetration resistance genes that offer opportunities for combining different resistance mechanisms in breeding programs for robust mildew resistance.
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Affiliation(s)
- Cynthia Ge
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Elzette Wentzel
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Nola D'Souza
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Kefei Chen
- Statistics for the Australian Grains Industry-West, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Richard P Oliver
- School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
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13
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Valizadeh N, Holasou HA, Mohammadi SA, Khawar KM. A Comparison of Genomic DNA Extraction Protocols in Artemisia annua L. for Large Scale Genetic Analyses Studies. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2021. [DOI: 10.1007/s40995-021-01170-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels. Mol Phylogenet Evol 2021; 160:107123. [PMID: 33610647 DOI: 10.1016/j.ympev.2021.107123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 12/30/2022]
Abstract
Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.
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15
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Angthong P, Uengwetwanit T, Pootakham W, Sittikankaew K, Sonthirod C, Sangsrakru D, Yoocha T, Nookaew I, Wongsurawat T, Jenjaroenpun P, Rungrassamee W, Karoonuthaisiri N. Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform. PeerJ 2020; 8:e10340. [PMID: 33240651 PMCID: PMC7668203 DOI: 10.7717/peerj.10340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.
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Affiliation(s)
- Pacharaporn Angthong
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Tanaporn Uengwetwanit
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kanchana Sittikankaew
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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16
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Hale H, Gardner EM, Viruel J, Pokorny L, Johnson MG. Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11337. [PMID: 32351798 PMCID: PMC7186906 DOI: 10.1002/aps3.11337] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 05/19/2023]
Abstract
The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low-cost sequencing in non-model plant systems.
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Affiliation(s)
- Haley Hale
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Elliot M. Gardner
- The Morton ArboretumLisleIllinois60532USA
- Department of BiologyCase Western Reserve UniversityClevelandOhio44106USA
- Singapore Botanic GardensNational Parks Board1 Cluny Road259569Singapore
| | - Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Lisa Pokorny
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
- Present address:
Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIA28223Pozuelo de Alarcón (Madrid)Spain
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
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17
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Rodrigues KA, Rocha RT, Mulinari FF, Guedes AV, Teixeira MDM, Motta DDO, Fernandes L, Magalhães BS, Felipe MSS, Pappas GJ, Parachin NS. Exploring the Brazilian diversity of Aspergillus sp. strains for lovastatin and itaconic acid production. Fungal Genet Biol 2020; 138:103367. [PMID: 32198121 DOI: 10.1016/j.fgb.2020.103367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022]
Abstract
Filamentous fungi are well known for producing secondary metabolites applied in various industrial segments. Among these, lovastatin and itaconic acid, produced by Aspergillus terreus, have applications in the pharmaceutical and chemical industries. Lovastatin is primarily used for the control of hypercholesterolemia, while itaconic acid is a building block for the production of synthetic fibers, coating adhesives, among others. In this study, for the first time, 35 strains of Aspergillus sp. from four Brazilian culture collections were evaluated for lovastatin and itaconic acid production and compared to a reference strain, ATCC 20542. From an initial screening, the strains ATCC 20542, URM 224, URM1876, URM 5061, URM 5254, URM 5256, URM 5650, and URM 5961 were selected for genomic comparison. Among tested strains, the locus corresponding to the lovastatin genomic cluster was assembled, showing that all genes essential for lovastatin biosynthesis were present in producing URM 5961 and URM 5650 strains, with 100% and 98.5% similarity to ATCC 20542, respectively. However, in the no producing URM 1876, URM 224, URM 5254, URM 5061, and URM 5256 strains, this cluster was either fragmented or missing. Among the 35 strains evaluated for itaconic acid production in this study, only three strains had titers above 0.5 g/L, 16 strains had production below 0.5 g/L, and the remaining 18 strains had no production, with the highest production of itaconic acid observed in the URM 5254 strain with 2.2 g/L. The essential genes for itaconic acid production, mttA, cadA msfA were also mapped, where all three genes linked to itaconic acid production were found in a single contig in the assembly of each strain. In contrast to lovastatin loci, there is no correlation between the level of itaconic acid production and genetic polymorphisms in the genes associated with its biosynthesis.
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Affiliation(s)
- Kelly Assis Rodrigues
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil
| | - Rodrigo Theodoro Rocha
- Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Computational Genomics Group, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, CEP 70790-900, Brazil
| | - Flávia Furtado Mulinari
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Adevilton Viana Guedes
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Marcus de Melo Teixeira
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil; Faculdade de Medicina, Universidade de Medicina, Brasília, DF CEP 70910-900, Brazil
| | - Dielle de Oliveira Motta
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Larissa Fernandes
- Laboratório de Imunologia Aplicada, Instituto de Biologia, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Beatriz Simas Magalhães
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Maria Sueli Soares Felipe
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Georgios Joannis Pappas
- Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Computational Genomics Group, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, CEP 70790-900, Brazil
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil.
