http://lod.bco-dmo.org/id/dataset/982240
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-08-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Infectivity assays and ultrastructural characterization of Thalassia testudinum agroinfected with Turtle grass virus X (TGVX) in laboratory aquaria, February-May 2024
2025-08-11
publication
2025-08-11
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2025-12-03
publication
https://doi.org/10.26008/1912/bco-dmo.982240.1
Mya Breitbart
University of South Florida
principalInvestigator
Bradley Furman
Florida Fish and Wildlife Commission
principalInvestigator
Luis Alvarado Marchena
University of South Florida
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Alvarado Marchena, L., Breitbart, M., Furman, B. (2025) Infectivity assays and ultrastructural characterization of Thalassia testudinum agroinfected with Turtle grass virus X (TGVX) in laboratory aquaria, February-May 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-08-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.982240.1 [access date]
Methods and Sampling: <div>
<p><span style="font-size:13px"><strong>Site</strong><br />
Study sites were located in Tampa Bay, Florida, USA. The viral genome was sourced from naturally infected Thalassia testudinum at Terra Ceia Aquatic Preserve (27.5838°N, 82.6161°W), a shallow coastal seagrass meadow. Experimental host plants were collected from Lassing Park in St. Petersburg (27.7538°N, 82.6281°W), another nearshore seagrass habitat.<br />
<br />
<strong>Sample Collection and Preparation</strong><br />
Young&nbsp;Thalassia testudinum&nbsp;plants were collected from Lassing Park, St. Petersburg, Florida, USA (27.7538°N, 82.6281°W) on March 4th, 2024. Collected specimens were transported in ambient seawater to the Knight Oceanographic Research Center Aquarium (University of South Florida), transplanted into 6-cm diameter pots with beach sand, and maintained in 10-liter aquaria. Artificial seawater was prepared using Instant Ocean at a salinity of 30 PSU (±0.5). The aquaria system was maintained at 30°C (±0.5) with constant aeration and a 16:8 light:dark photoperiod.</span></p>
<p><span style="font-size:13px">Prior to agroinfection, plants were screened for potexviruses using multiplex RT-PCR with specific primers targeting the TGVX coat protein (MBL5: 5′-CACAGATGAAGAGCTGACC-3′ and MBL6: 5′-TTCGATGAAGTAAGTGGCGG-3′) and degenerate primers for the potexvirus replicase gene (Potex-5/Potex-2RC), as described by van der Vlugt and Berendsen (2002). Mitochondrial&nbsp;nad5&nbsp;gene primers (nad5-F/nad5-R; Menzel et al. 2002) were included as internal control.</span></p>
<p><span style="font-size:13px"><strong>Viral Source and Clone Construction</strong><br />
TGVX genomic RNA was extracted from naturally infected&nbsp;T. testudinum&nbsp;leaves collected at Terra Ceia Aquatic Preserve, Tampa Bay, Florida (27.5838°N, 82.6161°W) on February 5th, 2024 (Van Bogaert et al. 2019). Viral RNA was isolated following the protocol of Sánchez-Navarro et al. (2013) and amplified using the SuperScript IV One-Step RT-PCR System (Invitrogen) with genome-specific primers (MBL1 and MBL2) designed based on the full TGVX genome (GenBank accession MH077559; Van Bogaert et al. 2019). The full-length cDNA (6.3 kb) was assembled into a pLX mini binary vector (Pasin et al. 2018) using a BsmBI-based directional cloning strategy. Resulting constructs were transformed into&nbsp;Escherichia coli&nbsp;DH5α, screened by colony PCR, and validated via whole-plasmid sequencing with Oxford Nanopore technology.</span></p>
<p><span style="font-size:13px"><strong>Agroinfection Assays</strong><br />
The pLX-TGVX plasmid and an empty vector (mock control) were transformed into&nbsp;Agrobacterium tumefaciens&nbsp;strain C58C1. Bacterial suspensions were prepared in induction buffer composed of 10 mM MES (pH 5.6), 10 mM MgCl₂, and 200 µM acetosyringone, and adjusted to an optical density of 0.6 at 600 nm. Plants were agroinfiltrated on the abaxial side of two leaves using a needleless syringe. At 17 days post-infiltration, systemic infection was confirmed by RT-PCR detection of the TGVX coat protein from upper, non-inoculated leaves.</span></p>
