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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
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Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
16.3K
DNA as a Genetic Template02:05

DNA as a Genetic Template

27.9K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

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Protocol: a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for

Craig B Anderson1, Benjamin K Franzmayr1,2, Soon Won Hong1

  • 11AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand.

Plant Methods
|September 6, 2018
PubMed
Summary

A new, inexpensive DNA extraction method provides high-quality genomic DNA suitable for genotyping-by-sequencing (GBS) and long-read sequencing. This high-throughput protocol is ideal for plant breeding and population genetics studies.

Keywords:
ArabidopsisFestucaFreeze-driedHigh-throughputLoliumMalusMedicagoNext-generation sequencingOryzaSecaleSilica gel-driedTrifolium

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Area of Science:

  • Plant genomics and molecular biology
  • Biotechnology and bioengineering

Background:

  • Next-generation sequencing (NGS) technologies like genotyping-by-sequencing (GBS) require high-quality DNA.
  • Existing high-throughput DNA extraction methods are often costly or yield suboptimal DNA quality.
  • Developing affordable, scalable DNA extraction is crucial for under-resourced species and large-scale projects.

Purpose of the Study:

  • To develop an inexpensive, high-throughput method for extracting sequencing-grade genomic DNA from diverse plant tissues.
  • To validate the suitability of the extracted DNA for both GBS and long-read sequencing platforms.

Main Methods:

  • Modification of a non-organic solvent-based protocol for DNA extraction.
  • Extraction performed in 96-well plates from fresh, freeze-dried, or silica gel-dried plant material.
  • Protocol assessed for scalability, automation, processing time, and cost-effectiveness.

Main Results:

  • Successfully extracted high molecular weight genomic DNA (1-13 μg) from various plant species.
  • Extracted DNA demonstrated suitability for restriction enzyme digestion and subsequent Illumina-based GBS library preparation.
  • DNA also proved effective for PacBio long-read sequencing, with low cost ($0.62/sample) and high throughput (384-576 samples/day).

Conclusions:

  • The developed protocol provides a versatile, scalable, and cost-effective solution for obtaining high-quality genomic DNA.
  • This method supports diverse NGS applications, including GBS and long-read sequencing, from various plant sample types.
  • It is well-suited for large-scale genotyping and breeding programs, especially for under-resourced species.