The genomics of a model organism

1. Submitted by:
Kumar Kashyap
M. Tech Marine Biotechnology
NCAAH, CUSAT
Ist Semester
Marine Genomics and Proteomics

2.  Model Organisms: A non human species,
extensively studied, discovery made in this
can be applied in others.
 Example: Escherichia coli are the first model
organism used in molecular biology.
 Cell cycle is almost similar to humans and
regulated by homologous proteins.

3.  Easily grown and easy maintainance
 Easy to provide necessary nutrients for
growth
 Short generation time
(birth→reproduction→death)
 Well understood growth and development
 Closely resemble to other organisms

4.  Model organisms of marine origin are called
marine model organisms. A few examples
include Ectocarpus, a filamentous brown
algae, Chondus crispus also known as Irish
moss (a red sea weed) etc.
 Any non-human species, which is used to
understand biological processes, is called a
model organism. A marine model organism is
model organism of marine origin.

5.  Ostreococcus tauri:
 Eukaryotic picophytoplankton
 Smallest free living eukaryote
 Used to study conserved biological functions such
as the circadian clock and the response to
environmental stress

6.  Chondrus crispus:
o Irish moss
o red sea weed
o rocky shores and other hard substrata
o Northern North Atlantic.

7.  Ectocarpus:
filamentous brown algae
found in temperate coastal regions worldwide
used to study a broad range of aspects of brown
algal biology
life cycle regulation, sex determination,
morphogenesis
ecology and population genetics
resistance to abiotic and biotic stress and cell
wall metabolism

8.  Ectocarpus, a brown algae with a complex
photosynthetic mechanism
 An evolutionary tree showing the five major groups that
have evolved into complex multicellularity

9.  From the diagram we can see that though
the group brown algae has evolved into
complex multicellularity, but its evolution
pathway is different from that of the rest
of the four groups.

10.  Dominant in rocky coastal systems and have
adaptations for that harsh environment.
 Developed an extended set of light
harvesting and pigment biosynthesis genes
 New metabolic pathways such as halide
metabolism
 To withstand the highly variable tidal
environment

11.  The Ectocarpus genome sequence represents
an important step towards developing this
organism as a model organism.
 Genome size – 214 million base pairs
 16,256 protein coding genes
 They are rich in introns (seven per gene on
an average)
 Also have long 3’ UTR’s upto 845 base pairs
long
 These genes are often very close to each
others on chromosome

12.  Repeated sequences, including DNA
transposons, retrotransposons and helitrons,
make upto 22.7%
 Also small RNAs are mapped preferentially on
these transposons, indicating that they have
certain role in silencing these transposons
elements

14.  Sequencing also revealed the presence of an
integrated copy of large DNA virus
Found to be closely related to Ectocarpus
Phaeovirus EsV-1
 In nature, about 50% of the individuals show
symptoms of viral infection
 One of the strains, strain EC 32, was never
observed to produce any virus particles
 Also expression analysis showed that almost
all of the viral genes were silent in this strain

16.  (a). It shows a circular DNA from the
Ectocarpus Phaeovirus EsV-1 and its linear
form present in the genome of Ectocarpus.
 (b). This figure shows the absence of
protein expression from the viral DNA
sequence that has been incorporated in the
Ectocarpus genome. The red line shows no
protein expression.

17.  Habitat is shallow water of inter tidal region
 This area is a hostile environment
 Cope up with tidal changes in light intensity,
temperature, salinity and wave action, etc
 It has evolved effective mechanism for survival
in its harsh environment
 For e.g., a large family of Light Harvesting
Complex (LHC) genes is present in Ectocarpus
(present at 53 loci, although some are probably
pseudogenes)
 Also there are a cluster of 11 genes, with highest
similarity to the LI818 family of light stress
realted LHCs

18.  Encode for a light independent
protochlorophyllide reductase (DPOR), allowing
efficient synthesis of chlorophyll under dim
light
 Together the above data clearly indicates
that Ectocarpus has a very complex
photosynthetic system that enables it to adapt
to an environment with highly variable light
conditions
 High level of phenolic compounds present in
the brown algae may be responsible for its
protection from ultraviolet light
 The diverse complement of enzymes
involved in the metabolism of reactive oxygen
species is also likely to represent an important
adaptation to osmotic and light stresses.

19.  Codes for 21 putative dehalogenases and two
haloalkane dehalogenases
 Protect the organism from the halogenated
compounds produced by kelps
 Cell wall contains some unusual
polysaccharides namely – alginates and
fucans, which provide resistance from
mechanical stress and protection from
predators

20.  Ecotoxicology detection. Tigriopus species.
Respond to natural or artificial stress. Short
life cycle and is easily cultured under
laboratory conditions.
 Oryzias melastigma, toxicological studies.
Effects of chemical pollutants in the marine
environment.
 Euplotes crassus, used to detect copper and
oxytetracycline temperature related
toxicity.

21.  http://www.nih.gov/science/models/
 http://genome.wellcome.ac.uk/doc_WTD020803.html
 foothilltech.org/dperez/.../model%20organisms%202b/Lecture.ppt
 http://mmo.embrc-france.fr/
 Raisuddin, S. et al. “The copepod Tigriopus: A promising marine model organism
for ecotoxicology and environmental genomics”. Aquatic toxicology, vol – 83
(2007), pages 161-173.
 Chen, X., et al. “Molecular staging of marine medaka: A model organism for
marine ecotoxicity study”. Marine pollution bulletin, volume – 63 (2011), issue
5 – 12, pages 309-317.
 Goemiro, A., et al. “Effects of elevated temperature on the toxicity of copper
and oxytetracycline in the marine model Euplotus crassus: A climate change
perspective”. Environmental pollution, volume 194 (2014), pages 262-271.
 Matranga, V., et al. “Toxic effects of engineered nanoparticals in the marine
environment: model organisms and molecular approaches.” Marine
environmental research, May 2012, pages 32-40.
 Philipp, E., et al. “Marine bivalves as model organisms for ageing research”.
 thomaspradeu.com/wp-content/.../10/Chenevert-_Model-organisms.pdf
 Cock, J. M., et al. “The Ectocarpus genome and the independent evolution of
multicellularity in brown algae” (2010). Nature, Volume 465, pages 617 – 621