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18
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Hämälä T, Guiltinan MJ, Marden JH, Maximova SN, dePamphilis CW, Tiffin P. Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao. Mol Biol Evol 2020; 37:110-123. [PMID: 31501906 DOI: 10.1093/molbev/msz206] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Separating footprints of adaptation from demography is challenging. When selection has acted on a single locus with major effect, this issue can be alleviated through signatures left by selective sweeps. However, as adaptation is often driven by small allele frequency shifts at many loci, studies focusing on single genes are able to identify only a small portion of genomic variants responsible for adaptation. In face of this challenge, we utilize coexpression information to search for signals of polygenetic adaptation in Theobroma cacao, a tropical tree species that is the source of chocolate. Using transcriptomics and a weighted correlation network analysis, we group genes with similar expression patterns into functional modules. We then ask whether modules enriched for specific biological processes exhibit cumulative effects of differential selection in the form of high FST and dXY between populations. Indeed, modules putatively involved in protein modification, flowering, and water transport show signs of polygenic adaptation even though individual genes that are members of those groups do not bear strong signatures of selection. Modeling of demography, background selection, and the effects of genomic features reveal that these patterns are unlikely to arise by chance. We also find that specific modules are enriched for signals of strong or relaxed purifying selection, with one module bearing signs of adaptive differentiation and an excess of deleterious mutations. Our results provide insight into polygenic adaptation and contribute to understanding of population structure, demographic history, and genome evolution in T. cacao.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Mark J Guiltinan
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Siela N Maximova
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
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19
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González-Martínez S, Galindo-Sánchez C, López-Landavery E, Paniagua-Chávez C, Portillo-López A. Aspergillus loretoensis, a single isolate from marine sediment of Loreto Bay, Baja California Sur, México resulting as a new obligate halophile species. Extremophiles 2019; 23:557-568. [PMID: 31227903 DOI: 10.1007/s00792-019-01107-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/09/2019] [Indexed: 10/26/2022]
Abstract
An obligate halophile fungal was isolated from 275 m deep marine sediments and is characterized here for the first time. Its optimal growth was at 15% NaCl even though it was able to grow at 25% and is incapable of growth with no NaCl. Based on its morphological characteristics as conidia chain production in a single phialide, the fungal is related to the genus Aspergillus, subgenus Polypaecilum. Phylogenetic molecular analysis using several markers (ITS1-2; RPB1; RPB2; Cct8; TSR1; CaM; BenA) places the fungal isolate closer to Aspergillus salinarus and A. baarnensis. However, its morphological and molecular differences establish it as a new species, Aspergillus loretoensis sp. nov.
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Affiliation(s)
- Sophia González-Martínez
- Facultad de Ciencias, Universidad Autónoma de Baja California, Km 103, Carretera Tijuana-Ensenada, Ensenada, 22860, Baja California, Mexico
| | - Clara Galindo-Sánchez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, 22860, Baja California, Mexico
| | - Edgar López-Landavery
- Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, 22860, Baja California, Mexico
| | - Carmen Paniagua-Chávez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, 22860, Baja California, Mexico
| | - Amelia Portillo-López
- Facultad de Ciencias, Universidad Autónoma de Baja California, Km 103, Carretera Tijuana-Ensenada, Ensenada, 22860, Baja California, Mexico.
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20
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Johnson G. High throughput DNA extraction of legume root nodules for rhizobial metagenomics. AMB Express 2019; 9:47. [PMID: 30969386 PMCID: PMC6458200 DOI: 10.1186/s13568-019-0771-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022] Open
Abstract
A novel combination of tissue homogenization, cell lysis, and DNA purification techniques was developed for isolating total DNA from whole legume root nodules on an automated robotic system. Silica dehydrated root nodules from soy bean, Glycine max cv. Tara, and mung bean, Vigna radiata cv. Crystal, were homogenized in 96-well plates and were enzymatically and chemically lysed before being loaded into the AutoGenprep 965 for automated phenol–chloroform based DNA isolation. The resulting DNAs were of relatively high concentration, low fragmentation, and free of phenolic and polysaccharide contaminants. In contrast to manual methods, this adaptation of the Autogen Prep automated DNA extraction instrument allows for 100’s to 1000’s of samples to be prepared in a fraction of the time and cost.
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21
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Safi H, Belgaroui N, Masmoudi K, Brini F. Promoter of the wheat lipid transfer protein, TdLTP4, drives leaf-preferential expression in transgenic Arabidopsis plants. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:275-285. [PMID: 32172770 DOI: 10.1071/fp18040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 10/15/2018] [Indexed: 06/10/2023]
Abstract
In a previous report, a gene encoding a durum wheat lipid transfer protein, TdLTP4, was characterised as induced by abiotic and biotic stresses. In the present work, we investigated the regulation of the gene TdLTP4. A TdLTP4 promoter (PrTdLTP4) region of around 868-bp was isolated and sequenced. Its analysis revealed the presence of several DNA boxes known to be important mainly in the regulation of genes expressed under abiotic stress (salt and dehydration), abscisic acid (ABA) and pathogen responsiveness. The whole PrTdLTP4 fragment was fused to the reporter gene β-glucuronidase (gusA) and analysed in transgenic Arabidopsis plants. Histochemical assays of transgenic Arabidopsis plants showed that the 868-bp fragment of TdLTP4 gene promoter was found to be sufficient for both spatial and temporal patterns of its expression. Under control conditions, GUS histochemical staining was observed significantly only in young leaves of 8- and 12-day-old plants. Whereas after stress challenge especially with NaCl and mannitol, GUS transcripts expression increased substantially in leaves of 30-day-old transgenic seedlings. Real-time qPCR expression analysis of the gusA gene, confirmed the results of histochemical assays. Taken together these data provide evidence that PrTdLTP4 functions as abiotic-stress-inducible promoter in a heterologous dicot system and could be an excellent tool for future crop improvement.
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Affiliation(s)
- Héla Safi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, BP '1177' 3018, Sfax - Tunisia
| | - Nebras Belgaroui
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, BP '1177' 3018, Sfax - Tunisia
| | - Khaled Masmoudi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, BP '1177' 3018, Sfax - Tunisia
| | - Faiçal Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, BP '1177' 3018, Sfax - Tunisia
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22
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Ahmed B, Khan MS, Musarrat J. Toxicity assessment of metal oxide nano-pollutants on tomato (Solanum lycopersicon): A study on growth dynamics and plant cell death. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 240:802-816. [PMID: 29783198 DOI: 10.1016/j.envpol.2018.05.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 05/20/2023]
Abstract
The present study for the first time demonstrated the interactions of metal oxide (MO) nano-pollutants (CuO and Al2O3-NPs) with tissues and cellular DNA of tomato plants grown in soil sand: silt: clay (667:190:143) and Hoagland-hydroponic system and assessed the hazardous effects of NPs on cell physiology and biochemistry. Results of SEM equipped with EDX revealed attachment of variably shaped CuO-NPs (18 nm) and Al2O3-NPs (21 nm) on roots, and internalization followed by translocation in plants by ICP-MS and TEM. Significant variations in foliage surface area, chlorophyll, proteins, LPO, and antioxidant enzymes were recorded. Roots and shoots accumulated 225.8 ± 8.9 and 70.5 ± 4 μgAl g-1 DW, whereas Cu accumulation was 341.6 ± 14.3 (roots) and 146.9 ± 8.1 μg g-1 DW (shoots) which was significant (p ≤ 0.0005) as compared to control. The total soluble protein content in roots, shoots, and leaves collected from Al2O3-NPs treated plants increased by 120, 80, and 132%, respectively while in CuO-NPs treatments, the increase was 68 (roots), 36 (shoots), and 86% (leaves) over control. The level of antioxidant enzymes in plant tissues was significantly (p ≤ 0.05) higher at 2000 μg ml-1 of MONPs over control. A dose-dependent increase in reactive oxygen species (ROS), biphasic change of lower and higher fluorescence in mitochondria due to dissipation of mitochondrial membrane potential (ΔΨm) and membrane defects using propidium iodide were observed. Comparatively, CuO-NPs induced higher toxicity than Al2O3-NPs. Perceptible changes in proteins (amide-I & II), cellulose, glucose, galactose and other carbohydrates were observed under FT-IR. The binding studies with TmDNA showed fluorescence quenching of EtBr-TmDNA and acridine orange-TmDNA complex only by CuO-NPs with -ΔG and +ΔH and +ΔS values. However, Al2O3-NPs induced lesser change in TmDNA conformation. Conclusively, the results are novel in better demonstrating the mechanistic basis of nano-phyto-toxicity and are important which could be used to develop strategies for safe disposal of Al2O3-NPs and CuO-NPs.
