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Humberto J. Debat - One of the best experts on this subject based on the ideXlab platform.
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Complete genome sequence of a divergent strain of Tibetan frog hepatitis B virus associated with a concave-eared torrent frog (Odorrana tormota)
Archives of Virology, 2019Co-Authors: Humberto J. DebatAbstract:Viruses of the family Hepadnaviridae are characterized by partially dsDNA circular genomes of approximately 3.2 kb, which are reverse transcribed from RNA intermediates. Hepadnaviruses have a broad host range, which includes humans (hepatitis B virus), other mammals (genus Orthohepadnavirus ), and birds (genus Avihepadnavirus ). The known host specificity of hepadnaviruses has been expanded by reports of new viruses infecting fish, amphibians, and reptiles. Tibetan frog hepatitis B virus (TFHBV) was recently discovered in a member of the species Nanorana parkeri (family Dicroglossidae) from Tibet. To increase our understanding of hepadnaviruses that infect amphibian hosts, we identified the full-length genome of a divergent strain, TFHBV-Ot, associated with a concave-eared torrent frog ( Odorrana tormota , family Ranidae) from China by searching deep-sequencing data. TFHBV-Ot shared a genomic organization and 76.6% overall genome sequence nucleotide identity with the prototype TFHBV associated with N. parkeri (TFHBV-Np). The pairwise amino acid sequence identity between the predicted gene products of TFHBV-Ot and TFHBV-Np ranged between 63.9% and 77.9%. Multiple tissue/organ-specific RNAseq datasets suggested a broad tropism of TFHBV, including muscle, gonads and brain. In addition, we provide information about putative virus-derived small RNAs from an amphibian hepadnavirus. The results presented here expand the known genetic diversity and host range of TFHBV to Ranidae frogs, and warrant an investigation of hepadnaviral infection of amphibian brains.
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Complete genome sequence of a divergent strain of Tibetan frog hepatitis B virus associated to concave-eared torrent frog Odorrana tormota
2018Co-Authors: Humberto J. DebatAbstract:The family Hepadnaviridae is characterized by partially dsDNA circular viruses of approximately 3.2 kb, which are reverse transcribed from RNA intermediates. Hepadnaviruses (HBVs) have a broad host range which includes humans (Hepatitis B virus), other mammals (genus Orthohepadnavirus), and birds (Avihepadnavirus). HBVs host specificity has been expanded by reports of new viruses infecting fish, amphibians, and reptiles. The tibetan frog hepatitis B virus (TFHBV) was recently discovered in Nanorana parkeri (Family Dicroglossidae) from Tibet. To increase understanding of hepadnavirus in amphibian host, we identified the full-length genome of a divergent strain TFHBV-Ot associated to the concave-eared torrent frog Odorrana tormota (Family Ranidae) from China by searching deep sequencing data. TFHBV-Ot shared the genomic organization and a 76.6% overall genome nucleotide identity to the prototype TFHBV associated to N. parkeri (TFHBV-Np). TFHBV-Ot amino acid pairwise identity with TFHBV-Np predicted gene products ranged between 63.9% and 77.9%. Multiple tissue/organ specific RNAseq datasets suggest a broad tropism of TFHBV including muscles, gonads and brains. In addition, we provide for the first time evidence of virus derived small RNA from an amphibian hepadnavirus, tentatively enriched in 19-20 nt species and cytidine as first base. The results presented here expand the genetic diversity and the host range of TFHBV to Ranidae frogs, and warrant investigation on hepadnaviral infection of amphibian brains.
Jungyoun Park - One of the best experts on this subject based on the ideXlab platform.
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rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish the mottled skate raja pulchra
International Journal of Molecular Sciences, 2012Co-Authors: Jungha Kang, Jungyoun ParkAbstract:The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.
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Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish<em>,</em> the Mottled Skate<em>, Raja </em><em>p</em><em>ulchra</em>
MDPI AG, 2012Co-Authors: Jungha Kang, Jungyoun ParkAbstract:The mottled skate, <em>Raja pulchra</em>, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two <em>R. pulchra </em>populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other <em>Rajidae</em> family species; three loci were polymorphic. A monomorphic locus was amplified in all three <em>Rajidae</em> family species and the <em>Dasyatidae</em> family. Two <em>Rajidae</em> polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species
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Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate,
2012Co-Authors: Raja Pulchra, Jungha Kang, Jungyoun ParkAbstract:Abstract: The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Tw
Jim R Ellis - One of the best experts on this subject based on the ideXlab platform.
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lengths at maturity and conversion factors for skates Rajidae around the british isles with an analysis of data in the literature
Ices Journal of Marine Science, 2012Co-Authors: Sophy R Mccully, Finlay Scott, Jim R EllisAbstract:Biological data on skates (Rajidae) from around the British Isles were collected between 1992 and 2010. The relationship between total length and weight for nine species (Amblyraja radiata, Dipturus batis-complex, Leucoraja fullonica, L. naevus, Raja brachyura, R. clavata, R. microocellata, R. montagui, and R. undulata) are provided for each sex and ICES ecoregion (when significantly different). Conversion factors for disc width to total length are provided. The lengths at first maturity and of the largest immature skates are reported for each sex, and the lengths at 50% maturity are estimated. Spatial differences in the length at maturity of R. clavata (females only) and L. naevus (both sexes) were observed. The lengths at maturity are discussed in relation to the results of earlier studies, and methodological differences are considered to have influenced reputed decreases in the length at maturity. A more standardized approach to collecting and reporting maturity information is required if potential spatial differences and temporal changes are to be investigated.