<p><span style="font-size:13px">Experimental treatments were categorized as mock-inoculated, pre-inoculation (baseline control), and post-inoculation (TGVX-infected).</span></p>
<p><span style="font-size:13px"><strong>Microscopy and Symptom Analysis</strong><br />
Phenotypic changes were documented using photography, capturing leaf deformation, curling, and wrinkling in both infected and control plants.</span></p>
<p><span style="font-size:13px">Transmission electron microscopy (TEM) was used to visualize virus-like particles and evaluate cytopathological effects. Leaf tissue was processed using the leaf-dip method and standard fixation, embedding, and ultrathin sectioning protocols (Brandes and Wetter 1959; Alvarado et al. 2019). Observed abnormalities included chloroplast swelling, loss of thylakoid grana, formation of replication organelles, and laminar aggregates, consistent with potexvirus infections.</span></p>
<p><span style="font-size:13px">TEM analysis was performed on both published and unpublished samples to support figure-based interpretation as well as broader ultrastructural screening.</span></p>
<p><strong><span style="font-size:13px">Image Data and Inventory</span></strong></p>
<p><span style="font-size:13px">The dataset includes three categories of image data:</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;1. RT-PCR gel electrophoresis images: Bands confirming presence/absence of TGVX coat protein and potexvirus replicase.</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;2.&nbsp;Phenotypic photographs: Images showing visible plant morphology differences between mock and infected conditions.</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;3.&nbsp;TEM images: Visual evidence of cytopathology caused by TGVX infection, including filamentous virus-like particles, swollen or disorganized chloroplasts, reduced thylakoid grana, membrane-bound replication organelles, and laminar aggregates.</span></p>
<p><strong><span style="font-size:13px">Each image file is cataloged in the file inventory table (file_inventory.csv), which includes:</span></strong></p>
<p><span style="font-size:13px">&nbsp; &nbsp;- Filename and folder name</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Experimental treatment group (mock, pre-inoculation, post-inoculation)</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Image category (RT-PCR, phenotype, TEM)</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Short description of observed features</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Scale bar (when applicable)</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Publication status&nbsp;</span></p>
<p><span style="font-size:13px">The TEM component of this dataset is complete and includes all ultrastructural images generated during the agroinfection experiments. RT-PCR and phenotype images correspond to figures published in the associated manuscript, while some TEM images remain unpublished but are provided here to support broader reuse and interpretation.</span><br />
<br />
<strong>Terms and&nbsp;parameter definitions</strong>&nbsp;(used in files within<strong> </strong><span style="font-size:13px">TGVX_agroinfection_turtlegrass_files.zip)</span><strong>:</strong></p>
<p>Plant_ID, "Unique identifier assigned to each individual <em>Thalassia testudinum</em> plant used in the experiment", unitless, NA<br />
Treatment, "Type of inoculation applied to the plant; pLX-TGVX = virus clone treatment, Mock = empty vector control", unitless, NA<br />
Days_Post_Agroinfection, "Time elapsed since agroinfiltration was performed on the plant", days, N/A<br />
TGVX_RT-PCR_Result, "Detection of TGVX RNA in plant tissues using coat protein-specific primers; Positive = viral RNA detected, Negative = not detected", unitless, NA<br />
Infection_Symptoms, "Visual symptoms associated with viral infection; Yes = symptoms present, No = no symptoms", unitless, NA<br />
VLP_Observed_TEM, "Presence of virus-like particles as observed by transmission electron microscopy; Yes = VLPs seen, No = not observed", unitless, NA<br />