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Affiliation(s)
- Bilal Ahmed
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India.
| | - Mohammad Saghir Khan
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - Javed Musarrat
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India; School of Biosciences and Biodiversity, Baba Ghulam Shah Badshah University, Rajouri, J & K, India
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23
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Tounsi S, Feki K, Saïdi MN, Maghrebi S, Brini F, Masmoudi K. Promoter of the TmHKT1;4-A1 gene of Triticum monococcum directs stress inducible, developmental regulated and organ specific gene expression in transgenic Arbidopsis thaliana. World J Microbiol Biotechnol 2018; 34:99. [DOI: 10.1007/s11274-018-2485-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/16/2018] [Indexed: 11/30/2022]
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24
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Syme RA, Martin A, Wyatt NA, Lawrence JA, Muria-Gonzalez MJ, Friesen TL, Ellwood SR. Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host-Pathogen Genetic Interactions. Front Genet 2018; 9:130. [PMID: 29720997 PMCID: PMC5915480 DOI: 10.3389/fgene.2018.00130] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
Pyrenophora teres, P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes. Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. PTT has a longer cultivated host association and, notably, a greater range of host-pathogen genetic interactions compared to other Pyrenophora spp., a property which associates better with genome size than pathogen lifestyle. The two forms possess similar complements of TE families with Tc1/Mariner and LINE-like Tad-1 elements more abundant in PTT. Tad-1 was only detectable as vestigial fragments in PTM and, within the forms, differences in genome sizes and the presence and absence of several TE families indicated recent lineage invasions. Gene differences between P. teres forms are mainly associated with gene-sparse regions near or within TE-rich regions, with many genes possessing characteristics of fungal effectors. Instances of gene interruption by transposons resulting in pseudogenization were detected in PTT. In addition, both forms have a large complement of secondary metabolite gene clusters indicating significant capacity to produce an array of different molecules. This study provides genomic resources for functional genetics to help dissect factors underlying the host-pathogen interactions.
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Affiliation(s)
- Robert A. Syme
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Nathan A. Wyatt
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Julie A. Lawrence
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Mariano J. Muria-Gonzalez
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Timothy L. Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Simon R. Ellwood
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
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25
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Simplified methodology for large scale isolation of homozygous transgenic lines of lettuce. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Osorio-Guarín JA, Berdugo-Cely J, Coronado RA, Zapata YP, Quintero C, Gallego-Sánchez G, Yockteng R. Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L. FRONTIERS IN PLANT SCIENCE 2017; 8:1994. [PMID: 29209353 PMCID: PMC5702303 DOI: 10.3389/fpls.2017.01994] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 05/17/2023]
Abstract
Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world's production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica's cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao's breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica's germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica's collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica's collection showed highest genetic diversity [Expected Heterozygosity (HE = 0.314), Observed Heterozygosity (HO = 0.353)] that is reduced when reference populations were included in the dataset (HE = 0.294, HO = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.
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Affiliation(s)
- Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria – Corpoica, Cundinamarca, Colombia
| | - Jhon Berdugo-Cely
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria – Corpoica, Cundinamarca, Colombia
| | - Roberto Antonio Coronado
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria – Corpoica, Cundinamarca, Colombia
| | | | | | | | - Roxana Yockteng
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria – Corpoica, Cundinamarca, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
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27
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DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods. Appl Microbiol Biotechnol 2017; 101:8077-8088. [PMID: 28942548 DOI: 10.1007/s00253-017-8493-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/11/2017] [Accepted: 08/30/2017] [Indexed: 12/12/2022]
Abstract
This review covers a developmental progression on early to modern taxonomy at cellular level following the advent of electron microscopy and the advancement in deoxyribonucleic acid (DNA) extraction for expatiation of biological classification at DNA level. Here, we discuss the fundamental values of conventional chemical methods of DNA extraction using liquid/liquid extraction (LLE) followed by development of solid-phase extraction (SPE) methods, as well as recent advances in microfluidics device-based system for DNA extraction on-chip. We also discuss the importance of DNA extraction as well as the advantages over conventional chemical methods, and how Lab-on-a-Chip (LOC) system plays a crucial role for the future achievements.
