Zhang et al ecn 2016 building an accessible weevil tissue collection for genomic research
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Transcript of Zhang et al ecn 2016 building an accessible weevil tissue collection for genomic research
Acknowledgments: NSF DEB-1155984, USDA Agreement 58-1275-1-335 (N. Franz). ESA STEP travel
award (G. Zhang). Lourdes Chamorro and Robert Anderson provided input towards this project.
Model Purpose Adoptab-
ility
Access
(online)
Access
(loan)
Sustainability Researcher
empowerment
Lab Research High Poor Discretionary 20-30 years High
Museum Collection Moderate Variable Variable Long-term Variable
GGBN Res & Coll Unclear Good Variable Unclear Low
WTC Res & Coll High Good Available Long-term High
Building an accessible weevil tissue collection for genomic research Guanyang Zhang, Sangmi Lee, Bukola Obayomi, Joseph Hunter, Salvatore Anzaldo, Nico Franz
School of Life Sciences, Arizona State University, Tempe, Arizona, USA
[email protected], [email protected], [email protected], @GYZhang2 @taxonbytes
Fresh specimens are critical for molecular phylogenetic and -genomic
research, but can be difficult to obtain. Reasons for this bottleneck
include: (1) Monophyletic lineages are distributed across international
borders. (2) Individual, short-termed, international collecting trips often
fail to yield target species while generating “rare species” represented
by singletons or few specimens. (3) Locally common species are usually
neglected by local collectors, but may be important to foreign
researchers that cannot readily obtain them. (4) Entomological
museums and collections typically do not curate tissue collections
(TCs), due to special curatorial and resource challenges.
Fresh specimens – bottleneck in genomic research
We summarize and evaluate four models of TCs in the table below: Lab:
TCs curated by individual researchers. Museum: museum-based TCs.
GGBN (Global Genome Biodiversity Network, ggbn.org): network of
large museums. WTC: WeevilTissueCollection. Models may overlap.
The issues – accessibility, sustainability & empowerment
The Franz Lab and Hasbrouck Insect Collection at Arizona State
University (ASUHIC) are building the WTC. This collection combines the
advantages of other models with the following features. (1) Specimen
data and images are accessible on-line through the SCAN (Symbiota
Collections of Arthropods Network) portal. (2) Globally located
researchers can participate in on-line curation. (3) Specimens are
available for loan to all researchers and kinds of research, with minimal
administrative burden. (4) Long-term sustainability highly likely in a
public research university with a permanent commitment to collection
staff. In summary, the WTC model is designed to empower researchers.
WTC enables access & empowers researchers
Collecting: Existing specimens curated in WTC have been acquired in the course of multiple international field
trips, each lasting 2-3 weeks, spanning five Neotropical countries (Cuba, Dominica, Dominican Republic, Guatemala
and Panama). The main collecting method used are beating sheets targeting plants near ground level. Habitats
comprise primarily tropical dry and rainforests. Elevations of localities range from sea level to 2,500 m.
Sorting: Specimens were sorted to morpho-species, and each was
assigned a “WTCsp” number (Fig. 1). At least one specimen/species
was used as a WTC voucher, preserved in 95% ethanol, and stored in
-20°C or -80°C freezers. Duplicates, if present, serve as additional
WTC vouchers and dry specimens. All specimens were assigned
locally unique identifiers (catalogue numbers, e.g., ASUHIC0071465).
Two undergraduate students sorted and imaged 534 morpho-species,
taking altogether ~350 hours (= one semester + one summer).
Digitization: Voucher WTC specimens were imaged with a Leica M205C stereoscope equipped with an imaging
system. Specimens were temporarily dried and placed in a small glass, laying on glass beads to facilitate
positioning (Fig. 1D). Specimen occurrence records and images were recorded in, and uploaded to, SCAN
(http://symbiota4.acis.ufl.edu/scan/portal/).
On-line access: WTC voucher specimen records and images (Figs. 2,4) are
accessible using this link tinyurl.com/weeviltissuecollection (redirect to SCAN,
Fig. 3). Specimen records can also be interactively viewed on Google map (Fig. 5).
Remote identification & annotation of WTC
specimens can be performed in SCAN, by
taxonomic experts examining specimen records
and images (Fig. 8). Genus-level identification
is often achievable based on images. This
process is enabled by SCAN’s multi-user
platform. A community of researchers can
participate in the on-line curation of WTC
specimens and request loans. Other researchers
have shown interests in WTC (Fig. 7).
Loan policy: All WTC specimens are
available for loan to any researcher,
and including diverse research foci.
Figure 7. E-mail from a weevil researcher showing interest in the WTC holdings.
Figure 8. Online identification and annotation of a specimen record representing an undescribed new species.
Figure 2. A specimen record with habitus images.
Figure 4. WeevilTissueCollection (WTC) data portal snippet.
Figure 5. Interactive distribution map of WTC specimens.
Molecular work: DNA extraction from whole
bodies is recommended for small weevils (<5
mm), which constitute the WTC majority. For
larger specimens, a hindleg can be used. If in
need of high quantities of DNA, muscle tissues
from the thorax may be dissected out.
Extracted whole specimens will be mounted
and integrated with regular dry specimens.
Curation of genomic extracts: DNA extracts obtained by the
local or external researchers will be deposited at ASUHIC and
stored in a -80°C freezer. In the future we will explore
methods of preserving and transporting genomic DNA extracts
under dry conditions, and also best practices to make genomic
extracts available for loan. SCAN is developing a DNA module.
Morphological work: WTC specimens are also available for
research that is exclusively morphological. DNA extraction will
be performed by the owner institution (ASUHIC) before
specimen loans are issued. New species are evidently present
in WTC (Fig. 6), and making the respective specimens
available for description and publication is a top priority. Figure 6. A WTC specimen from Cuba representing possibly a new species of Sicoderus.
Figure 1. Specimen labeling, storage, and temporary mount systems.
(A) Collecting data label, WTCsp code, and catalogue number label.
(B) As in (A), showing a large specimen.
(C) Storage tubes (2ml & 5ml).
(D) Temporary mount in a glass dish bedded with glass beads for imaging.
(A) (B) (C)
(D)
[Researcher X]
Figure 3. QR code for WTC access link