Chloroplast_Alterations, "Presence of cytopathological changes in chloroplasts due to viral infection; Yes = observed, No = not observed", unitless, NA<br />
RO_Presence, "Detection of viral replication organelles in tissue sections via TEM; Yes = present, No = absent", unitless, NA<br />
Grana_Reduction_Level, "Qualitative classification of thylakoid grana reduction in infected chloroplasts; None, Moderate, or Severe", unitless, NA</p>
<p><span style="font-size:13px"><strong>Organism identifiers </strong>(</span>name, Life Science Identifier (LSID), ncbi_txid)<span style="font-size:13px">:<br />
Thalassia testudinum, urn:lsid:marinespecies.org:taxname:374720,&nbsp;NCBI:txid55497<br />
Agrobacterium tumefaciens, urn:lsid:marinespecies.org:taxname:1501465,&nbsp;NCBI:txid358<br />
"Escherichia coli DH5[alpha]", , NCBI:txid668369<br />
"Turtle grass virus X", ,&nbsp;NCBI:txid2292642</span></p>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2219547 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2219547
completed
Mya Breitbart
University of South Florida
(727) 553-3520
USF College of Marine Sciences 140 7th Avenue South
St Petersburg
FL
33701
USA
mya@marine.usf.edu
pointOfContact
Bradley Furman
Florida Fish and Wildlife Commission
bradley.furman@myfwc.com
pointOfContact
Luis Alvarado Marchena
University of South Florida
luis.alvarado.ccr@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Eppendorf 5424
JEOL JEM-1400
Bio-Rad PowerPac Basic with Bio-Rad Sub-Cell Model 96
Fisher Scientific Isotemp 650D
Glass Aquaria
GLP24ADJS/19W/LED
Syngene Ingenius 3
AirClean 600 PCR Workstation
Leica EM UC6
Eppendorf BioPhotometer
Eppendorf Mastercycler X50a
theme
None, User defined
Centrifuge
Electron Microscope
Electrophoresis Chamber
Immersion heater
Incubator
no_bcodmo_term
no_bcodmo_term
no_bcodmo_term
no_bcodmo_term
no_bcodmo_term
no_bcodmo_term
Salinity Sensor
Spectrometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: VIDA Seagrass: Viral Infection Dynamics Among Seagrass
https://osprey.bco-dmo.org/project/877244
Collaborative Research: VIDA Seagrass: Viral Infection Dynamics Among Seagrass
<p><em>NSF Award Abstract:</em><br />
Seagrasses are marine flowering plants (or angiosperms) that create expansive underwater meadows that form the basis of highly productive and valuable ecosystems in coastal oceans. Unlike terrestrial systems where angiosperms dominate plant diversity, seagrasses are the only flowering plants in marine environments. Based on the profound impacts of viral infections on terrestrial plants, viruses are expected to influence seagrass ecology. However, no prior work has investigated viral infection dynamics in seagrasses or the impact of viruses on seagrass health. This project provides fundamental knowledge about seagrass-virus interactions through field and laboratory studies of Thalassia testudinum (i.e., turtlegrass, a climax species and key ecosystem engineer), and turtlegrass virus X (TVX), the only seagrass virus currently reported from experimental research. The lack of a seagrass-virus study system has kept the scientific community from learning which factors drive viral infection in marine angiosperms. By establishing the first seagrass-virus study system, a novel virus-host pathosystem for which virtually nothing is known, this project contributes to a more comprehensive understanding of seagrass ecology and serves as a model for investigating the growing number of seagrass viruses discovered through sequencing efforts. This multifaceted project trains one postdoctoral researcher, two graduate students, and six undergraduate students. Dissemination of results and data through open access channels informs the broader community and provides scientists with data for their own research to propel the field of seagrass virology. This project also engages educators and students participating in programs that strive to increase participation from underrepresented groups in STEM fields. Teachers from the Jacksonville Teacher Residency Program are getting involved through development of lessons that dive into seagrass biology. Students from Girls Incorporated, Girl Scouts, and the University of South Florida’s Oceanography Camp for Girls are participating as citizen scientists by photographing Tampa Bay’s seagrass ecosystems and contributing their observations to the Seagrass Spotter website. This project also increases awareness of seagrass ecosystems and challenges the public perception that all viruses are pathogenic through hands-on activities at the annual St. Petersburg Science Festival.</p>
