Evolution 2023: Gene family expansions underlying a host-plant shift in Manduca sp. - Jay Goldberg
Summary
TLDRJay, a post-doctoral researcher, discusses his work on gene duplications in the Manduca genus, focusing on ecological co-evolution. He highlights the challenges of confirming co-evolution in plant-insect interactions and presents his findings on gene family changes in Manduca species, particularly involving glutathione transferases and odorant receptors. These genes may play roles in detoxification and host plant shifts. Jay aims to understand how natural selection shapes these interaction genes and their role in co-evolution, supported by extensive genome sequencing and analysis.
Takeaways
- đŹ Jay's research focuses on gene duplications across the Manduka genus.
- đ± His broader research interest lies in co-evolution, which involves reciprocal selection during biological interactions.
- đ Jay distinguishes between ecological co-evolution (species interactions in nature) and cellular/molecular co-evolution (molecular interactions within organisms).
- 𧏠Current research emphasizes ecological co-evolution, particularly in plant-insect interactions.
- đŠ Microbial systems are often used to study co-evolution due to clear fitness effects and rapid generation times.
- đ Jay mentions the debunking of the textbook example of garter snakes and toxic newts, highlighting the complexity of co-evolution.
- đŒ His work involves studying the Manduka genus and their interactions with the Datura plant, noting the innate attraction of Manduka moths to Datura's floral volatiles.
- đ Jay uses whole genome sequencing and gene family analysis to study gene gain or loss events underlying host plant shifts.
- đ§Ș Significant findings include the duplication of glutathione transferase genes in Manduka and extra copies of odorant receptor 67c in Manduka sexta.
- đ The research aims to identify interaction genes mediating these co-evolutionary processes, contributing to the understanding of natural selection shaping these genes.
Q & A
What is the primary focus of Jay's post-doc research?
-Jay's post-doc research primarily focuses on gene duplications across the Manduca genus, with a broader emphasis on co-evolution, particularly ecological co-evolution.
What are the two types of co-evolution mentioned in the script?
-The two types of co-evolution mentioned are ecological co-evolution, which occurs when species interact in nature, and cellular or molecular co-evolution, which occurs when different molecules interact within an organism.
Why are microbial systems suitable for studying co-evolution?
-Microbial systems are suitable for studying co-evolution because they have clear fitness effects and rapid generation times, allowing for the observation of evolutionary changes in real time.
What challenge is associated with empirically assessing co-evolution in plant-insect interactions?
-Empirically assessing co-evolution in plant-insect interactions is challenging because there are many different interactions occurring, and any given trait of interest might be influenced by various environmental factors.
What recent findings have debunked a textbook example of co-evolution involving garter snakes and toxic newts?
-Recent findings have shown that the levels of toxins in newt populations are more closely related to their population structure than to the levels of resistance in their predators, indicating that selection is one-sided. The newts' toxins select for resistance in garter snakes, but the snakes' resistance does not select for higher toxin levels in the newts.
What is unique about the interaction between Datura plants and Manduca moths?
-The interaction between Datura plants and Manduca moths is unique because the floral volatiles of Datura plants are innately attractive to the moths, the larvae thrive on the toxic plants, and at least one species of Datura can be completely defoliated without any cost to seed production.
What method is Jay using to understand gene family changes in Manduca species?
-Jay is using whole genome sequencing and de novo assembly of Manduca species genomes, utilizing PacBio's HiFi reads for high accuracy and coverage.
What specific gene family did Jay's research find to have duplicated early in the evolution of the Manduca genus?
-Jay's research found that a glutathione transferase subfamily appears to have duplicated early in the evolution of the Manduca genus, with each species sampled having six to seven copies of this gene versus only one to two in the outgroups.
Why are the duplicated glutathione transferase genes interesting in the context of host plant colonization?
-The duplicated glutathione transferase genes are interesting because they are involved in detoxification of dietary compounds, which could have allowed Manduca species to colonize a diverse array of host plants by sub-functionalizing to detoxify different compounds.
