By Shruti Gupta
GENOME
 Entirety of an organism's hereditary information
 Includes both the genes and the non-coding sequences of the

D...
Background
 Biologists have
organized living things
into large groups called
kingdoms.
 There are six of them:
 Archaeb...
Some recent findings…


In 1996, scientists decided to split Monera into two groups of bacteria:
Archaebacteria and Eubac...
The domain

ARCHAEA
 “Ancient” bacteria
 Some of the first archaebacteria were

discovered in Yellowstone National
Park’...
Basic Facts
 They live in extreme environments (like hot springs or salty

lakes) and normal environments (like soil and ...
3 Main Types
Methanogens
Euryarchaeota
Crenarchaeota
Nanoarchaeota
Korarchaeota
Thaumoarchaeota.
Thermoacidophiles
Halophi...
Why to study ARCHAEA?
 As one of the most ancient lineages of living organisms, the archaea

set a boundary for evolution...
Archaea with sequenced genome or ongoing
genome projects
Published studies involving genomic analyses
Genome analysis of some cultivated archaea
published in NCBI
a. Methanobrevibacter smithii
(Human gut methanogen)

b. Sulf...
A genomic analysis of the archaeal
system Ignicoccus hospitalisNanoarchaeum equitans
 The crenarchaeaote Ignicoccus hospitalis is a specific

host for Nanoarchaeum equitans.
 Both the organisms represent h...
General features of I. hospitalis genome
Materials & Method
Genome sequencing and functional annotation
DNA isolation
proteinase K digestion method

Sequencing & assembly
Automated g...
Comparative genomic analysis
Analysis of the I. hospitalis and N. equitans genomes
IMG system

operons were identified
Phy...
Phylogenetic analysis
protein sequence was blasted
sequences with significant hits were retrieved
CLUSTALW
and aligned wit...
Conclusion…..
 Pioneering groundwork in the archaeal research field has been the isolation

and cultivation of hypertherm...


Although the study of model organisms remains crucial, it has become
clear over the past years of archaeal research tha...
REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA
REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA
REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA
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REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA

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REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA

  1. 1. By Shruti Gupta
  2. 2. GENOME  Entirety of an organism's hereditary information  Includes both the genes and the non-coding sequences of the DNA/RNA  The genome is vast in terms of its informational content. Composed of chemical symbols designated by a four-letter alphabet of A's, T's, C's, and G's, the human genome is some 3.2 billion letters in length  Availability of genome sequences provides opportunity to explore genetic variability both between organisms and within the individual organism
  3. 3. Background  Biologists have organized living things into large groups called kingdoms.  There are six of them:  Archaebacteria  Eubacteria  Protista  Fungi  Plantae  Animalia
  4. 4. Some recent findings…  In 1996, scientists decided to split Monera into two groups of bacteria: Archaebacteria and Eubacteria  Because these two groups of bacteria were different in many ways scientists created a new level of classification called a DOMAIN.  Now we have 3 domains 1. Bacteria 2. Archaea 3. Eukarya
  5. 5. The domain ARCHAEA  “Ancient” bacteria  Some of the first archaebacteria were discovered in Yellowstone National Park’s hot springs and geysers.  Numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.  Recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle.
  6. 6. Basic Facts  They live in extreme environments (like hot springs or salty lakes) and normal environments (like soil and ocean water).  All are unicellular (each individual is only one cell).  No peptidoglycan in their cell wall.  Some have a flagella that aids in their locomotion.
  7. 7. 3 Main Types Methanogens Euryarchaeota Crenarchaeota Nanoarchaeota Korarchaeota Thaumoarchaeota. Thermoacidophiles Halophiles
  8. 8. Why to study ARCHAEA?  As one of the most ancient lineages of living organisms, the archaea set a boundary for evolutionary diversity and have the potential to offer key insights into the early evolution of life, including the origin of the eukaryotes.  Many archaea are also extremophiles that flourish at high temperature, low or high pH, or high salt and delineate another boundary for life, the biochemical and geochemical boundary, which sets the physical limits of the biosphere.  Finally, some archaea are fundamental components of the biogeochemical cycles on earth or dominate special ecosystems that are of great interest (such as the methanogens).
  9. 9. Archaea with sequenced genome or ongoing genome projects
  10. 10. Published studies involving genomic analyses
  11. 11. Genome analysis of some cultivated archaea published in NCBI a. Methanobrevibacter smithii (Human gut methanogen) b. Sulfolobus islandicus (Hyperthermophilic acidophilic sulfur-metabolizing archeon)
  12. 12. A genomic analysis of the archaeal system Ignicoccus hospitalisNanoarchaeum equitans
  13. 13.  The crenarchaeaote Ignicoccus hospitalis is a specific host for Nanoarchaeum equitans.  Both the organisms represent hyperthermophilic lineages and inhabit types of ecosystems that are often considered to be ancient.  The genome of I. hospitalis consists of a single circular chromosome
  14. 14. General features of I. hospitalis genome
  15. 15. Materials & Method
  16. 16. Genome sequencing and functional annotation DNA isolation proteinase K digestion method Sequencing & assembly Automated gene prediction Sequence translation tRNAScanSE tool tRNA genes were fined BLASTn rRNA genes were fined
  17. 17. Comparative genomic analysis Analysis of the I. hospitalis and N. equitans genomes IMG system operons were identified Phyre tool Structure fold prediction blastclust analyses frequency of paralogs
  18. 18. Phylogenetic analysis protein sequence was blasted sequences with significant hits were retrieved CLUSTALW and aligned with the query sequence PAUP tool Phylogenetic trees were then constructed
  19. 19. Conclusion…..  Pioneering groundwork in the archaeal research field has been the isolation and cultivation of hyperthermophilic organisms and other extremophiles. This has not only led to the discovery of novel metabolisms and special adaptations of archaea, but also to a more fundamental understanding of the features that unify the organisms of this third domain of life.  It will be as exciting and important to isolate species of those archaeal groups that have so far solely been studied by molecular techniques. In particular, some of the organisms that are commonly found in moderate, aerobic environments should eventually be brought into culture, perhaps assisted by predictions made in metagenomic studies.
  20. 20.  Although the study of model organisms remains crucial, it has become clear over the past years of archaeal research that cultivation independent techniques, including population genomics, will be indispensable if we want to fully understand the diversity and ecological impact of archaea.

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