TAILIEUCHUNG - Sequencing of plant genomes - a review

The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called “next-generation” sequencing. | Turkish Journal of Agriculture and Forestry Review Article Turk J Agric For (2015) 39: 361-376 © TÜBİTAK doi: Sequencing of plant genomes – a review 1 2 3 Mine TÜRKTAŞ , Kuaybe YÜCEBİLGİLİ KURTOĞLU , Gabriel DORADO , 4 5 1, Baohong ZHANG , Pilar HERNANDEZ , Turgay ÜNVER * 1 Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı, Turkey 2 Department of Biology, Faculty of Arts and Sciences, Marmara University, İstanbul, Turkey 3 Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Córdoba, Córdoba, Spain 4 Department of Biology, College of Arts and Sciences, East Carolina University, Greenville, NC, USA 5 Institute for Sustainable Agriculture-National Research Council (IAS-CSIC), Córdoba, Spain Received: Accepted: Published Online: Printed: Abstract: The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called “next-generation” sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome .

• Nông nghiệp
• Sequencing of plant genomes
• ChIP Seq
• Deep sequencing
• High throughput Sequencing technologies
• RNA Seq
• Genome Biology
• Long read sequencing
• Chromosome level draft genome
• High molecular weight DNA extraction
• Genomic standardized workflow
• BMC Genomics
• Copy number variation
• Structural variation
• Plant adaptation
• Machine learning
• BMC Plant Biology
• Genome rearrangement
• Gene order
• Plastid genome
• Mitochondrial genome
• Arabidopsis thaliana
• Metabolomic analysis
• Sequencing total RNA
• Organellar genomes
• BMC Bioinformatics
• Gene expression
• Next generation sequencing
• Library bias correction
• Standard RNAseq methods
• Ribosomal RNA
• Illumina RNAseq
• Cell line samples
• Ribosomal depletion
• Single cell RNAseq
• Rare cell population composition
• Tumor heterogeneity
• Alternative splicing
• BMC Cancer
• RNAseq expression patterns
• Invasive urothelial carcinoma
• Pathologic presentation
• Molecular subtypes
• Human bladder tumors
• Chromatin remodeling
• SNF2 type ATPases
• Detailed RNAseq analyses
• RNAseq analyses
• Arginine rich splicing factors
• Oryza sativa
• Robust principal component analysis
• Outlier detection
• High dimensional data
• Anomaly detection
• SL trans splicing
• De novo assembly
• RNAseq data
• Spliced Leader trans splicing
• Gene ontology
• Differential gene expression
• Sequencing messenger RNA
• RNA sequencing
• Gene expression analysis
• Read depth
• Sample number
• Matataki outperformed conventional methods
• Meta analyses
• Sequence variant
• Splicing event
• DNA mutation
• RNA editing
• High throughput RNA Sequencing
• Biologically accurate gene
• Plant Biology
• Plastid transcriptome
• Plastomic rearrangement
• Strand specific RNAseq
• Salicylic acid
• Jasmonic acid
• Web application
• Signaling pathway
• Phenotypic observation
• Collaborative cross
• Sex differences
• High fat diet
• Environmental factors
• Cell line authentication
• Cell line identification
• RNA Seq variant profiles
• Disease biology
• DNA polymorphisms
• Bioinformatics pipeline
• Black poplar
• Populus nigra
• Single Nucleotide Polymorphisms
• Primary tissue preservation without dissociation
• Hypothermic preservation
• Organ transplant preservation
• Organ transplant preservative
• Aneuploidy detection
• Single cell
• Copy number
• Hepatocellular carcinoma
• Transcript expression
• Supervised cell typing
• Reference dataset construction
• Computational performance
• Single cell RNA sequencing
• In silico lineage tracing
• Neural stem cells
• Schmidtea mediterranea
• Transgenic labeling
• BMC Pulmonary Medicine
• Bronchial epithelial cells
• Hereditary COPD pathogenesis
• Non hispanic white
• Cis regulatory
• Tandem mass tag
• Parallel reaction monitoring
• Dictyostelium discoideum
• Autophagy related