How does Jay's research contribute to understanding co-evolution between Datura and Manduca?
-Jay's research aims to identify interaction genes mediating the interactions between Datura and Manduca, which will help understand how natural selection has shaped these genes and whether co-evolution has played a role in their adaptation.
Outlines
đŹ Jay's Post-Doc Research on Gene Duplications and Co-evolution
Jay introduces his post-doctoral research on gene duplications within the Manduca genus, focusing on the ecological aspects of co-evolution. He explains the difference between ecological and molecular co-evolution, emphasizing the challenge of empirically assessing co-evolution in plant-insect interactions. Jay provides an example involving garter snakes and toxic newts, demonstrating one-sided selection. He compares this to his study on Datura plants and Manduca moths, which are seemingly adapted to each other. Jay highlights that despite extensive research, empirical tests to confirm co-evolution in these systems are lacking. His current focus is on the Manduca side of the interaction, with particular attention to their diverse adaptations across different host plants.
đŠ Manduca Genus Host Plant Shifts and Genomic Analysis
Jay delves into the diversity within the Manduca genus, noting the different host plants utilized by various species. He aims to understand if gene gain or loss events underpin these host plant shifts, focusing on the shift to solanaceous plants in particular. Using whole genome sequencing and de novo assembly, Jay has generated new genomic data for several Manduca species. He explains the annotation process using different pipelines and highlights a gene family analysis performed with OrthoFinder. His research indicates a specific gene duplication event in a glutathione transferase subfamily across the Manduca genus, suggesting its role in detoxification and adaptation to diverse host plants. Additionally, he finds multiple copies of an odorant receptor gene in Manduca sexta, potentially linked to host plant colonization.
đ Identifying Interaction Genes in Co-evolution
Jay discusses his broader research goals of identifying interaction genes that mediate plant-insect co-evolution. He aims to understand how natural selection has shaped these genes, particularly within the Datura plant and its specialist insect community. His work includes annotating and assembling multiple genomes, not just for Manduca and Datura but also for other herbivores and plant species. He highlights the significance of understanding these interactions, including the costs and benefits for the plants involved. Jay concludes by acknowledging the support he received from various collaborators, sequencing services, and funding sources. He invites further questions and provides his contact information.
Mindmap
Keywords
đĄGene duplications
đĄCo-evolution
đĄEcological co-evolution
đĄMolecular co-evolution
đĄManduca genus
đĄDatura plants
đĄObligate interactions
đĄFitness effects
đĄFloral volatiles
đĄGenomic sequencing
đĄGlutathione transferase
đĄOdorant receptor 67c
Highlights
Introduction to ongoing post-doc research on gene duplications across the Manduca genus.
Research focuses on co-evolution, which is the reciprocal process of selection during biological interactions.
Two types of co-evolution: ecological (species interactions) and molecular (molecular interactions within organisms).
Current research emphasis on the ecological aspects of co-evolution.
Few confirmed examples of co-evolution, primarily in obligate interactions and microbial systems.
Microbial systems are advantageous for experimental manipulation due to rapid generation times.
Challenges in empirically assessing co-evolution in plant-insect interactions due to multiple environmental interactions.
Use of sequencing data to detect co-evolution by looking for evidence of past selection.
Recent study debunked a textbook example of co-evolution between garter snakes and toxic newts.
Research on Manduca sexta and its adaptation to Datura plants.
Manduca species' host plants vary significantly, indicating potential gene gain or loss events underlying host plant shifts.
Whole genome sequencing used to study gene family changes in Manduca species.
Glutathione transferase subfamily duplicated early in Manduca evolution, with multiple copies found in sampled species.
Manduca sexta has extra copies of odorant receptor 67c, potentially allowing colonization of new, highly toxic host plants.
Focus on finding interaction genes mediating plant-insect interactions to understand natural selection's role.
