Rapid transcriptional plasticity
of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
The divergent evolution
of a duplicated gene results in genetic incompatibilities between strains of the plant Arabidopsis.
In theory, excess genes are superfluous and should soon be lost, but in fact many
of the duplicated genes survive to this day — around a third of our genes can be traced back to these two ancient events.
Unexpectedly, they show that the appearance
of duplicated genes was not caused by a simple duplication of the whole genome but rather by a mating («hybridization») event between two different species.
This ancestor «started off with a whole new set
of duplicate genes,» says Michael Clegg, a plant geneticist at the University California, Irvine, who was not involved with the work.
Contribution to the understanding of how the evolution of gene families relates to functional divergence, including the fate
of duplicated genes, horizontal transfer and interspecies hybridization, as well as the characterization of the ancestral patterns of evolution among archosaurs, and the discovery of the late acquisition of mitochondria in eukaryotes (Gabaldón's group, Science 2014, PLoS Biology 2015, PLoS Genetics 2015, Nature 2016).
Not exact matches
And contrary to your cited reference's claim
of a loss
of specificity, to the contrary, these
duplicate genes were then refined by further mutation to make them better.
Over the course
of evolution, some
duplicate genes are short - lived, losing functionality and ultimately being removed.
Armed with the both the king cobra and Burmese python genome the team was able to show that, despite previous hypotheses that venom
genes evolve «early» in the lineage leading to snakes, venom
gene families do not
duplicate early, in fact the study shows that the rapid and extensive expansion
of functionally important venom toxin families is restricted to the venomous «advanced» snake lineage.
So Aoife McLysaght
of Trinity College Dublin, Ireland, set out to investigate why so many
duplicated genes were retained.
Rather than supporting a genome duplication event at the time when yeast evolved to have twice the number
of chromosomes, their data indicated that the
duplicated genes had begun to diverge long before.
All this enabled them to systematically whittle away
genes that either had nonessential functions or
duplicated the function
of another
gene.
Within the
duplicate regions, Carmona - Mora and her colleagues discovered many switches, known as enhancers, important for controlling activity
of genes.
Some evidence hints that
duplicate enhancers may help control
genes important in other parts
of the brain.
Some
duplicated genes were lost over time but others took on new functions, including contributions to the development
of floral organs.
After the
gene was
duplicated — now I just mention [ed] that duplication takes place all
of the time, they are common sort
of genetic accidents — but after the
genes were
duplicated, now there was the opportunity to divide the labor that was once stored by a single
gene; now divide that labor into two
genes, and what happened is, a series a mutations have taken place that has optimized each role — that the regulatory sensor role
of GAL3 and the enzymatic - converting role
of GAL1.
In this episode, Scientific American news editor Phil Yam discusses how veterinarians, physicians and multinational food companies need to work together in the global fight against animal - borne infectious diseases; and University
of Wisconsin evolutionary biologist Sean Carroll talks about recent research tracking the evolution
of yeast
genes with specific functions descended from a single,
duplicated gene with multiple functions.
Hence, the offspring derives all its
genes from the mother, but they are not a
duplicate of her genome.
But even making an elephant whose
genes are 9 % mammoth might take 20 years, and we may never re-create an exact
duplicate of the extinct species, Church says.
Many
genes were
duplicated even more extensively, with four, five or six copies sometimes present, instead
of the usual two.
The process begins when a
gene for a molecule with a potentially toxic function, like a protein - chopping enzyme, is accidentally
duplicated, typically during the formation
of egg cells and sperm.
«First
of all, we know it is not a white pig because it is missing a
duplicated KIT
gene which would make it this colour.
This interaction is explained by divergent evolution occurring among paralogs
of an essential
duplicate gene, for which the functional copy is not located at the same locus in different accessions.
The team discovered that the stretch
of DNA in question has undergone major changes; chunks
of genes have been deleted, other chunks
duplicated or even triplicated.