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28
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Corcoll N, Österlund T, Sinclair L, Eiler A, Kristiansson E, Backhaus T, Eriksson KM. Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing. FEMS Microbiol Lett 2017; 364:3898816. [DOI: 10.1093/femsle/fnx139] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/27/2017] [Indexed: 01/07/2023] Open
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29
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Cunha NBD, Barbosa AEADD, de Almeida RG, Porto WF, Maximiano MR, Álvares LCS, Munhoz CBR, Eugênio CUO, Viana AAB, Franco OL, Dias SC. Cloning and characterization of novel cyclotides genes from South American plants. Biopolymers 2017; 106:784-795. [PMID: 27554590 DOI: 10.1002/bip.22938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 08/10/2016] [Accepted: 08/21/2016] [Indexed: 01/06/2023]
Abstract
Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and establishing heterologous expression strategies, but also to understand local plant evolution in the context of host-pathogen relationships. Here, two species from the Brazilian Cerrado, Palicourea rigida (Rubiaceae) and Pombalia lanata (A.St.-Hil.) Paula-Souza (Violaceae), were used for cloning and characterizing novel cyclotide genes. Using 3' and 5' RACE PCR and sequencing, two full cDNAs, named parigidin-br2 (P. rigida) and hyla-br1 (P. lanata), were isolated and shown to have similar genetic structures to other cyclotides. Both contained the conserved ER-signal domain, N-terminal prodomain, mature cyclotide domain and a C-terminal region. Genomic sequencing of parigidin-br2 revealed two different gene copies: one intronless allele and one presenting a rare 131-bp intron. In contrast, genomic sequencing of hyla-br1 revealed an intronless gene-a common characteristic of members of the Violaceae family. Parigidin-br2 5' and 3' UTRs showed the presence of 12 putative candidate sites for binding of regulatory proteins, suggesting that the flanking and intronic regions of the parigidin-br2 gene must play important roles in transcriptional rates and in the regulation of temporal and spatial gene expression. The high degree of genetic similarity and structural organization among the cyclotide genes isolated in the present study from the Brazilian Cerrado and other well-characterized plant cyclotides may contribute to a better understanding of cyclotide evolution.
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Affiliation(s)
- Nicolau Brito da Cunha
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | | | - Renato Goulart de Almeida
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - William Farias Porto
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Mariana Rocha Maximiano
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Luana Cristina Silva Álvares
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Cassia Beatriz Rodrigues Munhoz
- Departamento de Botânica, Instituto de Ciências Biológicas. Bloco D. Universidade de Brasília. Campus Darcy Ribeiro 70904-970, Asa Norte. Brasília, DF, Brazil
| | - Chesterton Ulysses Orlando Eugênio
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Antônio Américo Barbosa Viana
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Octavio Luiz Franco
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil.,S-Inova Biotech, Pós Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Simoni Campos Dias
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
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30
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Farr DF, Elliott M, Rossman AY, Edmonds RL. Fusicoccum arbutisp. nov. causing cankers on Pacific madrone in western North America with notes onFusicoccum dimidiatum,the correct name forScytalidium dimidiatumandNattrassia mangiferae. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832803] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- David F. Farr
- Systematic Botany & Mycology Laboratory, USDA Agricultural Research Service, Room 304, B011a, 10300 Baltimore Ave., Beltsville, Maryland 20705
| | - Marianne Elliott
- College of Forest Resources, University of Washington, Seattle, Washington 98195
| | - Amy Y. Rossman
- Systematic Botany & Mycology Laboratory, USDA Agricultural Research Service, Room 304, B011a, 10300 Baltimore Ave., Beltsville, Maryland 20705
| | - Robert L. Edmonds
- College of Forest Resources, University of Washington, Seattle, Washington 98195
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31
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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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32
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Ploch S, Rose LE, Bass D, Bonkowski M. High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae. J Eukaryot Microbiol 2016; 63:635-41. [PMID: 27005328 PMCID: PMC5031217 DOI: 10.1111/jeu.12314] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/20/2016] [Accepted: 03/12/2016] [Indexed: 02/06/2023]
Abstract
The largest biological surface on earth is formed by plant leaves. These leaf surfaces are colonized by a specialized suite of leaf-inhabiting microorganisms, recently termed "phyllosphere microbiome". Microbial prey, however, attract microbial predators. Protists in particular have been shown to structure bacterial communities on plant surfaces, but virtually nothing is known about the community composition of protists on leaves. Using newly designed specific primers targeting the 18S rDNA gene of Cercozoa, we investigated the species richness of this common protist group on leaves of four Brassicaceae species from two different locations in a cloning-based approach. The generated sequences revealed a broad diversity of leaf-associated Cercozoa, mostly bacterial feeders, but also including known plant pathogens and a taxon of potential endophytes that were recently described as algal predators in freshwater systems. This initial study shows that protists must be regarded as an integral part of the microbial diversity in the phyllosphere of plants.
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Affiliation(s)
- Sebastian Ploch
- Institute of Population Genetics, Cluster of Excellence in Plant Sciences, University of Düsseldorf, Universitätsstr. 1, D-40225, Düsseldorf, Germany
- Senckenberg Biodiversity and Climate Research Center, Georg-Voigt-Street 14-16, D-60325, Frankfurt, Germany
| | - Laura E Rose
- Institute of Population Genetics, Cluster of Excellence in Plant Sciences, University of Düsseldorf, Universitätsstr. 1, D-40225, Düsseldorf, Germany
| | - David Bass
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, United Kingdom
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, United Kingdom
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Street 47b, D-50674, Köln, Germany
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33
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Athanasio CG, Chipman JK, Viant MR, Mirbahai L. Optimisation of DNA extraction from the crustacean Daphnia. PeerJ 2016; 4:e2004. [PMID: 27190714 PMCID: PMC4867708 DOI: 10.7717/peerj.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
Daphnia are key model organisms for mechanistic studies of phenotypic plasticity, adaptation and microevolution, which have led to an increasing demand for genomics resources. A key step in any genomics analysis, such as high-throughput sequencing, is the availability of sufficient and high quality DNA. Although commercial kits exist to extract genomic DNA from several species, preparation of high quality DNA from Daphnia spp. and other chitinous species can be challenging. Here, we optimise methods for tissue homogenisation, DNA extraction and quantification customised for different downstream analyses (e.g., LC-MS/MS, Hiseq, mate pair sequencing or Nanopore). We demonstrate that if Daphnia magna are homogenised as whole animals (including the carapace), absorbance-based DNA quantification methods significantly over-estimate the amount of DNA, resulting in using insufficient starting material for experiments, such as preparation of sequencing libraries. This is attributed to the high refractive index of chitin in Daphnia's carapace at 260 nm. Therefore, unless the carapace is removed by overnight proteinase digestion, the extracted DNA should be quantified with fluorescence-based methods. However, overnight proteinase digestion will result in partial fragmentation of DNA therefore the prepared DNA is not suitable for downstream methods that require high molecular weight DNA, such as PacBio, mate pair sequencing and Nanopore. In conclusion, we found that the MasterPure DNA purification kit, coupled with grinding of frozen tissue, is the best method for extraction of high molecular weight DNA as long as the extracted DNA is quantified with fluorescence-based methods. This method generated high yield and high molecular weight DNA (3.10 ± 0.63 ng/µg dry mass, fragments >60 kb), free of organic contaminants (phenol, chloroform) and is suitable for large number of downstream analyses.
