Targeted amplicon resequencing of chelonid alphaherpesvirus 5 from tumor samples collected from Chelonia mydas (green turtle) inhabiting Hawaiian and Florida coastal waters
Dates
Publication Date
2018-01-31
Start
1996-03-25
End
2012-11-08
Citation
Morrison, C.L., Cornman, R.S., Iwanowicz, Luke, Iwanowicz, Deborah, Adams, C.R., and Sanders, L.R., 2018, Targeted amplicon resequencing of chelonid alphaherpesvirus 5 from tumor samples collected from Chelonia mydas (green turtle) inhabiting Hawaiian and Florida coastal waters: U.S. Geological Survey data release, https://doi.org/10.5066/F73B5Z3T.
Summary
The files in this data release are the processed DNA consensus sequence alignment files for the chelonid herpesvirus 5 (ChHV-5) genome plus 66 open reading frames representing protien-coding genes. DNA was extracted from tumor biopsies from green sea turtles (Chelonias mydas) with fibropapillomatosis sampled from Florida and Hawaii coastal waters. We used high-throughput short-read sequencing (Illumina MiSeq and Ion Torrent Personal Genome Machine) of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. The raw sequence data is available at the NCBI Sequence Read Archive under bioproject number PRJNA360405, including biosample numbers [...]
Summary
The files in this data release are the processed DNA consensus sequence alignment files for the chelonid herpesvirus 5 (ChHV-5) genome plus 66 open reading frames representing protien-coding genes. DNA was extracted from tumor biopsies from green sea turtles (Chelonias mydas) with fibropapillomatosis sampled from Florida and Hawaii coastal waters. We used high-throughput short-read sequencing (Illumina MiSeq and Ion Torrent Personal Genome Machine) of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. The raw sequence data is available at the NCBI Sequence Read Archive under bioproject number PRJNA360405, including biosample numbers SAMN06210144- SAMN06210150.
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ChHV5_resequencing_metadata.xml Original FGDC Metadata
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Purpose
Samples were collected to assess genomic variation in ChHV-5 among five Hawaii and three Florida green sea turtles infected with fibropapillomatosis. , This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.