<p>Seagrass-virus interactions are being investigated through a two-tiered approach involving field studies in Tampa Bay, Florida and microcosm experiments. Field surveys focus on elucidating the nature of turtlegrass-TVX interactions (positive, neutral or negative) and the relationship between turtlegrass genotypic diversity and virus distribution in a natural population where TVX has persisted for at least five years. TVX load is monitored bimonthly over two years to assess how viral load relates to turtlegrass genotype and performance (growth, health, reproductive effort), and abiotic parameters. The investigated turtlegrass meadow contains TVX-positive and negative specimens, thus providing a perfect natural laboratory with homogenous environmental characteristics that allow exploration of the drivers of viral infection. Given that environmental changes may alter host-microbe interactions, complementary microcosm experiments are evaluating turtlegrass responses to TVX infection at the physiological (survival, photochemical capacity, cellular responses) and molecular (transcriptomic) levels in a controlled environment under normal conditions and in the context of salinity changes, an important seagrass stressor. Microcosm experiments also provide the first profiles of seagrass gene expression and measurement of cellular metabolites in response to viral infection. Expected results have direct implications for understanding seagrass production and resilience in the face of global climate change and anthropogenic stress.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
VIDA Seagrass
largerWorkCitation
project
eng; USA
oceans
-82.635578
-82.607178
27.583468
27.758566
2024-02-01
2024-05-31
Tampa Bay, Florida
0
BCO-DMO catalogue of parameters from Infectivity assays and ultrastructural characterization of Thalassia testudinum agroinfected with Turtle grass virus X (TGVX) in laboratory aquaria, February-May 2024
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://doi.org/10.26008/1912/bco-dmo.982240.1
download
onLine
dataset
<div>
<p><span style="font-size:13px"><strong>Site</strong><br />
Study sites were located in Tampa Bay, Florida, USA. The viral genome was sourced from naturally infected Thalassia testudinum at Terra Ceia Aquatic Preserve (27.5838°N, 82.6161°W), a shallow coastal seagrass meadow. Experimental host plants were collected from Lassing Park in St. Petersburg (27.7538°N, 82.6281°W), another nearshore seagrass habitat.<br />
<br />
<strong>Sample Collection and Preparation</strong><br />
Young&nbsp;Thalassia testudinum&nbsp;plants were collected from Lassing Park, St. Petersburg, Florida, USA (27.7538°N, 82.6281°W) on March 4th, 2024. Collected specimens were transported in ambient seawater to the Knight Oceanographic Research Center Aquarium (University of South Florida), transplanted into 6-cm diameter pots with beach sand, and maintained in 10-liter aquaria. Artificial seawater was prepared using Instant Ocean at a salinity of 30 PSU (±0.5). The aquaria system was maintained at 30°C (±0.5) with constant aeration and a 16:8 light:dark photoperiod.</span></p>
<p><span style="font-size:13px">Prior to agroinfection, plants were screened for potexviruses using multiplex RT-PCR with specific primers targeting the TGVX coat protein (MBL5: 5′-CACAGATGAAGAGCTGACC-3′ and MBL6: 5′-TTCGATGAAGTAAGTGGCGG-3′) and degenerate primers for the potexvirus replicase gene (Potex-5/Potex-2RC), as described by van der Vlugt and Berendsen (2002). Mitochondrial&nbsp;nad5&nbsp;gene primers (nad5-F/nad5-R; Menzel et al. 2002) were included as internal control.</span></p>
<p><span style="font-size:13px"><strong>Viral Source and Clone Construction</strong><br />
