Bioinformatics: A Way Forward to Explore “Plant Omics”

Rahman, Mehboob‐ur; Shaheen, Tayyaba; Rahman, Muhammad Atif Iqbal Mahmood-ur; Zafar, Yusuf

doi:10.5772/64043

Cited by 4 publications

(3 citation statements)

References 98 publications

(98 reference statements)

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“…So, DNA sequencing was introduced in endophyte study. The sequences are then deposited in Gene Bank, NCBI and EMBL by using bioinformatic tools (Mehboob-ur-Rahman, Mahmood-ur-Rahman et al, 2016).…”

Section: Dna Sequencing Methodsmentioning

confidence: 99%

A Brief History of Endophyte Detection Techniques in Grasses

Ahmad¹,

Ameen²,

Khalid³

et al. 2019

SAR

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Endophytes are the plant mutualists that live asymptomatically inside plant tissue and are found in nearly whole plant kingdom. Endophytic fungi receive shelter and nutrition from host plants and in return provide great advantages to the host. Grasses are a useful forage species and are of great agricultural and socio-economic value. The presence of endophytes in these grasses provide protection, persistence and improved yield against herbivores, insects, pathogens, drought and several other biotic and abiotic stresses. This review summarizes traditional and modern molecular techniques to identify endophytes from turf and forage grasses. Traditional approaches include direct observation, staining, laser micro dissection and pressure catapulting and cultivation-dependent methods that provide a morphological identification of endophytic mycobiota in grass tissues. Earlier studies on endophytes using these methods resulted in several technical implications which molecular approaches are able to solve now-a-days. Molecular approaches include DNA extraction, PCR based DNA Fingerprinting techniques, Denaturing Gradient Gel Electrophoresis, Sanger sequencing, Pyrosequencing, Immunoblot assay, Biosensors, DNA Barcoding and Molecular Phylogenetics etc. A comparison of these detection techniques will facilitate other researchers as well to develop new ways for the detection of endophytes that will contribute to the improvement of grassland in future.

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Section: Dna Sequencing Methodsmentioning

confidence: 99%

A Brief History of Endophyte Detection Techniques in Grasses

Ahmad¹,

Ameen²,

Khalid³

et al. 2019

SAR

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“…208 Considering biological data, information can be classified into (1) primary (sequences), (2) secondary (structure, expression, metabolic pathways, types of drugs, etc), and (3) specialized, for example, containing information on a species or on a class of protein. 209 Within this third group, some references to AMPs can be mentioned, such as CAMPR3 196 and APD 198 that compile sequence data and structure retrieved from diverse sources, and also the Defensin knowledgebase 203 and the CyBase 205 which are dedicated to specific classes of peptides (defensins and cyclotides, respectively), in addition to PhytAMP, 206 a specific database of plant AMPs ( Supplementary Table 2 ).…”

Section: Bioinformatic Tools and Databases For Plant Ampsmentioning

confidence: 99%

Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era

Santos-Silva

Zupin

Oliveira-Lima

et al. 2020

Bioinform Biol Insights

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Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.

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“…Moreover, biotechnological studies can use the obtained results to manipulate the biosynthesis pathways, for higher secondary metabolite production. 73,74…”

Section: Use Of Bioinformaticsmentioning

confidence: 99%

Ascertaining the Paradigm of Secondary Metabolism Enhancement through Gene Level Modification in Therapeutic Plants

Sinha¹,

Sandhu²,

Bisht³

et al. 2019

JYP

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Since ages plants with therapeutic effects are used for curing several human ailments. With the development in modern biotechnological tools, these therapeutic compounds could be overexpressed in the plants. This review aims to compile the valuable information from the examples in the literature, regarding the biotechnological tools those could be useful for the overproduction of health-promoting biochemicals in the medicinal plants. Gene level modification is all about creating improved variety of plants that are highly resistant to pests and pesticides or contain higher levels of nutrients than conventional plants. Plant secondary metabolites constitute an exciting and vital aspect of research, due to their chemical diversity, varied biological functions and pharmacological activities. Gene modification, through Agrobacterium mediated transformation , RNA interference or CRISPER/Cas9, has opened avenues of improvement in medicinal plants and provide an alternative production system of pharmaceutically important secondary metabolites for their commercial exploitation.

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Bioinformatics: A Way Forward to Explore “Plant Omics”

Cited by 4 publications

References 98 publications

A Brief History of Endophyte Detection Techniques in Grasses

A Brief History of Endophyte Detection Techniques in Grasses

Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era

Ascertaining the Paradigm of Secondary Metabolism Enhancement through Gene Level Modification in Therapeutic Plants

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