DNA Sequencing and Crop Protection

Tedeschi, Rosemarie

doi:10.5772/38461

Cited by 3 publications

(5 citation statements)

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“…Electrophoresis is used to separate, analyze, identify, and purify DNA fragments, enabling the visualization of Polymerase Chain Reaction) products [10]. Electrophoresis began with the preparation of a 1.5% agarose gel for DNA visualization.…”

Section: Electrophoresismentioning

confidence: 99%

Potential invasive species detection of Demospongiae using environmental DNA in Sabang and Lhokseumawe Ports

Lestari,

Yonatika,

Hartanto

et al. 2024

BIO Web Conf.

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Sabang and Lhokseumawe Ports are located in the province of Aceh and constitute part of the northern Malacca Strait, sharing direct borders with neighboring countries such as Malaysia, Thailand, and India. Strategic geographical location significantly influences the oceanographic conditions and biodiversity of the area. As marine organisms, sponges play a crucial role in the ecosystem, yet research on their identification in the Sabang and Lhokseumawe regions is limited. The analysis of community structure and identification of species can be conducted using various approaches, including environmental DNA (e-DNA) analysis. This study aimed to assess water quality and identify the presence of potentially invasive Demospongiae using DNA Metabarcoding in Sabang and Lhokseumawe Ports. The measurement results of the water conditions indicate that the waters around Sabang and Lhokseumawe ports generally exhibit values that support sponge life. e-DNA analysis successfully detected the presence of the Demospongiae class, with 260 Operational Taxonomic Units (OTUs) in Sabang waters and 148 OTUs in Lhokseumawe waters. One commonly found genus, Cliona sp., has the potential to become invasive in both locations, posing a risk of bioerosion to corals under specific conditions.

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Section: Electrophoresismentioning

confidence: 99%

Potential invasive species detection of Demospongiae using environmental DNA in Sabang and Lhokseumawe Ports

Lestari,

Yonatika,

Hartanto

et al. 2024

BIO Web Conf.

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“…Symptomatogical identification is usually followed by laboratory analyses based on morphological identification using microscopy. This method required isolation and culturing of the organisms, which sometimes encounter serious challenges as not all the microorganisms are cultivable in vitro (Tedeschi, 2012). There are several types of microscopy such Phase contrast Microscope, Stereoscopic Microscope, Electron Microscope (Scanning and Transmission), Fluorescence Microscope, Luminescence Microscope and Immunofluorescence microscopy.…”

Section: Microscopymentioning

confidence: 99%

“…The improvement of the sequencing technology and in particular the advent of NGS together with the evolution of bioinformatics enable large-scale sequencing projects permitting a new comparative genomics approach and thus facilitate the identification of candidate genes to be used in plant protection. The possibility to down-regulate or over express genes in plants or in plant pathogenic organisms is a very powerful tool, within pest management and agriculture in general, to meet farmer and consumer demands (Tedeschi, 2012;Huq et al, 2016). The advent of NGS technologies has led to the development of rapid genome-wide SNP detection applications in various plant species (Peterson et al, 2014;Chung et al, 2017).…”

Section: Dna Sequencingmentioning

confidence: 99%

“…Genotyping by sequencing (GBS) for plant genetic diversity analysis (Peterson et al, 2014;He et al, 2014;Huqet al, 2016;Thottathil et al, 2016;Chung et al, 2017;Rasheed et al, 2017) 16S rRNA, 23S rRNA gene and ITS region Sequencing (Tadesch, 2012; De Boer andLopez, 2012, Patel et al, 2016) 16S and 12S subunits of mitochondrial DNA as well as the (ITS1 and ITS2), the 18S and 28S subunits of the rDNA (Fakrudin et al, 2006;Tedeschi, 2012;Wang et al, 2016) DNA Sequencing (Shaiket al, 2016); ITS region (Du, et al, 2010). Chloroplast DNA sequencing (Wallinger et al, 2012) Microarray Diversity analysis (Galbraith and Edwards, 2010;Kiyama, 2017) Identification of pathogens (Rodrigo et al, 2014 Nanoencapsulated material delivery to plants and benefits in precision farming (Duhanet al, 2017;Kumar et al, 2017a;Mishra et al, 2017;Prasad et al, 2017;Abobatta 2018;Thaku et al, 2018) plant disease detection (Fang and Ramasamy.…”