TGVX genomic RNA was extracted from naturally infected&nbsp;T. testudinum&nbsp;leaves collected at Terra Ceia Aquatic Preserve, Tampa Bay, Florida (27.5838°N, 82.6161°W) on February 5th, 2024 (Van Bogaert et al. 2019). Viral RNA was isolated following the protocol of Sánchez-Navarro et al. (2013) and amplified using the SuperScript IV One-Step RT-PCR System (Invitrogen) with genome-specific primers (MBL1 and MBL2) designed based on the full TGVX genome (GenBank accession MH077559; Van Bogaert et al. 2019). The full-length cDNA (6.3 kb) was assembled into a pLX mini binary vector (Pasin et al. 2018) using a BsmBI-based directional cloning strategy. Resulting constructs were transformed into&nbsp;Escherichia coli&nbsp;DH5α, screened by colony PCR, and validated via whole-plasmid sequencing with Oxford Nanopore technology.</span></p>
<p><span style="font-size:13px"><strong>Agroinfection Assays</strong><br />
The pLX-TGVX plasmid and an empty vector (mock control) were transformed into&nbsp;Agrobacterium tumefaciens&nbsp;strain C58C1. Bacterial suspensions were prepared in induction buffer composed of 10 mM MES (pH 5.6), 10 mM MgCl₂, and 200 µM acetosyringone, and adjusted to an optical density of 0.6 at 600 nm. Plants were agroinfiltrated on the abaxial side of two leaves using a needleless syringe. At 17 days post-infiltration, systemic infection was confirmed by RT-PCR detection of the TGVX coat protein from upper, non-inoculated leaves.</span></p>
<p><span style="font-size:13px">Experimental treatments were categorized as mock-inoculated, pre-inoculation (baseline control), and post-inoculation (TGVX-infected).</span></p>
<p><span style="font-size:13px"><strong>Microscopy and Symptom Analysis</strong><br />
Phenotypic changes were documented using photography, capturing leaf deformation, curling, and wrinkling in both infected and control plants.</span></p>
<p><span style="font-size:13px">Transmission electron microscopy (TEM) was used to visualize virus-like particles and evaluate cytopathological effects. Leaf tissue was processed using the leaf-dip method and standard fixation, embedding, and ultrathin sectioning protocols (Brandes and Wetter 1959; Alvarado et al. 2019). Observed abnormalities included chloroplast swelling, loss of thylakoid grana, formation of replication organelles, and laminar aggregates, consistent with potexvirus infections.</span></p>
<p><span style="font-size:13px">TEM analysis was performed on both published and unpublished samples to support figure-based interpretation as well as broader ultrastructural screening.</span></p>
<p><strong><span style="font-size:13px">Image Data and Inventory</span></strong></p>
<p><span style="font-size:13px">The dataset includes three categories of image data:</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;1. RT-PCR gel electrophoresis images: Bands confirming presence/absence of TGVX coat protein and potexvirus replicase.</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;2.&nbsp;Phenotypic photographs: Images showing visible plant morphology differences between mock and infected conditions.</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;3.&nbsp;TEM images: Visual evidence of cytopathology caused by TGVX infection, including filamentous virus-like particles, swollen or disorganized chloroplasts, reduced thylakoid grana, membrane-bound replication organelles, and laminar aggregates.</span></p>
<p><strong><span style="font-size:13px">Each image file is cataloged in the file inventory table (file_inventory.csv), which includes:</span></strong></p>
<p><span style="font-size:13px">&nbsp; &nbsp;- Filename and folder name</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Experimental treatment group (mock, pre-inoculation, post-inoculation)</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Image category (RT-PCR, phenotype, TEM)</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Short description of observed features</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Scale bar (when applicable)</span></p>
<p><span style="font-size:13px">&nbsp; &nbsp;-&nbsp;Publication status&nbsp;</span></p>
