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In-Depth Information
10
Lila Kari and Laura F. Landweber
Ciliates are unicellular protists that may have arisen more than a billion years
ago. They have since diverged into thousands of species, many uncharacterized,
the genetic divergence among ciliates being at least as deep as that between
plants and animals [17]. Despite their diversity, ciliates are united by two com-
mon features; the presence of short threads called cilia on their surface, whose
rhythmic beating causes movement and is also useful for food capture, and the
presence of two types of nuclei. The
macronucleus
contains DNA encoding
functional copies of all the genes that regulate vegetative growth and cell pro-
liferation. The
micronucleus
contains encrypted versions of the macronuclear
DNA, is mostly functionally inert, and is only used for sexual exchange of
DNA. In this chapter we study the decryption of the macronuclear DNA from
a computational perspective.
INTRODUCTION
When two cells mate, they exchange micronuclear information. After they sep-
arate, the old micronuclei and macronuclei degenerate, while the newly formed
micronuclei develop into new macronuclei over hours or days, depending on
the species. Few ciliates have so far been studied at the level of molecular ge-
netics:
Tetrahymena
and
Paramecium
representing the
Oligohymenophorans
and
Oxytricha
(recently renamed
Sterkiella
), and
Stylonichia
and
Euplotes
rep-
resenting
Spirotrichs
. The DNA molecule in each of the approximately 120
202