Transcripts
hello my name is Jay
and I'm going to tell you about some of
my ongoing post-doc research looking at
Gene duplications across the manduka
genus
my research broadly speaking focuses on
co-evolution which is the reciprocal
process of selection that can occur
during biological interactions broadly
speaking there are two types ecological
co-evolution which occurs when species
Collide in nature and also cellular or
molecular coevolution that occurs when
different molecules Collide within an
organism
right now my research is focusing on the
ecological aspects of this process
I would argue that there aren't really
that many known examples of co-evolution
that have really been confirmed
but of the ones that there are they are
primarily obligate interactions and
microbial systems this is because there
are clear Fitness effects that make them
very very suitable to experimental
manipulation and microbial systems are
particularly cool and a little jealous
that you can observe evolutionary
changes often in real time due to their
rapid generation times
in the plant insect interactions that I
work with co-evolution is often assumed
but can be difficult to empirically
assess because as shown in this figure
there are a number of different
interactions occurring and so any given
trait that you might be interested in
and want to understand if co-evolution
has shaped it
um it could be shaped by a lot of other
things that are going on in the
environment
nowadays we can detect covolution using
sequencing data and looking for evidence
of past selection
and this has actually led to textbook
examples being debunked recently and so
quite literally this was in the textbook
that I had to read as a biology
undergrad the Garter snakes and the
toxic newts that they eat in the Pacific
Northwest and so the functional trait
matching that we see in this system is
often cited as evidence of co-evolution
garter snakes that are feeding on
non-toxic newts have low if any levels
of resistance to their Toxin and the
Garter snakes that feed on highly toxic
nudes tend to have high levels of
resistance but a recent study found that
the levels of the toxins in the new
populations actually more closely relate
to their population structure and not to
the levels of resistance found in their
predators
whereas we do see signatures of
selection in the Garter snakes those
they feed on non-toxic newts have little
if any copies of the resistance genes
whereas the frequency of different
resistance alleles is much much higher
in any population of snakes that's
feeding on toxic nudes this indicates
that selection is one-sided the newts
and their toxins are selecting for
resistance in the Garter snakes but the
resistance of the Garter snakes is not
selecting for higher levels of toxins in
the newts
so in a similar fashion these systems
that I work with datura and maduka
interactions are seemingly adapted to
each other which could be the result of
co-evolution the floral volatiles of
Doterra plants are innately attractive
to the adult manduka mods there's no
learning involved on behalf of the moth
they know exactly what sense to follow
and find these flowers
the larvae of this species thrive on
these highly highly toxic host plants
and perhaps most importantly for
maintaining the mutualistic side of this
interaction there is no cost of
herbivory for at least one species of
detera they can be almost completely
defoliated and bounce back and produce
as many seeds as if they had never
experienced herbivory at all
but despite years if not Decades of
research into the traits mediating this
interaction there haven't really been
any empirical tests that show it is the
result of co-evolution
I'm doing research on both sides of this
interaction but today I'm only going to
show you um the manduca side of things
and so many of you are probably familiar
with manduka sexta the most Supreme
model insect in my opinion
but there are dozens of species in this
genus that have been described and
they're found all over North South and
Central America from Southern Canada all
the way to Argentina and Chile
and in Southern Arizona where I was
doing this research there are six
species the ones pictured
I'd hope to sample all of them for this
study but unfortunately I was only able
to acquire four of them
and I find them a fascinating study
clade because host plants vary
considerably from species to species
they're over positing on a diverse array
of plants
and I want to understand if any Gene
gain or loss events are underlying their
host plant shifts and there's one in
particular that I'm very interested in
so here we see the mandible phylogeny
most species fall within a few species
complexes
and these species complexes on the top
of the tree all exclusively feed on
non-solinacious host plants so there's a
diverse array of plant families that you
can find their caterpillars on but none