<p><span style="font-size:13px">The TEM component of this dataset is complete and includes all ultrastructural images generated during the agroinfection experiments. RT-PCR and phenotype images correspond to figures published in the associated manuscript, while some TEM images remain unpublished but are provided here to support broader reuse and interpretation.</span><br />
<br />
<strong>Terms and&nbsp;parameter definitions</strong>&nbsp;(used in files within<strong> </strong><span style="font-size:13px">TGVX_agroinfection_turtlegrass_files.zip)</span><strong>:</strong></p>
<p>Plant_ID, "Unique identifier assigned to each individual <em>Thalassia testudinum</em> plant used in the experiment", unitless, NA<br />
Treatment, "Type of inoculation applied to the plant; pLX-TGVX = virus clone treatment, Mock = empty vector control", unitless, NA<br />
Days_Post_Agroinfection, "Time elapsed since agroinfiltration was performed on the plant", days, N/A<br />
TGVX_RT-PCR_Result, "Detection of TGVX RNA in plant tissues using coat protein-specific primers; Positive = viral RNA detected, Negative = not detected", unitless, NA<br />
Infection_Symptoms, "Visual symptoms associated with viral infection; Yes = symptoms present, No = no symptoms", unitless, NA<br />
VLP_Observed_TEM, "Presence of virus-like particles as observed by transmission electron microscopy; Yes = VLPs seen, No = not observed", unitless, NA<br />
Chloroplast_Alterations, "Presence of cytopathological changes in chloroplasts due to viral infection; Yes = observed, No = not observed", unitless, NA<br />
RO_Presence, "Detection of viral replication organelles in tissue sections via TEM; Yes = present, No = absent", unitless, NA<br />
Grana_Reduction_Level, "Qualitative classification of thylakoid grana reduction in infected chloroplasts; None, Moderate, or Severe", unitless, NA</p>
<p><span style="font-size:13px"><strong>Organism identifiers </strong>(</span>name, Life Science Identifier (LSID), ncbi_txid)<span style="font-size:13px">:<br />
Thalassia testudinum, urn:lsid:marinespecies.org:taxname:374720,&nbsp;NCBI:txid55497<br />
Agrobacterium tumefaciens, urn:lsid:marinespecies.org:taxname:1501465,&nbsp;NCBI:txid358<br />
"Escherichia coli DH5[alpha]", , NCBI:txid668369<br />
"Turtle grass virus X", ,&nbsp;NCBI:txid2292642</span></p>
</div>
Specified by the Principal Investigator(s)
<p><strong>Molecular data (RT-PCR results)</strong> were processed by visualization on agarose gels stained with ethidium bromide and photographed using the Syngene Ingenius 3 imaging system. Digital images were cropped and labeled using Microsoft PowerPoint 365 to organize figures in a clear and consistent manner.</p>
<p><strong>Transmission electron microscopy (TEM)</strong> images were acquired using Gatan DigitalMicrograph software and exported as uncompressed TIFF files. Brightness and contrast levels were uniformly adjusted using GIMP 2.10.32 to enhance visual clarity without altering scientific information. Scale bars were standardized across micrographs using ImageJ (Fiji distribution).</p>
<p><strong>Phenotypic data (visual leaf symptoms)</strong> were documented photographically, and images were organized and annotated in Microsoft PowerPoint 365, then exported as TIFF files.</p>
<p><strong>Sequencing reads for validation of the TGVX genome </strong>assembly were basecalled and assembled using Oxford Nanopore (Eurofins), then aligned to the reference TGVX genome (GenBank accession MH077559) using SnapGene v8.1.1. Sequence identity and coverage were quantified, and the assembled genome was deposited in GenBank (accession number PP887953).</p>
<p>No statistical analyses or graphical outputs were performed at this stage. All data files and processed images are available in both original and presentation-ready formats.</p>
Specified by the Principal Investigator(s)
* Files within submitted file set under "TGVX_agroinfection_turtlegrass/" were packaged into TGVX_agroinfection_turtlegrass_files.zip and attached to this dataset. The associated file descriptions and metadata were uploaded as supplemental file file_inventory.csv.
* Organism names in this dataset were matched to Life Science Identifiers (LSIDs) using the World Register of Marine Species (WoRMS) on 2025-11-20 and added to the Methods&Sampling metadata section. Identifiers at NCBI were also added.