Section: Dna Sequencingmentioning

confidence: 99%

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Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

Alemu

2020

Int J Appl Sci Biotechnol

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The second Sustainable Developmental Goals (SDG), among the seventeen SDG, is concerned with the pursuit of global food security and agricultural sustainability, which become the key to the success of the entire SDG. Whereas agricultural production and productivity are heavily threatened by the incidence of pests that inflict huge losses in various forms. This calls for prompt applications of biotechnology for the fast, accurate and reliable means for characterization of plant generic resources and pests as it is the pre-requisite and gateway for designing appropriate plant protection and production strategies. It is imperative that pests be identified properly so that judicious use of the literature can be made and sustainable management strategies can be implemented at the right stage. To this end, the application of biotechnology has made significant advances for reliable characterization of plant genetic resources as well as accurate diagnosis of pests, study of their genetic diversity and variability, detailed mechanisms of their transmission and evolutionary relationships. Accordingly, this review article covers the comprehensive account of the various molecular techniques, genome mapping and OMICS sciences utilized for characterization plants and pests that ultimately allow the detailed study of the biology and epidemiology of pests at any stage of their life cycle. The resulting data are eventually employed for enhancing successful implementation of sustainable plant protection and production strategies. In conclusion, the increasing projections of transboundary pests, environmental and abiotic factors together with the continuous scientific advancements and breakthroughs have made biotechnology to be an important engine of bioeconomy for generating invaluable products, processes and services. Int. J. Appl. Sci. Biotechnol. Vol 8(3): 247-288

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“…In short, DNA barcodes from standard gene region(s) compliment taxonomy, population analysis, and phylogenetic and evolutionary studies at genetic level. They are also utilized for identification of species, particularly for eggs, larvae, and commercial products [19,20].…”

Section: Introductionmentioning

confidence: 99%

Molecular Markers and Their Optimization: Addressing the Problems of Nonhomology Using Decapod COI Gene

Jose¹,

Harikrishnan²

2020

Biochemical Analysis Tools - Methods for Bio-Molecules Studies

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Advancements in DNA sequencing and computational technologies influenced almost all areas of biological sciences. DNA barcoding technology employed for generating nucleotide sequences (DNA barcodes) from standard gene region(s) is capable of resolving the complexities caused due to morphological characters. Thus, they complement taxonomy, population analysis, and phylogenetic and evolutionary studies. DNA barcodes are also utilized for species identification from eggs, larvae, and commercial products. Sequence similarity search using Basic Local Alignment Search Tool (BLAST) is the most reliable and widely used strategy for characterizing newly generated sequences. Similarity searches identify "homologous" gene sequence(s) for query sequence(s) by statistical calculations and provide identity scores. However, DNA barcoding relies on diverse DNA regions which differ considerably among taxa. Even, region-specific variations within barcode sequences from a single gene leading to "nonhomology" have been reported. This causes complications in specimen identification, population analysis, phylogeny, evolution, and allied studies. Hence, the selection of appropriate barcode region(s) homologous to organism of interest is inevitable. Such complications could be avoided using standardized barcode regions sequenced using optimized primers. This chapter discusses about the potential problems encountered due to the unknown/unintentional/intentional use of nonhomologous barcode regions and the need for primer optimization.

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DNA Sequencing and Crop Protection

Cited by 3 publications

References 142 publications

Potential invasive species detection of Demospongiae using environmental DNA in Sabang and Lhokseumawe Ports

Potential invasive species detection of Demospongiae using environmental DNA in Sabang and Lhokseumawe Ports

Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

Molecular Markers and Their Optimization: Addressing the Problems of Nonhomology Using Decapod COI Gene

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