CPGAVAS2, an integrated plastome sequence annotator and analyzer

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: 47(W1), P. W65 - W73

Published: April 25, 2019

We previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the into CPGAVAS2 to address following challenges: (i) inaccurate annotation in reference sequence likely causing propagation errors; (ii) difficulty small exons genes petB, petD rps16 trans-splicing gene rps12; (iii) lack other genome features their visualization, such as repeat elements; (iv) modules diversity analysis plastomes. In particular, provides two datasets annotation. The first dataset contains 43 plastomes whose have been validated or corrected by RNA-seq data. second one 2544 curated with alignment. Two new algorithms are also implemented correctly annotate genes. Tandem dispersed repeats identified, results displayed on circular map together annotated DNA-seq data can be uploaded identification single-nucleotide polymorphism sites RNA-editing sites. case studies show that annotates better than several servers. will become an indispensible tool research accessed from http://www.herbalgenomics.org/cpgavas2.

Language: Английский

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PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

Plant Methods, Journal Year: 2019, Volume and Issue: 15(1)

Published: May 21, 2019

Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although rapid development high-throughput sequencing technology has led to an explosion plastome sequences, annotation remains a significant bottleneck plastomes. User-friendly batch multiple plastomes is urgent need.We introduce Plastid Genome Annotator (PGA), standalone command line tool that can perform rapid, accurate, flexible newly generated target based on well-annotated reference In contrast current existing tools, PGA uses as query unannotated subject locate genes, which we refer reverse query-subject BLAST search approach. accurately identifies gene intron boundaries well loss. The program outputs GenBank-formatted files log file assist users in verifying annotations. Comparisons against other available tools demonstrated high accuracy PGA, with little or no post-annotation verification necessary. Likewise, flexibility within by annotating Rosa roxburghii using Amborella trichopoda reference. program, user manual example data sets are freely at https://github.com/quxiaojian/PGA.PGA facilitates across For projects generated, time savings high-quality especially significant.

Language: Английский

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Role of Recombinant DNA Technology to Improve Life

International Journal of Genomics, Journal Year: 2016, Volume and Issue: 2016, P. 1 - 14

Published: Jan. 1, 2016

In the past century, recombinant DNA technology was just an imagination that desirable characteristics can be improved in living bodies by controlling expressions of target genes. However, recent era, this field has demonstrated unique impacts bringing advancement human life. By virtue technology, crucial proteins required for health problems and dietary purposes produced safely, affordably, sufficiently. This multidisciplinary applications potential to deal with important aspects life, instance, improving health, enhancing food resources, resistance divergent adverse environmental effects. Particularly agriculture, genetically modified plants have augmented harmful agents, enhanced product yield, shown increased adaptability better survival. Moreover, pharmaceuticals are now being used confidently rapidly attaining commercial approvals. Techniques gene therapy, genetic modifications also widely purpose bioremediation treating serious diseases. Due tremendous broad range application review article mainly focuses on its importance possible daily

Language: Английский

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What can we do with 1000 plastid genomes?

The Plant Journal, Journal Year: 2017, Volume and Issue: 90(4), P. 808 - 818

Published: Jan. 23, 2017

The plastid genome of plants is the smallest and most gene-rich three genomes in each cell one generally present highest copy number. As a result, obtaining DNA sequence particularly cost-effective way discovering genetic information about plant. Until recently, gathered this was limited to small portions amplified by polymerase chain reaction, but recent advances sequencing technology have stimulated substantial rate increase complete genomes. Within last year, number accessible public repositories has exceeded 1000. This sudden flood data raises numerous challenges analysis interpretation, also offers keys potential insights across large swathes plant biology. We examine what been learnt so far, more could be if we look at right way, might gain from tens thousands sequences that will surely arrive next few years. exciting new discoveries are likely made interdisciplinary interfaces between molecular biology ecology.

Language: Английский

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The chloroplast genome: a review

Acta Physiologiae Plantarum, Journal Year: 2020, Volume and Issue: 42(6)

Published: May 18, 2020

Abstract Chloroplasts are the metabolically active, semi-autonomous organelles found in plants, algae and cyanobacteria. Their main function is to carry out photosynthesis process involving a conversion of light energy into chemical bonds used for synthesis organic compounds. The Chloroplasts’ proteome consists several thousand proteins that, besides photosynthesis, participate biosynthesis fatty acids, amino hormones, vitamins, nucleotides secondary metabolites. Most chloroplast nuclear-encoded. During course evolution, many genes ancestral chloroplasts have been transferred from genome cell nucleus. However, these which essential retained genome. This review aims provide relatively comprehensive summary knowledge field arrangement expression based on widely model plant genetic research, namely Arabidopsis thaliana .