of them are in the nightshade family
which includes datura wild tobaccos and
tomato plants as well
whereas the species complexes on the
bottom of this tree the sexta and
occulta complexes exclusively use
solanaceous plants in the nitrate family
as their larval hosts
and so this shift to a soul and AC
specialist lifestyle appears to have
occurred once when Rustica diverged from
the common ancestor of the sexta and the
culta complexity
to address this question and what sort
of Gene family changes were current I
used whole genome sequencing and de novo
assembled some new genomes of manduka
species using path bios HiFi reads these
are highly accurate long reads
um I had no other sequencing data just
lots and lots of Hi-Fi reads
and in fact over 50x coverage for the
two genomes that I assembled and um my
friend and collaborator Dr Keaton
Godfrey was very generous and donated uh
commanduka Rustico assembly that she has
worked on to this project
I annotated all these genomes with the
fun annotate pipeline although I'm
currently redoing it with Helix sir
which is a brand new annotation pipeline
that I found much easier to work with
and just as robust if not better than
both fun annotate and the breaker
pipeline which I believe is the standard
nowadays
and the gene family analyzes I'm about
to show you were done with ortho finder
So This research was done with the help
of two really outstanding high school
students that I was mentoring earlier
this year
for any Arizona folks in the audience
today I highly recommend that you
participate in sarsa Star Lab program it
was a really rewarding experience for me
and helped me refine my teaching and
mentoring skills
and we found that a glutathione
transferase subfamily appears to have
duplicated in early on in the evolution
of the manduka genus
each species that we sampled had six to
seven copies of this Gene in their
genomes versus only one to two in the
out groups that we were using which was
the domestic silk mall and highly's best
for tilio which is in the same family as
manduka but about as distantly related
as two species in the same family can
feed
just to emphasize all of these branches
here on the tree
were manduka-specific copies of this
Gene whereas the top three branches were
the ones found in our outgroups
we also found that manduka's sexta
specifically has extra copies of odorant
receptor 67c there were seven copies in
its genome versus three to four in the
other Hawk moths in its family and two
in the domestic silkmonts
and most of the manduka manduka sex the
specific duplications occurred on this
branch of the gene tree
so why are these genes so interesting to
me well gsts are broadly involved in
detoxification of dietary compounds mid
gut expression is induced by the
consumption of these chemicals and
selection on them often unrealize
resistance to insecticides by pests
having multiple copies of a gene like
this could have allowed them to
sub-functionalize which compounds
they're detoxifying and subsequently
colonize a diverse array of host plants
as the gene is Diversified
or 67c is under positive selection in a
species of cactophilic drostophila
and this selection is associated with
multiple very recent host shifts to
alkaloid-rich columnar cacti so perhaps
there's some sort of convergent or
parallel Evolution going on that is
mediated by this Gene and allowing
manduca and drosophila to colonize new
highly toxic host points
and so to tie this all back to
co-evolution the driving force of my
research program this is all focused on
finding the interaction genes that are
mediating these interactions so that I
can take further steps
to understand how natural selection has
shaped these interaction genes
and I am very broadly interested in
datura and its specialist insect
Community if and how co-evolution has
shaped them and what sort of genes are
involved in these interactions and so I
have quite a few genomes that I'm
working on right now most of the
assemblies and annotations are almost
done
and so uh not just manduka and datura
but also hamifter and herbivores a few
species of Weevil and another species of
datura that has um it is not quite so
well trait matched to its herbivores for
example there is a strong cost to
refrigerate if it's defoliated it
doesn't bounce back
and so with that I'd like to acknowledge
everyone who has helped me with this
project over the years both from
developing the ideas and also all the
various Labs that have helped me carry
out this research
um of course have to acknowledge the
sequencing services that I used
and also the funding that was generously
provided by the University of Arizona
Pacific bioscience and the National
Science Foundation
and you can find me on Mastodon if you
have any further questions or anyone
you're welcome to send me an email and
thank you for watching
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