One result stood out in the DNA
of the people who were less at risk for malaria: Two
genes that provide instructions for two proteins called glycophorin A and glycophorin B were snipped, fused together and
duplicated.
American geneticist Calvin Bridges discovered copy number variation in 1936, when he noticed that flies that inherit a
duplicate copy
of a
gene called Bar develop very small eyes.
They discovered that the number
of tumor suppressor
genes or oncogenes in a chromosome correlated with how often the whole chromosome or part
of the chromosome was deleted or
duplicated in cancers.
Next steps include trying to
duplicate the mutant
of this
gene in the pathogenic form
of mycobacteria, to demonstrate that the
gene is indeed essential as predicted for infection to take place, the microbiologists say.
They found that chickens with the Muffs and beard trait had three
duplicated regions
of chromosome 27, inserted next to one
of the original
gene regions.
In earlier work, James Sikela, a genome researcher at the University
of Colorado, Denver, and Jonathan Pollack from Stanford University and colleagues found 134
genes that had been
duplicated primarily after human ancestors split off from other primates.
A closer look revealed that the heavily -
duplicated gene contained its own duplications: six copies
of a domain called DUF1220.
This receptor is made using one
of two
duplicated copies
of the T - cell receptor
gene, called C1 or C2, at random.
A copy number variant may affect dozens
of genes, or it can disrupt or
duplicate a single
gene.
The researchers analyzed DNA sequences known as transposons, or «jumping
genes,» which can jump from one part
of the genome to another, often
duplicating themselves in the process.
As the authors note, «the presence
of duplicated and diverged genomic regions probably promotes functional novelty between resulting
gene copies, following positive selection.»
In 2008, Wigler proposed that such cases, characterized by changes in
gene copy number —
duplicated or deleted genome segments that leave an individual with extra or missing copies
of one or more
genes — likely account for at least half
of ASD cases.
Andy Peters and Ursula Storb show that the initiation
of Ig
gene transcription targets Ig
gene somatic hypermutation (SHM), by
duplicating the variable (V) region promoter upstream
of the constant (C) region and showing that a second wave
of mutations occurs over the C region.
Genes can be removed, altered, or
duplicated, and rates
of gene expression can be selectively increased or decreased.
Nearly a decade ago now, researchers demonstrated restoration
of more youthful levels
of liver function in old mice by adding a
duplicate gene to increase amounts
of this protein.
However, such CRISPR screens are sensitive to a phenomenon called the copy number effect, where
genes that have been repeatedly
duplicated within a cell (as commonly happens in cancer cells) can be flagged as essential regardless
of whether they are or not.
Estimates from Escherichia coli indicate that 46 %
of its 4100
genes are recognizable as
gene duplicates (Koonin et al., 1995).
The scientists also discovered that
genes modified only by one
of the epigenetic markers, H3K4me3, contain the DNA recipes for proteins that enable an ES cell to proliferate, or
duplicate itself.
In yeast, the published genomic sequences show that at least 14 %
of its 5800
genes are clear
duplicates.
In multicellular organisms, functional
duplicate copies
of a
gene can exist in a genome, but if their expression patterns do not overlap, their products are unable to compensate for each other if either
gene is mutated.
With no tell - tale signs
of whole genome duplication, the researchers say, the octopus must have instead
duplicated specific regions
of its genetic code — and acquired totally novel
genes — over the course
of its evolution.
Furthermore, recombination between
duplicated sequences introduces structural variation into the human genome and facilitates the formation
of clustered
gene families.
The ancient Cucurbita allotetraploid lost its
duplicated genes randomly from both
of the contributing diploids.
Therefore, the second protein is likely a more divergent
duplicate of the ancient Boule
gene, specific to the Cnidarian lineage.
Perhaps the most striking feature is the extent to which individual
genes and entire blocks
of chromosomal regions have been
duplicated in the Arabidopsis genome.
Massively parallel RNA sequencing (RNA - Seq) was used to investigate in an unbiased fashion the expression
of different
genes, comparing the control and DAXX K / D expression patterns in PC3 cells (
duplicate samples).