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species composition of skates Rajidae in commercial fisheries around the british isles and their discarding patterns
Journal of Fish Biology, 2012Co-Authors: Joana F Silva, Jim R Ellis, Thomas CatchpoleAbstract:Recent regulations have required European nations to report commercial landings of Rajidae (skates) to species level since 2008. Morphological similarities between some species, variability in colouration and regional differences in common names may compromise the accuracy of some of these data. An increased proportion of rajid landings reported by the U.K. (England, Wales and Northern Ireland) are now reported to species level (42% in 2008, rising to 92% in 2010). Recent landings (2007-2010) of Rajidae by the U.K. indicated that the majority of reported landings were made by otter trawl (55·9%), tangle and gillnet (18·7%) and beam trawl (15·5%). Approximately 70% of recent landings originated from four ICES Divisions: the Irish Sea (VIIa), western English Channel (VIIe), Bristol Channel (VIIf) and southern North Sea (IVc). Recent species-specific landings of Rajidae are appraised in terms of the species reported and the overall composition, and potential problems identified. Data from observer trips have been used to estimate the species composition of Rajidae taken in some of the main commercial fisheries operating around the British Isles, and these data are compared to landings. Although there was typically broad agreement between these data sets in terms of the main species landed, misidentification issues were apparent and Rajidae with highly patchy distributions may be under-represented in observer data. Data from observer trips were also used to examine the discard and retention pattern. Most rajid species were first retained from total lengths, L(T) , of 27-34 cm, with 50% retention occurring at between 49 and 51 cm and near-full retention at L(T) of 60-67 cm. Beam trawls captured a higher proportion of smaller individuals, whilst gillnets (>150 mm mesh size) caught proportionally more larger rajids.
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multiple paternity analysis in the thornback ray raja clavata l
Journal of Heredity, 2007Co-Authors: Malia Chevolot, Wytze T. Stam, Adriaan D. Rijnsdorp, Jim R Ellis, Jeanine L. OlsenAbstract:Skates (Rajidae) are characterized by slow growth rate, low fecundity, and late maturity and are thus considered to be vulnerable to exploitation. Although understanding mating systems and behavior are important for long-term conservation and fisheries management, this aspect of life history is poorly understood in skates. Using 5 highly polymorphic microsatellite loci, we analyzed egg clutches collected from 4 female Raja clavata captured in the wild to test for multiple paternity. Using the reconstructed multilocus genotypes method to explain the progeny genotype array, we showed that all 4 clutches were sired by a minimum of 4-6 fathers and, thus, female thornback rays are polyandrous. Whether polyandry in R. clavata is natural or a consequence of overexploitation remains uncertain. This is the first report of multiple paternity in a rajiform species and any oviparous elasmobranch.
Jungha Kang - One of the best experts on this subject based on the ideXlab platform.
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rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish the mottled skate raja pulchra
International Journal of Molecular Sciences, 2012Co-Authors: Jungha Kang, Jungyoun ParkAbstract:The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.
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Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish<em>,</em> the Mottled Skate<em>, Raja </em><em>p</em><em>ulchra</em>
MDPI AG, 2012Co-Authors: Jungha Kang, Jungyoun ParkAbstract:The mottled skate, <em>Raja pulchra</em>, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two <em>R. pulchra </em>populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other <em>Rajidae</em> family species; three loci were polymorphic. A monomorphic locus was amplified in all three <em>Rajidae</em> family species and the <em>Dasyatidae</em> family. Two <em>Rajidae</em> polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species
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Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate,
2012Co-Authors: Raja Pulchra, Jungha Kang, Jungyoun ParkAbstract:Abstract: The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Tw
Martin J. Genner - One of the best experts on this subject based on the ideXlab platform.
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Characterisation of polymorphic microsatellite markers for skates (Elasmobranchii: Rajidae) from expressed sequence tags
Conservation Genetics, 2009Co-Authors: Aliya El Nagar, Matthew J. Mchugh, Toby Rapp, David W. Sims, Martin J. GennerAbstract:Simple sequence repeat markers (SSRs, microsatellites) were characterised for skates (Elasmobranchii: Rajidae) from published expressed sequence tags (ESTs) of Leucoraja erinacea. These were tested in four European species (Raja clavata, Raja montagui, Dipturus batis, and Leucoraja naevus). Thirteen of the fourteen amplified loci were polymorphic in at least one species. Polymorphic loci possessed on average 4.5–5.9 alleles per species, and expected heterozygosity ranged from 0.05 to 0.88. Possible null alleles were detected at three loci, while one locus showed significant deviation from Hardy–Weinberg Equilibrium proportions. Three locus-pairs exhibited significant linkage disequilibrium in one or more species. This marker set will be valuable for population genetic analyses of the focal taxa, and may prove useful for studies of other skate species.