scholarly journals Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome

DNA Research ◽  
2018 ◽  
Vol 25 (5) ◽  
pp. 535-545 ◽  
Author(s):  
Orzenil Bonfim Silva-Junior ◽  
Dario Grattapaglia ◽  
Evandro Novaes ◽  
Rosane G Collevatti
Keyword(s):  
Snp Genotyping ◽  
Plant Genomes ◽  
Sequence Capture ◽  
Genome Wide ◽  
Heterozygous Plant ◽  
Hardwood Tree

scholarly journals Combination of Multiple Microsatellite Analysis and Genome-Wide SNP Genotyping Helps to Solve Wildlife Crime: A Case Study of Poaching of a Caucasian tur (Capra caucasica) in Russian Mountain National Park

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3416
Author(s):  
Andrey Rodionov ◽  
Tatiana Deniskova ◽  
Arsen Dotsev ◽  
Valeria Volkova ◽  
Sergey Petrov ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
National Park ◽  
Molecular Genetic ◽  
Dna Typing ◽  
Molecular Genetic Analysis ◽  
Snp Genotyping ◽  
Wildlife Crime ◽  
Wildlife Forensics ◽  
Genome Wide

Poaching is one of the major types of wildlife crime in Russia. Remnants of goats (presumably the wild endemic species, the Caucasian tur) were found in an area of the Caucasian mountains. The case study involves a suspected poacher whose vehicle was found to have two duffel bags containing pieces of a carcass, which he claimed was that of a goat from his flock. The aim of the forensic genetic analysis for this case was to (i) establish individual identity and (ii) perform species identification. DNA typing based on fourteen microsatellites revealed that STR-genotypes generated from pieces of evidence found at crime scene fully matched those obtained from the evidence seized from the suspect. The results of genome-wide SNP-genotyping, using Illumina Goat SNP50 BeadChip, provided evidence that the poached animal was a wild Caucasian tur (Capra caucasica). Thus, based on comprehensive molecular genetic analysis, evidence of poaching was obtained and sent to local authorities. To our knowledge, this case study is the first to attempt to use DNA chips in wildlife forensics of ungulates.

scholarly journals Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 506 ◽  
Author(s):  
Katherine H Fisher ◽  
Victoria M Wright ◽  
Amy Taylor ◽  
Martin P Zeidler ◽  
Stephen Brown
Keyword(s):  
Genome Wide ◽  
Stat Pathway

scholarly journals Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 183 ◽  
Author(s):  
Matthieu G Conte ◽  
Sylvain Gaillard ◽  
Gaetan Droc ◽  
Christophe Perin
Keyword(s):  
Plant Genomes ◽  
Genome Wide

Sequence capture across large phylogenetic scales by using pooled PCR‐generated baits: A case study of Lepidoptera

2019 ◽  
Vol 19 (4) ◽  
pp. 1037-1051 ◽  
Author(s):  
Yuan Zhang ◽  
Shaohong Deng ◽  
Dan Liang ◽  
Peng Zhang
Keyword(s):  
Sequence Capture

scholarly journals A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture

2015 ◽  
Vol 43 (6) ◽  
pp. 3389-3404 ◽  
Author(s):  
Henriette O'Geen ◽  
Isabelle M. Henry ◽  
Mital S. Bhakta ◽  
Joshua F. Meckler ◽  
David J. Segal
Keyword(s):  
Binding Specificity ◽  
Genome Wide Analysis ◽  
Sequence Capture ◽  
Genome Wide ◽  
A Genome ◽  
Targeted Sequence Capture

scholarly journals Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 749 ◽  
Author(s):  
Melanie Hiltbrunner ◽  
Gerald Heckel
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Common Vole ◽  
Natural Host ◽  
Sequence Information ◽  
Coding Region ◽  
Sequence Capture ◽  
Genome Wide ◽  
The Impact

Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.

scholarly journals Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 126 ◽  
Author(s):  
Wilson X. Guillory ◽  
Morgan R. Muell ◽  
Kyle Summers ◽  
Jason L. Brown
Keyword(s):  
Bayesian Methods ◽  
Evolutionary History ◽  
Conservation Status ◽  
Nuclear Data ◽  
Nuclear Markers ◽  
Poison Frog ◽  
Sequence Capture ◽  
Genome Wide ◽  
Frog Species ◽  
History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

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