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Affiliation(s)
| | - James K Chipman
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
| | - Mark R Viant
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
| | - Leda Mirbahai
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
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34
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Wang HM, To KY, Lai HM, Jeng ST. Modification of flower colour by suppressing β-ring carotene hydroxylase genes in Oncidium. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:220-9. [PMID: 26404515 DOI: 10.1111/plb.12399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/17/2015] [Indexed: 05/20/2023]
Abstract
Oncidium 'Gower Ramsey' (Onc. GR) is a popular cut flower, but its colour is limited to bright yellow. The β-ring carotene hydroxylase (BCH2) gene is involved in carotenoid biogenesis for pigment formation. However, the role of BCH2 in Onc. GR is poorly understood. Here, we investigated the functions of three BCH2 genes, BCH-A2, BCH-B2 and BCH-C2 isolated from Onc. GR, to analyse their roles in flower colour. RT-PCR expression profiling suggested that BCH2 was mainly expressed in flowers. The expression of BCH-B2 remained constant while that of BCH-A2 gradually decreased during flower development. Using Agrobacterium tumefaciens to introduce BCH2 RNA interference (RNAi), we created transgenic Oncidium plants with down-regulated BCH expression. In the transgenic plants, flower colour changed from the bright yellow of the wild type to light and white-yellow. BCH-A2 and BCH-B2 expression levels were significantly reduced in the transgenic flower lips, which make up the major portion of the Oncidium flower. Sectional magnification of the flower lip showed that the amount of pigmentation in the papillate cells of the adaxial epidermis was proportional to the intensity of yellow colouration. HPLC analyses of the carotenoid composition of the transgenic flowers suggested major reductions in neoxanthin and violaxanthin. In conclusion, BCH2 expression regulated the accumulation of yellow pigments in the Oncidium flower, and the down-regulation of BCH-A2 and BCH-B2 changed the flower colour from bright yellow to light and white-yellow.
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Affiliation(s)
- H-M Wang
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - K-Y To
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - H-M Lai
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - S-T Jeng
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
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de Oliveira RS, Oliveira-Neto OB, Moura HFN, de Macedo LLP, Arraes FBM, Lucena WA, Lourenço-Tessutti IT, de Deus Barbosa AA, da Silva MCM, Grossi-de-Sa MF. Transgenic Cotton Plants Expressing Cry1Ia12 Toxin Confer Resistance to Fall Armyworm (Spodoptera frugiperda) and Cotton Boll Weevil (Anthonomus grandis). FRONTIERS IN PLANT SCIENCE 2016; 7:165. [PMID: 26925081 PMCID: PMC4759279 DOI: 10.3389/fpls.2016.00165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/31/2016] [Indexed: 05/21/2023]
Abstract
Gossypium hirsutum (commercial cooton) is one of the most economically important fibers sources and a commodity crop highly affected by insect pests and pathogens. Several transgenic approaches have been developed to improve cotton resistance to insect pests, through the transgenic expression of different factors, including Cry toxins, proteinase inhibitors, and toxic peptides, among others. In the present study, we developed transgenic cotton plants by fertilized floral buds injection (through the pollen-tube pathway technique) using an DNA expression cassette harboring the cry1Ia12 gene, driven by CaMV35S promoter. The T0 transgenic cotton plants were initially selected with kanamycin and posteriorly characterized by PCR and Southern blot experiments to confirm the genetic transformation. Western blot and ELISA assays indicated the transgenic cotton plants with higher Cry1Ia12 protein expression levels to be further tested in the control of two major G. hirsutum insect pests. Bioassays with T1 plants revealed the Cry1Ia12 protein toxicity on Spodoptera frugiperda larvae, as evidenced by mortality up to 40% and a significant delay in the development of the target insects compared to untransformed controls (up to 30-fold). Also, an important reduction of Anthonomus grandis emerging adults (up to 60%) was observed when the insect larvae were fed on T1 floral buds. All the larvae and adult insect survivors on the transgenic lines were weaker and significantly smaller compared to the non-transformed plants. Therefore, this study provides GM cotton plant with simultaneous resistance against the Lepidopteran (S. frugiperda), and the Coleopteran (A. grandis) insect orders, and all data suggested that the Cry1Ia12 toxin could effectively enhance the cotton transgenic plants resistance to both insect pests.
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Affiliation(s)
- Raquel S. de Oliveira
- Catholic University of BrasiliaBrasilia, Brazil
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
| | - Osmundo B. Oliveira-Neto
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
- UNIEURO – University CenterBrasília, Brazil
| | - Hudson F. N. Moura
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
- Biology Institute, Brasilia UniversityBrasilia, Brazil
| | - Leonardo L. P. de Macedo
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
| | - Fabrício B. M. Arraes
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
- Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Wagner A. Lucena
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
- Embrapa CottonCampina Grande, Brazil
| | - Isabela T. Lourenço-Tessutti
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
| | - Aulus A. de Deus Barbosa
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
| | - Maria C. M. da Silva
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
| | - Maria F. Grossi-de-Sa
- Catholic University of BrasiliaBrasilia, Brazil
- Pest-Plant Molecular Interaction Laboratory, Embrapa Genetic Resources and Biotechnology, Brazilian Research Agricultural CorporationBrasilia, Brazil
- *Correspondence: Maria F. Grossi-de-Sa,
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Lalhmangaihi R, Ghatak S, Laha R, Gurusubramanian G, Kumar NS. Protocol for optimal quality and quantity pollen DNA isolation from honey samples. J Biomol Tech 2014; 25:92-5. [PMID: 25365793 DOI: 10.7171/jbt.14-2504-001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The present study illustrates an optimized sample preparation method for an efficient DNA isolation from low quantities of honey samples. A conventional PCR-based method was validated, which potentially enables characterization of plant species from as low as 3 ml bee-honey samples. In the present study, an anionic detergent was used to lyse the hard outer pollen shell, and DTT was used for isolation of thiolated DNA, as it might facilitate protein digestion and assists in releasing the DNA into solution, as well as reduce cross-links between DNA and other biomolecules. Optimization of both the quantity of honey sample and time duration for DNA isolation was done during development of this method. With the use of this method, chloroplast DNA was successfully PCR amplified and sequenced from honey DNA samples.