Language: Английский

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Therapeutic recombinant protein production in plants: Challenges and opportunities

Plants People Planet, Journal Year: 2019, Volume and Issue: 2(2), P. 121 - 132

Published: Nov. 28, 2019

Societal Impact Statement Therapeutic protein production in plants is an area of great potential for increasing and improving the proteins treatment or prevention disease humans other animals. There are a number key benefits this technique scientists society, as well regulatory challenges that need to be overcome by policymakers. Increased public understanding costs therapeutic will instrumental acceptance, thus medical veterinary impact, approach. Summary recombinant powerful tool combating many diseases which have previously been hard treat. The most utilized expression systems Chinese Hamster Ovary cells Escherichia coli , but all available strengths weaknesses regarding development time, cost, size, yield, growth conditions, posttranslational modifications approval. plant industry established growing harvesting crops easy affordable using current infrastructure. Growth conditions generally simple: sunlight, water, addition cheap, fertilizers. multiple options systems, including species, genetic constructs targeting, each best suited particular type production. Transient provide mechanism rapidly transfect produce matter weeks, rather than months it can take competing while targeted cereal seeds harvested, stored potentially purified much more easily systems. Current include lack approval, environmental containment concerns nonhuman glycosylation, may limit scope manufactured plants. specific could facilitate certain quickly cheaply near future.

Language: Английский

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Recent strategies of increasing metal tolerance and phytoremediation potential using genetic transformation of plants

Plant Biotechnology Reports, Journal Year: 2018, Volume and Issue: 12(1), P. 1 - 14

Published: Jan. 3, 2018

Avoidance and reduction of soil contamination with heavy metals is one the most serious global challenges. Nowadays, science offers us new opportunities utilizing plants to extract toxic elements from by means phytoremediation. Plant abilities uptake, translocate, transform metals, as well limit their toxicity, may be significantly enhanced via genetic engineering. This paper provides a comprehensive review recent strategies aimed at improvement plant phytoremediation potential using transformation employing current achievements in nuclear cytoplasmic genome transformation. Strategies for obtaining suitable effective clean-up tolerant excessive concentrations are critically assessed. Promising directions manipulations, such gene silencing cis- intragenesis, also discussed. Moreover, ways overcoming disadvantages approachare proposed. The knowledge gathered here could useful designing research biotechnological efficiency.

Language: Английский

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Chloroplast development in green plant tissues: the interplay between light, hormone, and transcriptional regulation

New Phytologist, Journal Year: 2021, Volume and Issue: 233(5), P. 2000 - 2016

Published: Nov. 3, 2021

Summary Chloroplasts are best known for their role in photosynthesis, but they also allow nitrogen and sulphur assimilation, amino acid, fatty nucleotide hormone synthesis. How chloroplasts develop is therefore relevant to these diverse fundamental biological processes, attempts at rational redesign. Light strictly required chloroplast formation all angiosperms directly regulates the expression of hundreds chloroplast‐related genes. modulates levels several hormones including brassinosteriods, cytokinins, auxins gibberellins, which themselves control development particularly during early stages plant development. Transcription factors such as GOLDENLIKE1&2 ( GLK1&2 ), GATA NITRATE‐INDUCIBLE CARBON METABOLISM‐INVOLVED GNC ) CYTOKININ‐RESPONSIVE FACTOR 1 CGA1 act downstream both light phytohormone signalling regulate Thus, green tissues transcription factors, form a complex network regulating chloroplast‐ photosynthesis‐related genes number per cell. We use this conceptual framework identify points regulation that could be harnessed modulate abundance increase photosynthetic efficiency crops, highlight future avenues overcome gaps current knowledge.

Language: Английский

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Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Genomics, Journal Year: 2019, Volume and Issue: 112(1), P. 581 - 591

Published: April 15, 2019

Language: Английский

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Green giant—a tiny chloroplast genome with mighty power to produce high‐value proteins: history and phylogeny

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(3), P. 430 - 447

Published: Jan. 23, 2021

Summary Free‐living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence chloroplast DNA was demonstrated in 1960s. The first genomes sequenced 1980s, followed ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop past three decades. Foreign genes expressed isolated chloroplasts or intact plant late 1980s stably integrated into genomes, with typically maternal inheritance shown 1990s. Since then, conferred highest reported levels tolerance resistance biotic abiotic stress. Although launching products agronomic traits important crops using this concept has been elusive, commercial developed include enzymes used everyday life from processing fruit juice, enhancing water absorption cotton fibre removal stains as laundry detergents dye textile industry. Plastid genome sequences have revealed framework green phylogeny well intricate history plastid transfer events other eukaryotes. Discordant historical signals among suggest possible variable constraints across plastome further understanding mitigation these may yield new opportunities for bioengineering. In review, we trace evolutionary chloroplasts, status autonomy recent advances use those advanced clinic, including treatment COVID‐19 patients SARS‐CoV‐2 vaccine.

Language: Английский

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