Agriculture Reference
In-Depth Information
Disproportionate removal of damaging invasive DNA would occur
because only diploid recombinate individuals that carry unbuffered
homo alleles of the damaging intragenic insertion regions would be
selected against, rather than selecting against all unbuffered haploid
genomes that carry any deleterious regions. In this way, recombined
genomes that have lost damaging alleles at many loci would retain many
bene
cial alleles and would not be under negative selection pressure.
This nucleotide pairing recombination process would allow quality
checking of the genome more ef
ciently than using a haploid phase
of the life cycle that produces an entire haploid organism (genome) that
is under selection and may be lost by extinction (Gu et al. 2003; Walbot
and Evans 2003).
B. Gene Silencing and Defense
Even though the evolution of sexual reproduction may have been as
important for rapidly removing deleterious mutations as it is for spread-
ing and rearranging bene
cial mutations through a population of
genomes, it may not have been suf
cient to continue a successful
defense against the spread of invasive TEs. At some point, mobility of
large numbers of TE-invasive DNAs may have overcome the ability to
recognize and remove them by an enzyme-mediated DNA elimination
process. If so, there would have been very high selection pressure to
evolve a mechanism to recognize TE insertions, such as the double
stranded RNAs by which Class I TEs spread, and then prevent their
mobilization (Baulcombe 2004; Chan et al. 2005; Slotkin et al. 2012). As
we shall see, the extant ciliates still use DNA elimination (excision), but
these organisms now occupy a small environmental niche. Sexual
reproduction by the haploid/diploid system therefore may have been
pressured to evolve into an epigenetic gene expression control system
that removes the dangers of TE insertion by silencing them through
nucleotide pairing recognition as it appears to operate now (Matzke and
Matzke 2004; Lisch and Bennetzen 2011; Nosaka et al. 2012). This would
have reduced the need for their removal by genetic recombination
through sexual reproduction, but more importantly, may have opened
the possibility that the TE silencing system could further evolve into a
mechanism that could achieve control of speci
c host gene activity and
thereby produce the organism phenotype alternations that we now see in
the alternation of haploid and diploid generations (Woodhouse et al.
2006). Just as in the maintenance of somatic cell identity, genes that
control haploid and diploid forms would require strong suppression,
while the organism is in the other form. This silencing ability would