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Moeller JR, Moehn NR, Waller DM, Givnish TJ. Paramagnetic cellulose DNA isolation improves DNA yield and quality among diverse plant taxa. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400048. [PMID: 25309836 PMCID: PMC4189495 DOI: 10.3732/apps.1400048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/25/2014] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY The chemical diversity of land plants ensures that no single DNA isolation method results in high yield and purity with little effort for all species. Here we evaluate a new technique originally developed for forensic science, based on MagnaCel paramagnetic cellulose particles (PMC), to determine its efficacy in extracting DNA from 25 plant species representing 21 families and 15 orders. • METHODS AND RESULTS Yield and purity of DNA isolated by PMC, DNeasy Plant Mini Kit (silica column), and cetyltrimethylammonium bromide (CTAB) methods were compared among four individuals for each of 25 plant species. PMC gave a twofold advantage in average yield, and the relative advantage of the PMC method was greatest for samples with the lowest DNA yields. PMC also produced more consistent sample purity based on absorbance ratios at 260:280 and 260:230 nm. • CONCLUSIONS PMC technology is a promising alternative for plant DNA isolation.
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Affiliation(s)
- Jackson R. Moeller
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Drive, Madison, Wisconsin 53706 USA
| | - Nicholas R. Moehn
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Drive, Madison, Wisconsin 53706 USA
| | - Donald M. Waller
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Drive, Madison, Wisconsin 53706 USA
| | - Thomas J. Givnish
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Drive, Madison, Wisconsin 53706 USA
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Feki K, Brini F, Ben Amar S, Saibi W, Masmoudi K. Comparative functional analysis of two wheat Na+/H+ antiporter SOS1 promoters in Arabidopsis thaliana under various stress conditions. J Appl Genet 2014; 56:15-26. [DOI: 10.1007/s13353-014-0228-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/03/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
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Ayadi M, Mieulet D, Fabre D, Verdeil JL, Vernet A, Guiderdoni E, Masmoudi K. Functional analysis of the durum wheat gene TdPIP2;1 and its promoter region in response to abiotic stress in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 79:98-108. [PMID: 24704987 DOI: 10.1016/j.plaphy.2014.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 02/22/2014] [Indexed: 06/03/2023]
Abstract
In a previous work, we demonstrated that expression of TdPIP2;1 in Xenopus oocytes resulted in an increase in Pf compared to water injected oocytes. Phenotypic analyses of transgenic tobacco plants expressing TdPIP2;1 generated a tolerance phenotype towards drought and salinity stresses. To elucidate its stress tolerance mechanism at the transcriptional level, we isolated and characterized the promoter region of the TdPIP2;1 gene. A 1060-bp genomic fragment upstream of the TdPIP2;1 translated sequence has been isolated, cloned, and designated as the proTdPIP2;1 promoter. Sequence analysis of proTdPIP2;1 revealed the presence of cis regulatory elements which could be required for abiotic stress responsiveness, for tissue-specific and vascular expression. The proTdPIP2;1 promoter was fused to the β-glucuronidase (gusA) gene and the resulting construct was transferred into rice (cv. Nipponbare). Histochemical analysis of proTdPIP2;1::Gus in rice plants revealed that the GUS activity was observed in leaves, stems and roots of stably transformed rice T3 plants. Histological sections prepared revealed accumulation of GUS products in phloem, xylem and in some cells adjacent to xylem. The transcripts were up-regulated by dehydration. Transgenic rice plants overexpressing proTdPIP2;1 in fusion with TdPIP2;1, showed enhanced drought tolerance, while wild type plants were more sensitive and exhibited symptoms of wilting and chlorosis. These findings suggest that expression of the TdPIP2;1 gene regulated by its own promoter achieves enhanced drought tolerance in rice.
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Affiliation(s)
- Malika Ayadi
- Plant Protection and Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, Route Sidi Mansour Km 6, B.P "1177", 3018 Sfax, Tunisia
| | | | - Denis Fabre
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | | | | | | | - Khaled Masmoudi
- Plant Protection and Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, Route Sidi Mansour Km 6, B.P "1177", 3018 Sfax, Tunisia; ICBA, P.O. Box 14660, Dubai, United Arab Emirates.
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Nagori R, Sharma P, Habibi N, Purohit SD. An Efficient Genomic DNA Extraction Protocol for Molecular Analysis in Annona reticulata. NATIONAL ACADEMY SCIENCE LETTERS-INDIA 2014. [DOI: 10.1007/s40009-013-0213-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J. "A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids". BMC Genomics 2013; 14:683. [PMID: 24094114 PMCID: PMC3852598 DOI: 10.1186/1471-2164-14-683] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 09/24/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213-217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety 'Pisang Klutuk Wulung' (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation. RESULTS The resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids. CONCLUSIONS We have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.
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Affiliation(s)
- Mark W Davey
- Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium
| | - Ranganath Gudimella
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Lee Wan Sin
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Norzulaani Khalid
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Johan Keulemans
- Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium
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Henderson DC, Hammond J. CKC: isolation of nucleic acids from a diversity of plants using CTAB and silica columns. Mol Biotechnol 2013; 53:109-17. [PMID: 22271458 DOI: 10.1007/s12033-012-9494-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To assay for viruses in plant samples, we required a method for nucleic acid isolation that is rapid, simple, and applicable to the widest possible variety of plants. A protocol for isolation of total nucleic acid (TNA) was developed by combining common CTAB methods with silica spin columns. We report data on TNA purity and RNA quality from over 30 plant genera representing 25 families. Measurements showed that RNA is of high quality, and one-step RT-PCR was successfully performed on all samples. The protocol can be completed in less than 2 h.
