Transcript Analysis Control Region

Mitochondrial Genomic
Rearrangements in Songbirds
1
Introduction
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Mitochondrial genome is conserved among
vertebrates.
Examination of similarity of mitochondrial
rearrangement can be used to classification.
Most avian orders have the rearrangement
between the cytochrome b and 12S rRNA.
The main mechanisms causing the avian
mitochondrial rearrangement were purposed to
tandem duplication and inversion and other gene
recombinations.
Two assumption:
1.Mitochondrial rearrangement are rare.
2.A shared organization reflect a common
ancestry.
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Key Words and Methods
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Control region (CR) and noncoding
region (NC)
Tandem duplication and inversion.
Polymerase chain reaction (PCR)
Sequencing
Ancestral arrangement
Derived arrangement
Willow warbler (Phylloscopus trochilus)
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Content
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Typical vertebrate gene order—single
translocation of NADH6 and tRNAGlu .
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Most avian orders gene order--tRNAThr /
tRNAPro / NADPH6 / tRNAGlu / CR /
tRNAPhe
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Another avian mitochondrial arrangement–
tRNAThr / CR / tRNAPro /NADPH6 / tRNAGlu
/ NC / tRNAPhe
has least two evolutionary changes.
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Fig.1
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Suppose
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Derived mitochondrial arrangement is
evolution from ancestral mitochondrial
arrangement and passed through a
tandem duplication and a deletion.
Noncoding region is a part of control
region.
Control region and noncoding region are
homologous.
Comparing the similarity of NC and CR
in different genus or spices can know
the relatives of the each kinds.
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Table 1
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Analysis Control Region
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We can find that the control regions are
about 1100 nt long in all of the
phylloscopus species.
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Table 2
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Analysis Control Region
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We can find that the control regions are
about 1100 nt long in all of the
Phylloscopus species.
The similarity between the control region
of the six Phylloscopus species showed
>63%
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Table 3
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Analysis Control Region
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We can find that the control regions are
about 1100 nt long in all of the
Phylloscopus species.
The similarity between the control region
of the six Phylloscopus species showed
>63%
Contrast the others warblers,the control
region is quite different.
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Table 1
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Analysis Control Region
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We can find that the control regions are
about 1100 nt long in all of the
Phylloscopus species.
The similarity between the control region
of the six Phylloscopus species showed
>63%
Contrast the others warblers,the control
region is quite different.
Suppose that the higher degrees of
similarity between the CR , the relatives
of the avian was closer.
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Analysis Noncoding Region
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The NC regions from the different
species were highly divergent the
alignment of these sequence was
complicated.
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Table 2
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Analysis Noncoding Region
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The NC regions from the different
species were highly divergent the
alignment of these sequence was
complicated.
For the more distantly related species,
comparisons of the NC regions gave
very low degrees of similarity.
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Compare Noncoding Region
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Analysis Noncoding Region
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The NC regions from the different
species were highly divergent the
alignment of these sequence was
complicated.
For the more distantly related species,
comparisons of the NC regions gave
very low degrees of similarity.
When comparing all six Phylloscopus
species, we were only able to find two
conserved parts in the NC region. First
was between position 152~207 and
second was between 246~325 . Apart
from these two regions, the alignments
were no better than random.
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Fig 2
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Comparisons Between the CR and the NC Region
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Only parts of the NC region of each
species could be aligned with the CR of
that species. However, each species’s
NC region had short stretches which
showed high similarity to a portion of the
CR from that species.
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Fig 3
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Comparisons Between the CR and the NC Region
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Only parts of the NC region of each
species could be aligned with the CR of
that species. However, each species’s
NC region had short stretches which
showed high similarity to a portion of the
CR from that species.
The detected similarity between the CR
and the NC region supports the
hypothesis that the control and NC
regions are homologous and that the
derived gene order arose through a
tandem duplication followed by deletions.
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Fig.1
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Conclusion and Discussion
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The high degree of similarity between positions 867
and 1136 of the CR and the NC region from each
Phylloscopus species, respectively, strongly
suggests that the CR and the NC region of each
species are homologous and that the mechanism
which caused this rearrangement was a tandem
duplication followed by multiple deletions.
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If we assume that the NC region is a partially
deleted and degraded copy of the CR and that the
rearrangement occurred in the common ancestor of
Phylloscopus, we would expect the NC region of
each species to be more similar to the NC regions
of other species than to the CR of that species.
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Discussion and Conclusion
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However, the similarities between the CR and the
NC region of each species were less pronounced
than those between the different NC regions when
we compared closely related species.
Why are the three genes tRNApro ,NADH6 ,and
tRNAGlu prone to move together and prone to
moving to the same site in different lineages? One
possible explanation is that most mitochondrial
rearrangements must be deleterious.
Even if duplications and deletions occur relatively
frequently , only a few gene combinations might be
viable and thus reach fixation.
Hence, the observed positions of the three genes
either downstream or upstream of the control region
in birds might be two of very few function location
for these genes.
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