genome annotation

Examples of genome annotation in the following topics:

• Use of Whole-Genome Sequences of Model Organisms

  • The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs).
  • Several other organelle and viral genomes were later sequenced.
  • It took this long because it was 60 times bigger than any other genome that had been sequenced at that point.
  • Having entire genomes sequenced aids these research efforts.
  • The process of attaching biological information to gene sequences is called genome annotation.

• Uses of Genome Sequences

  • Genome sequences and expression can be analyzed using DNA microarrays, which can contribute to detection of disease and genetic disorders.
  • Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome.
  • Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function.
  • Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities.
  • DNA microarrays can be used to analyze gene expression within the genome.

• Variations in Size and Number of Genes

  • The C-value is another measure of genome size.
  • For example, the predicted size of the human genome is not much larger than the genomes of some invertebrates and plants, and may even be smaller than the Indian rice genome.
  • In prokaryotic genomes, research has shown that there is a significant positive correlation between the C-value of prokaryotes and the amount of genes that compose the genome.
  • In eukaryotic organisms, there is a paradox observed, namely that the number of genes that make up the genome does not correlate with genome size.
  • It is also possible that genomes can shrink due to deletions.

• Biotechnology

  • Relying on the study of DNA, genomics analyzes entire genomes, while biotechnology uses biological agents for technological advancements.
  • Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species.
  • The advances in genomics have been made possible by DNA sequencing technology.
  • The ways in which genomic information can contribute to scientific understanding are varied and quickly growing.
  • In genomics, the DNA of different organisms is compared, enabling scientists to create maps with which to navigate the DNA of different organisms.

• Noncoding DNA

  • For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
  • The amount of total genomic DNA varies widely between organisms, and the proportion of coding and noncoding DNA within these genomes varies greatly as well.
  • The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes; approximately 90% of the Takifugu genome is noncoding DNA.
  • In 2013, a new "record" for most efficient genome was discovered.
  • This 3% has given this plant the title the 'most efficient' genome.

• Whole-Genome Duplication

  • Whole-genome duplication is characterized by an organisms entire genetic information being copied once or multiple times.
  • Genome doubling provides organisms with redundant alleles that can evolve freely with little selection pressure.
  • In 1997, Wolfe & Shields gave evidence for an ancient duplication of the Saccharomyces cerevisiae (Yeast) genome.
  • It was initially noted that this yeast genome contained many individual gene duplications.
  • They found 32 pairs of homologous chromosomal regions, accounting for over half of the yeast's genome.

• Genome Evolution

  • The evolution of the genome is characterized by the accumulation of changes.
  • There are various mechanisms that have contributed to genome evolution and these include gene and genome duplications, polyploidy, mutation rates, transposable elements, pseudogenes, exon shuffling and genomic reduction and gene loss.
  • Spontaneous mutations often occur which can cause various changes in the genome.
  • The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million times.
  • Good examples are the genomes of Mycobacterium tuberculosis and Mycobacterium leprae, the latter of which has a dramatically reduced genome.

• Predicting Disease Risk at the Individual Level

  • Genome analysis is used to predict the level of disease risk in healthy individuals.
  • The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information.
  • Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics.
  • The scientists used databases and several publications to analyze the genomic data.
  • Explain how analysis of an individual's genome can aid in predicting disease risk

• The Evolution of Craniata and Vertebrata

  • Both genomic and fossil evidence suggests that vertebrates evolved from craniates, which evolved from invertebrate chordates.
  • Based on the molecular analysis of vertebrate and invertebrate genomes (genomics), scientists can determine the evolutionary history of different phylogenetic groups.
  • According to these genomic analyses, vertebrates appear to be more closely related to the lancelets (cephalochordates) than to the tunicates (urochordates).
  • A comparison of the genomes of a lancelet, tunicate, lamprey, fish, chicken, and human confirmed that two whole-genome duplications occurred in the early history of the Vertebrata subphylum.
  • Both fossil and genomic evidence suggests that vertebrates arose during the Cambrian explosion.The Cambrian explosion was the relatively brief span of time during the Cambrian period during which many animal groups appeared and rapidly diversified.

• Genomics and Biofuels

  • Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria.
  • Pichia's recently-sequenced genome has revealed insights into the metabolic pathways responsible for this process, guiding efforts to optimize this capability in commercial production strains.
  • Explain the process of creating new biofuels by using microbial genomics