Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis

PeerJ
Cheryl L MorrisonRobert S Cornman

Abstract

Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing 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. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were...Continue Reading

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Citations

Jun 28, 2019·Diseases of Aquatic Organisms·Rocío Álvarez-VarasWashington B Cárdenas
Oct 18, 2019·Diseases of Aquatic Organisms·Donna J ShaverThomas F Backof
May 28, 2019·EcoHealth·Isabela G DomicianoAna Paula F R L Bracarense
May 25, 2021·Frontiers in Veterinary Science·God'spower Richard OkohEllen Ariel

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Datasets Mentioned

BETA
HQ870327
PRJNA360405

Methods Mentioned

BETA
transmission electron microscopy
PCR
biopsy
Assay
PCRs
electrophoresis
chips
amplicon sequencing

Software Mentioned

Geneious Tree Builder
BLAST
RDP4
GENECONV
CLC Genomics Workbench
samtools
PAML4
DnaSP
PartitionFinder
MEGA7

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