* Collection metadata included in Sampling_Metadata_Table/Thalassia_Plants_Sampling_Metadata.xlsx with the zip file package was also extracted as csv and attached as a supplemental file directly: Thalassia_Plants_Sampling_Metadata.csv
** Coordinates converted to individual Lat,Lon columns in decimal degrees
** Date format changed to ISO 8601 format.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Eppendorf 5424
Eppendorf 5424
PI Supplied Instrument Name: Eppendorf 5424 PI Supplied Instrument Description:Microcentrifuge: Eppendorf 5424 – used for pelleting and separation steps in nucleic acid extraction. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
JEOL JEM-1400
JEOL JEM-1400
PI Supplied Instrument Name: JEOL JEM-1400 PI Supplied Instrument Description:Transmission Electron Microscopy (TEM): JEOL JEM-1400 – used for imaging of virus-like particles and cytopathology at 80 kV. Instrument Name: Electron Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB07/
Bio-Rad PowerPac Basic with Bio-Rad Sub-Cell Model 96
Bio-Rad PowerPac Basic with Bio-Rad Sub-Cell Model 96
PI Supplied Instrument Name: Bio-Rad PowerPac Basic with Bio-Rad Sub-Cell Model 96 PI Supplied Instrument Description:Bio-Rad PowerPac Basic with Bio-Rad Sub-Cell Model 96 – used for agarose gel electrophoresis. Instrument Name: Electrophoresis Chamber Instrument Short Name: Instrument Description: General term for an apparatus used in clinical and research laboratories to separate charged colloidal particles (or molecules) of varying size through a medium by applying an electric field.
PI Supplied Instrument Name: PI Supplied Instrument Description:Temperature Control: Submersible aquarium heaters with digital thermometers – used to maintain stable temperature (~30°C). Instrument Name: Immersion heater Instrument Short Name:Immersion heater Instrument Description: Submersible heating element for water tanks and aquaria.
Fisher Scientific Isotemp 650D
Fisher Scientific Isotemp 650D
PI Supplied Instrument Name: Fisher Scientific Isotemp 650D PI Supplied Instrument Description:Oven: Fisher Scientific Isotemp 650D – used to polymerize Spurr resin during sample embedding for TEM. Instrument Name: Incubator Instrument Short Name:incubator (general) Instrument Description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled.
Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494).
Glass Aquaria
Glass Aquaria
PI Supplied Instrument Name: Glass Aquaria PI Supplied Instrument Description:Glass Aquaria: 10-liter capacity – used for maintaining Thalassia testudinum plants under controlled lab conditions. Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
PI Supplied Instrument Name: PI Supplied Instrument Description:Aeration System: Aquarium air pumps with diffusers – used to oxygenate water. Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
GLP24ADJS/19W/LED
GLP24ADJS/19W/LED
PI Supplied Instrument Name: GLP24ADJS/19W/LED PI Supplied Instrument Description:Plant Grow Light: GLP24ADJS/19W/LED (Home Depot) – used to simulate natural light photoperiod (16:8 L:D). Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
Syngene Ingenius 3
Syngene Ingenius 3
PI Supplied Instrument Name: Syngene Ingenius 3 PI Supplied Instrument Description:UV Transilluminator: Syngene Ingenius 3 – used for visualization of ethidium bromide-stained nucleic acids. Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
AirClean 600 PCR Workstation
AirClean 600 PCR Workstation
PI Supplied Instrument Name: AirClean 600 PCR Workstation PI Supplied Instrument Description:Biosafety Cabinet: AirClean 600 PCR Workstation – used to prevent contamination during RNA and PCR preparation. Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
Leica EM UC6
Leica EM UC6
PI Supplied Instrument Name: Leica EM UC6 PI Supplied Instrument Description:Ultramicrotome: Leica EM UC6 – used to prepare ultrathin sections for TEM. Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
PI Supplied Instrument Name: PI Supplied Instrument Description:Salinity Tester: Marine Line salinity meter – used to monitor artificial seawater salinity (target 30 PSU ± 0.5). Instrument Name: Salinity Sensor Instrument Short Name:Salinity Sensor Instrument Description: Category of instrument that simultaneously measures electrical conductivity and temperature in the water column to provide temperature and salinity data. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/350/
Eppendorf BioPhotometer
Eppendorf BioPhotometer
PI Supplied Instrument Name: Eppendorf BioPhotometer PI Supplied Instrument Description:Spectrophotometer: Eppendorf BioPhotometer – used to quantify nucleic acid concentrations. Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/
Eppendorf Mastercycler X50a
Eppendorf Mastercycler X50a
PI Supplied Instrument Name: Eppendorf Mastercycler X50a PI Supplied Instrument Description:Eppendorf Mastercycler X50a – used for RT-PCR amplification Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)