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Affiliation(s)
- David C Henderson
- USDA-ARS, United States National Arboretum, Floral and Nursery Plants Research Unit, B-010A, Beltsville, MD 20705, USA.
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Sairkar P, Chouhan S, Batav N, Sharma R. Optimization of DNA isolation process and enhancement of RAPD PCR for low quality genomic DNA of Terminalia arjuna. J Genet Eng Biotechnol 2013. [DOI: 10.1016/j.jgeb.2013.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sahu SK, Thangaraj M, Kathiresan K. DNA Extraction Protocol for Plants with High Levels of Secondary Metabolites and Polysaccharides without Using Liquid Nitrogen and Phenol. ISRN MOLECULAR BIOLOGY 2012; 2012:205049. [PMID: 27335662 PMCID: PMC4890884 DOI: 10.5402/2012/205049] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/18/2012] [Indexed: 11/23/2022]
Abstract
Mangroves and salt marsh species are known to synthesize a wide spectrum of polysaccharides and polyphenols including flavonoids and other secondary metabolites which interfere with the extraction of pure genomic DNA. Although a plethora of plant DNA isolation protocols exist, extracting DNA from mangroves and salt marsh species is a challenging task. This study describes a rapid and reliable cetyl trimethylammonium bromide (CTAB) protocol suited specifically for extracting DNA from plants which are rich in polysaccharides and secondary metabolites, and the protocol also excludes the use of expensive liquid nitrogen and toxic phenols. Purity of extracted DNA was excellent as evident by A260/A280 ratio ranging from 1.78 to 1.84 and A260/A230 ratio was >2, which also suggested that the preparations were sufficiently free of proteins and polyphenolics/polysaccharide compounds. DNA concentration ranged from 8.8 to 9.9 μg μL(-1). The extracted DNA was amenable to RAPD, restriction digestion, and PCR amplification of plant barcode genes (matK and rbcl). The optimized method is suitable for both dry and fresh leaves. The success of this method in obtaining high-quality genomic DNA demonstrated the broad applicability of this method.
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Affiliation(s)
- Sunil Kumar Sahu
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Tamil Nadu, Parangipettai 608 502, India
| | - Muthusamy Thangaraj
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Tamil Nadu, Parangipettai 608 502, India
| | - Kandasamy Kathiresan
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Tamil Nadu, Parangipettai 608 502, India
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Yu B, Gruber MY, Khachatourians GG, Zhou R, Epp DJ, Hegedus DD, Parkin IAP, Welsch R, Hannoufa A. Arabidopsis cpSRP54 regulates carotenoid accumulation in Arabidopsis and Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5189-202. [PMID: 22791829 PMCID: PMC3430994 DOI: 10.1093/jxb/ers179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
An Arabidopsis thaliana mutant, cbd (carotenoid biosynthesis deficient), was recovered from a mutant population based on its yellow cotyledons, yellow-first true leaves, and stunted growth. Seven-day-old seedlings and mature seeds of this mutant had lower chlorophyll and total carotenoids than the wild type (WT). Genetic and molecular characterization revealed that cbd was a recessive mutant caused by a T-DNA insertion in the gene cpSRP54 encoding the 54 kDa subunit of the chloroplast signal recognition particle. Transcript levels of most of the main carotenoid biosynthetic genes in cbd were unchanged relative to WT, but expression increased in carotenoid and abscisic acid catabolic genes. The chloroplasts of cbd also had developmental defects that contributed to decreased carotenoid and chlorophyll contents. Transcription of AtGLK1 (Golden 2-like 1), AtGLK2, and GUN4 appeared to be disrupted in the cbd mutant suggesting that the plastid-to-nucleus retrograde signal may be affected, regulating the changes in chloroplast functional and developmental states and carotenoid content flux. Transformation of A. thaliana and Brassica napus with a gDNA encoding the Arabidopsis cpSRP54 showed the utility of this gene in enhancing levels of seed carotenoids without affecting growth or seed yield.
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Affiliation(s)
- Bianyun Yu
- Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK, S7N 0X2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Margaret Y. Gruber
- Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK, S7N 0X2, Canada
- To whom correspondence should be addressed: E-mail:
and
| | - George G. Khachatourians
- Department of Food and Bioproduct Sciences, University of Saskatchewan51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Rong Zhou
- Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Delwin J. Epp
- Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Dwayne D. Hegedus
- Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Ralf Welsch
- Institute for Biology II, Cell BiologySchaenzlestr. 1, 79104 Freiburg, Germany
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada1391 Sandford Street, London, ON, N5V 4T3, Canada
- To whom correspondence should be addressed: E-mail:
and
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How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS One 2012; 7:e43808. [PMID: 22952770 PMCID: PMC3429509 DOI: 10.1371/journal.pone.0043808] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/26/2012] [Indexed: 11/19/2022] Open
Abstract
Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplification success as measured by using three differentially sized markers, the rbcL barcoding marker (cpDNA), the LEAFY exon 3 (nrDNA), and the trnL(UAA) P6 loop (cpDNA). Results reveal large differences between extraction methods, where DNA purity rather than yield is shown to be strongly correlated with PCR success. Amplicon size shows similarly strong correlation with PCR success, with the shortest fragment showing the highest success rate (78%, P6 loop, 10–143 base pairs (bp)) and the largest fragment the lowest success (10%, rbcL, 670 bp). The effect of specimen preparation method on PCR success was also tested. Results show that drying method strongly affects PCR success, especially the availability of fragments longer than 250 bp, where longer fragments are more available for PCR amplification in air dried material compared to alcohol dried specimens. Results from our study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions (<200–300 bp) in order to maximise outcomes. Development of shorter barcoding regions, or mini-barcodes within existing ones should be of high importance as only a few options are currently available; this is particularly important if we hope to incorporate the millions of herbarium samples available into barcoding initiatives and other molecular studies.
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Xin Z, Chen J. A high throughput DNA extraction method with high yield and quality. PLANT METHODS 2012; 8:26. [PMID: 22839646 PMCID: PMC3441248 DOI: 10.1186/1746-4811-8-26] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/20/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome), and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L.) Moench] leaves and dry seeds with high yield, high quality, and affordable cost. RESULTS We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. CONCLUSION A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.
