Migration of green tree frog (Hyla cinerea) into - Lycoming College

thingyoutstandingBiotechnology

Oct 1, 2013 (4 years and 13 days ago)

99 views


G
C
A
T
-
S
E
E
K
quence

The Genome Consortium for Active Teaching

NextGen Sequencing Group


NextGen Sequencing Request Form


Complete fields below, save file with your last name at the beginning of
the filename (e.g. newman
-
GCAT
-
SEEK Sequence request form.pdf) and
email to
Vincent Buonaccorsi
<BUONACCORSI@juniata.edu>


A.

Contact Information



1.

Name:

A. Malcolm Campbell
(lead PI)
and Michael Dorcas

2.

Department:

Biology

3.

Institution:

Davidson College

4.

Phone Number:

704
-
894
-
2692

5.

Email Address

macampbell@davidson.edu
,
midorcas@davidson.edu
,


B.

Project Information

1.

Title
:

Migration of green tree frog in
to historically more temperate regions
.
(
H
yla cinerea
)

2.

Category:

transcriptomes

(Wang

et al.
, 2009)

3.

Total amount of sequence requested:

We will need two to three lanes.

4.

Preferred technology:

Illumina

5.

Do you have funds for a partial run next Spring?

no


C.

Describe the
background, hypotheses and
specific aims (500 words max)


The green tree frog

(
Hyla cinerea
)

historical
ly

was

limited to the
Coastal Plain and lower Piedmont of the
Carolinas

However, within the last 10 years, this species has expanded its range to encompass much of the
Piedmont

(unpublished data)
.

We want to understand
whether

the transcriptome is changing by comparing
transcriptome
s

of
green tree
frogs isolated in the
upper

Piedmont to

those isolated from the
Coastal Plain
.
We would also like to compare the green tree frog with the gray tree frog
(Hyla chrysoscelis), a species
that
has
always lived
throughout both North and South Carolina
. What
has changed? Is climate change

the cause
and the transcriptomes are unchanged

(Stuart
et al.
, 2004; Araújo,
et al.
, 2006; Lips,
et al.
, 2008)
? Or is the
green tree frog evolving and producing a different transcriptome that permits it to survive the colder
conditions?


It is worth
noting that the only
anuran

genomic data publicly available is
the west African
X. tropicalis

(
http://faculty.virginia.edu/xtropicalis/
)
. Searching NCBI database revealed very few entries for any
anu
ran

genes or proteins. To our knowledge, this would be the first genomic
-
level project on any
anuran

from the
Americas. We hope to use this information to provide a good starting place to sequence complete genomes
in the future.

D.

Describe the methods [samp
le prep,
calculation of
amount of sequence required, analysis plan]


One lane would give 37.5GBp of PE sequence.

We will need around 30X coverage for assembly.

This
would be 1.5% of 4GBp * 30 which works out to about 2GBp per transcriptome.

We will
barcode and get 15
samples analyzed in the same lane. We will sample three different sources of RNA: 1) gray tree frog endemic
to Piedmont of NC; 2) green tree frog from endemic
Coastal Plain
; 3) green tree frog from
the
Piedmont of
NC. We will sample
tadpoles and metamorph
os
ing young frogs

at five different developmental stages to
produce 15 samples of mRNA
. We will
prepare the 15 sample
s in triplicate from three different
collections
of biological material to provide greater population diversity and r
edundancy for assembly
.


We are searching for two teaching postdocs funded by Davidson College to lead this interdisciplinary
effort. The bioinformatics postdoc will work with undergraduates to assemble the reads and annotate the
deduced transcripts/g
enes.
We
w
ould assemble the reads using NextGENe, and count using NextGENe or
Galaxy programs.

The conservation biologist will
head up all field work in collaboration with undergraduate
researchers at Davidson College.


E.

Describe
the role
and number
of
unde
rgraduates

involved in

the project
,

and how they would benefit.


Undergraduates from the Dorcas lab will be responsible for collecting the biological samples and
documenting their age and geographical location. Undergraduates from the Campbell lab will

be responsible for
isolating the RNA and keeping track of each biological source. Dorcas and Campbell will mentor the two teaching
postdocs as they work with undergraduates. The postdocs will work collaboratively to assemble and annotate
the transcriptome

in conjunction with all the students enrolled in Laboratory Methods in Genomics which is
required for the Genomics Concentration. In addition, the conservation biology postdoc will work with
undergraduates to survey the region to document the distribution

of gray and green tree frogs. This team of
students and postdocs will integrate the animal distribution data with historical weather records and species
distribution records to better understand the migration of the green tree frog.


The conservation

biology team and the bioinformatics/genomics team will work collaboratively to

determine

if climate and
/
or genomic changes best explain the new migration of green tree frogs.
Dorcas
and Campbell
each
typically mentor about 8 undergraduates a year. In addi
tion, the postdocs will be teaching courses related
to this collaborative project. Over the three
-
year period, we estimate approximately 60 undergraduates will be
directly involved in this transcriptome project.


F.

I agree to administer the GCAT
-
SEEK pre
-

a
nd post
-
activity assessment test for students and to complete the
faculty post
-
utilization survey
.

_
X

yes, ____ no


G.

Describe any other broader impact or intellectual merit considerations.

Xenopus

tropicalis

is the only anuran that
has been sequenced and
this would be the first North American
anuran

sequenced. Since
amphibians

are suffering a radical decline in numbers globally, it would be good to
know the genomes of many species to help us understand what might permit one species to survive but not
another one.





H.

References

Araújo
,

M. B., W. Thuiller
, and R. G. Pearson. 2006.
Climate warming and the decline of amphibians and reptiles
in Europe
.
Journal of Biogeography
. Vol. 33:

1712

1728
.


Lips
,

Karen R., Jay Diffendorfer, Joseph R. Mendelson III, Michael W. Sears.
2008.
Riding the Wave: Reconciling
t
he Roles of Disease and Climate Change in Amphibian Declines. PLoS Biology. Volume 6(3):
441


454.


Stuart
,

Simon N., Janice S. Chanson, Neil A. Cox,

Bruce E. Young, Ana S. L. Rodrigues, Debra L. Fischman,

Robert
W. Waller.
2004.
Status and Trends of Amp
hibian

Declines and Extinctions Worldwide
.
Science. Vol.
306
:
1783


1786.


Wang, Zhong, Mark Gerstein and Michael Snyder. 2009.
RNA
-
Seq: a revolutionary tool for transcriptomics.
Nature Reviews. Vol. 10: 57


63.