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Evolutionary comparisons of Chelonid alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-afflicted green (Chelonia mydas), Olive ridley (Lepidochelys olivacea) and Kemp’s ridley (Lepidochelys kempii) sea turtles

Citation

Whitmore, Liam et al. (2021), Evolutionary comparisons of Chelonid alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-afflicted green (Chelonia mydas), Olive ridley (Lepidochelys olivacea) and Kemp’s ridley (Lepidochelys kempii) sea turtles, Dryad, Dataset, https://doi.org/10.5061/dryad.wwpzgmsk6

Abstract

The spreading global sea turtle fibropapillomatosis (FP) epizootic is threatening some of Earth’s ancient reptiles, adding to the plethora of threats faced by these keystone species. Understanding this neoplastic disease and its likely aetiological pathogen, chelonid alphaherpesvirus 5 (ChHV5), is crucial to understand how the disease impacts sea turtle populations and species and the future trajectory of disease incidence. We generated 20 ChHV5 genomes, from three sea turtle species, to better understand the viral variant diversity and gene evolution of this oncogenic virus. We revealed previously underappreciated genetic diversity within this virus (with an average of 2035 single nucleotide polymorphisms (SNPs), 1.54% of the ChHV5 genome) and identified genes under the strongest evolutionary pressure. Furthermore, we investigated the phylogeny of ChHV5 at both genome and gene level, confirming the propensity of the virus to be interspecific, with related variants able to infect multiple sea turtle species. Finally, we revealed unexpected intra-host diversity, with up to 0.15% of the viral genome varying between ChHV5 genomes isolated from different tumours concurrently arising within the same individual. These findings offer important insights into ChHV5 biology and provide genomic resources for this oncogenic virus.

Usage Notes

This 1._ChHV5_consensus_genome_sequences.txtreadme.txt file was generated on 2021-07-01 by Liam Whitmore

GENERAL INFORMATION

1. Title of Dataset: 1._ChHV5_consensus_genome_sequences.txt

2. Author Information
    A. Principal Investigator Contact Information
        Name: Liam Whitmore
        Institution: University of Limerick
        Address: University of Limerick, Limerick, V94 T9PX, Ireland​
        Email: Liam.Whitmore@ul.ie

3. Date of data collection (single date, range, approximate date): 
Data collection spanned multiple papers as we used collaborators data as well as our own.
Information regarding this can be found in the methods section of this research paper (https://doi.org/10.3390/ani11092489).

4. Geographic location of data collection: 
Samples collected from turtles for data analysis were collected
from coast of eastern USA (from Massachusetts to Texas).

5. Information about funding sources that supported the collection of the data: 
Funding was generously provided by an Irish Research Council Government of Ireland Postgraduate Scholarship, 
under project number GOIPG/2020/1056, by the National Save The Sea Turtle Foundation, Inc., and this research 
was also supported by Gumbo Limbo Nature Center, Inc. d/b/a Friends of Gumbo Limbo (a 501c3 non-profit organization) 
through a generous donation through their Graduate Research Grant programme.

SHARING/ACCESS INFORMATION

Links to publications that cite or use the data: 
Whitmore, L., Yetsko, K., Farrell, J.A., Page-Karjian, A., Daniel, W., Shaver, D.J., Frandsen, H.R., Walker, J.S., Crowder, W., Bovery, C. 
and Rollinson Ramia, D., 2021. Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted 
Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles. Animals, 11(9), p.2489
https://doi.org/10.3390/ani11092489 

Recommended citation for this dataset: 
Whitmore, L., Yetsko, K., Farrell, J.A., Page-Karjian, A., Daniel, W., Shaver, D.J., Frandsen, H.R., Walker, J.S., Crowder, W., Bovery, C. 
and Rollinson Ramia, D., 2021. Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted 
Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles. Animals, 11(9), p.2489
https://doi.org/10.3390/ani11092489 

DATA & FILE OVERVIEW

File information: 
Dataset consists of 21 ChHV5 consensus sequences (genomes, including reference ChHV5 genome) generated from FP tumour tissue samples from three species of marine turtle (Green, Kemp's ridley and olive ridley) 
in the western Atlantic (MA - TX). Please see associated paper for table with sample information.

Are there multiple versions of the dataset? no

METHODOLOGICAL INFORMATION

Please see published manuscript with detailed information regarding data processing, along with additional information of how data was processed by collaborators
(https://doi.org/10.3390/ani11092489).

DATA-SPECIFIC INFORMATION FOR: 1._ChHV5_consensus_genome_sequences.txt

1. Number of variables: 21

2. Number of cases/rows: N/A

Funding

Irish Research Council for Science, Engineering and Technology, Award: GOIPG/2020/1056

National Save the Sea Turtle Foundation, Award: NSTSTF FPTRI

Gumbo Limbo Nature Center

Gumbo Limbo Nature Center