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Affiliation(s)
- Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, 3810 4th Street, Lubbock, TX, 79415, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, 3810 4th Street, Lubbock, TX, 79415, USA
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Ganesan G, Sankararamasubramanian HM, Harikrishnan M, Ganpudi A, Ashwin G, Parida A. A MYB transcription factor from the grey mangrove is induced by stress and confers NaCl tolerance in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4549-61. [PMID: 22904269 DOI: 10.1093/jxb/ers135] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
MYB transcription factor genes play important roles in developmental and various other processes in plants. In this study, functional characterization of AmMYB1, a single-repeat MYB transcription factor isolated from the salt-tolerant mangrove tree Avicennia marina is reported. AmMYB1 cDNA was 1046 bp in length with an open reading frame of 783 bp, encoding 260 amino acids. The corresponding gene had two introns and three exons and was present as a single copy in A. marina. The deduced amino acid sequence showed similarities to MYB proteins reported in other plants, including the conserved MYB binding domain. RNA gel blot analysis showed that the AmMYB1 transcript expression was more pronounced in green photosynthetic tissue and was strongly induced by stresses such as salt (500 mM), light (500 µE m(-2) s(-1)), and the exogenous application of ABA (100 µM). An analysis of the upstream sequence of AmMYB1 gene revealed the presence of regulatory elements identical to those present in the promoters of stress inducible genes. The promoter was responsive to NaCl and could enhance reporter gene expression in planta. An in vitro DNA binding assay using the promoter region (TGGTTAG) of the AtRD22 gene and a transactivation assay in yeast cells suggest the possibility of AmMYB1 protein regulating the expression of other genes during salt stress. Transgenic tobacco plants constitutively expressing the AmMYB1 transcription factor showed better tolerance to NaCl stress.
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Affiliation(s)
- G Ganesan
- M. S. Swaminathan Research Foundation, Biotechnology, Taramani, Chennai 600113, India
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Ghaffariyan S, Mohammadi SA, Aharizad S. DNA isolation protocol for the medicinal plant lemon balm (Melissa officinalis, Lamiaceae). GENETICS AND MOLECULAR RESEARCH 2012; 11:1049-57. [PMID: 22614273 DOI: 10.4238/2012.april.27.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Lemon balm (Melissa officinalis) is a medicinal plant that is widely used as a sedative or calmant, spasmolytic and antibacterial agent and sleep aid. This has led to a high demand for lemon balm products, resulting in the extinction of this species in some of its natural habitats. Molecular techniques have increasingly been used in plant diversity conservation and isolation of PCR amplifiable genomic DNA is an important pre-requisite. Lemon balm contains high levels of polyphenols and polysaccharides, which pose a major challenge for the isolation of high-quality DNA. We compared different genomic DNA extraction protocols, including traditional phenol-chloroform DNA extraction protocols and two commercial kits for DNA purification for their ability to produce good-quality DNA from fresh leaves of five lemon balm genotypes. Quality and quantity of the DNA samples were determined using 0.8% agarose gel electrophoresis and a spectrophotometer. The DNA purity was further confirmed by PCR amplification using barley retrotransposon LTR base primers. The spectral quality of DNA as measured by the A(260)/A(280) ratio ranged from 1.46 to 2.37. The Fermentase genomic DNA purification kit and the CTAB extraction protocol using PVP and ammonium acetate to overcome the high levels of polyphenols and polysaccharides yielded high-quality DNA with a mean A(260)/A(280) ratio of 1.87. The quantity of DNA and its PCR purity were similar with all the protocols, but considering the time and cost required for extraction of DNA from a large number of samples, the CTAB protocol using PVP and ammonium acetate is suitable for lemon balm.
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Affiliation(s)
- S Ghaffariyan
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Saad RB, Romdhan WB, Zouari N, Azaza J, Mieulet D, Verdeil JL, Guiderdoni E, Hassairi A. Promoter of the AlSAP gene from the halophyte grass Aeluropus littoralis directs developmental-regulated, stress-inducible, and organ-specific gene expression in transgenic tobacco. Transgenic Res 2011; 20:1003-18. [PMID: 21188636 DOI: 10.1007/s11248-010-9474-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 12/10/2010] [Indexed: 11/26/2022]
Abstract
In our recent published work it has been demonstrated that AlSAP, a gene encoding an A20/AN1 zinc-finger protein (stress-associated protein) of the C4 halophyte grass Aeluropus littoralis, is inducible by various abiotic stresses and by hormonal stimuli. To further investigate the regulation of the gene, a 586-bp genomic fragment upstream of the AlSAP translated sequence has been isolated, cloned, and designated as the "Pr ( AlSAP )" promoter. Sequence analysis of "Pr ( AlSAP )" revealed the presence of cis-regulatory elements which could be required for abiotic stress, abscisic acid (ABA), and salicylic acid (SA) responsiveness and for tissue-specific and vascular expression. The Pr ( AlSAP ) promoter was fused to the β-glucuronidase (gusA) gene and the resulting construct transferred into tobacco. Histochemical assays of stably transformed tobacco plants showed that Pr ( AlSAP ) is active in this heterologous C3 system. While full-length gusA transcripts accumulated in whole 15, 30, and 45-day-old plants, GUS histochemical staining was only observed in leaves and stems of 45-day-old, or older, transgenic seedlings. Histological sections prepared at this stage revealed activity localized in leaf veins (phloem and bundle sheath) and stems (phloem and cortex) but not in roots. Furthermore, gusA transcripts accumulated in an age-dependent manner with a basipetal pattern in leaf and stem tissues throughout the plant. In flowers, GUS expression was detected in sepals only. The accumulation of gusA transcripts was up-regulated by salt, dehydration, ABA, and SA treatment. Altogether, these results show that, when used in a heterologous dicot system, Pr ( AlSAP ) is an age-dependent, abiotic-stress-inducible, organ-specific and tissue-specific promoter.
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Affiliation(s)
- Rania Ben Saad
- University of Sfax, Centre of Biotechnology of Sfax, BP1117, 3018 Sfax, Tunisia
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