scholarly journals Whole-genome analysis of introgression between the spotted owl and barred owl (Strix occidentalis and Strix varia, respectively; Aves: Strigidae) in western North America

2018 ◽  
Author(s):  
Zachary R. Hanna ◽  
John P. Dumbacher ◽  
Rauri C.K. Bowie ◽  
James B. Henderson ◽  
Jeffrey D. Wall
Keyword(s):  
North America ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Western North America ◽  
Whole Genome Analysis ◽  
Spotted Owl ◽  
Strix Varia ◽  
Local Selection ◽  
Spotted Owls

AbstractAs the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix varia and S. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of western S. varia that suggested admixture with S. occidentalis appear unrelated to S. occidentalis ancestry and may instead reflect local selection.

scholarly journals Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies potential targets of allele-specific immunity to clinical malaria

2020 ◽  
Author(s):  
Zalak Shah ◽  
Myo T Naung ◽  
Kara A Moser ◽  
Matthew Adams ◽  
Andrea G Buchwald ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Clinical Malaria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Multiple Alleles ◽  
Vaccine Candidates ◽  
Genome Wide ◽  
Allele Specific

Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. This immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode likely targets of naturally acquired immunity and that should be further characterized for their potential as vaccine candidates.

scholarly journals Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials

2015 ◽  
Vol 82 (2) ◽  
pp. 596-607 ◽  
Author(s):  
Stacey M. Broomall ◽  
Mohamed Ait Ichou ◽  
Michael D. Krepps ◽  
Lauren A. Johnsky ◽  
Mark A. Karavis ◽  
...  
Keyword(s):  
Sequence Data ◽  
454 Sequencing ◽  
Forensic Analysis ◽  
Whole Genome Sequence ◽  
High Dose ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Potential Sources ◽  
Gamma Irradiated ◽  
Sequencing Platforms

ABSTRACTEffective microbial forensic analysis of materials used in a potential biological attack requires robust methods of morphological and genetic characterization of the attack materials in order to enable the attribution of the materials to potential sources and to exclude other potential sources. The genetic homogeneity and potential intersample variability of many of the category A to C bioterrorism agents offer a particular challenge to the generation of attributive signatures, potentially requiring whole-genome or proteomic approaches to be utilized. Currently, irradiation of mail is standard practice at several government facilities judged to be at particularly high risk. Thus, initial forensic signatures would need to be recovered from inactivated (nonviable) material. In the study described in this report, we determined the effects of high-dose gamma irradiation on forensic markers of bacterial biothreat agent surrogate organisms with a particular emphasis on the suitability of genomic DNA (gDNA) recovered from such sources as a template for whole-genome analysis. While irradiation of spores and vegetative cells affected the retention of Gram and spore stains and sheared gDNA into small fragments, we found that irradiated material could be utilized to generate accurate whole-genome sequence data on the Illumina and Roche 454 sequencing platforms.

scholarly journals Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria

PLoS Genetics ◽  
2021 ◽  
Vol 17 (5) ◽  
pp. e1009576
Author(s):  
Zalak Shah ◽  
Myo T. Naung ◽  
Kara A. Moser ◽  
Matthew Adams ◽  
Andrea G. Buchwald ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Clinical Malaria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Multiple Alleles ◽  
Vaccine Candidates ◽  
Genome Wide ◽  
Allele Specific

Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. Immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode possible targets of naturally acquired immunity that should be validated immunologically and further characterized for their potential as vaccine candidates.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽  
2020 ◽  
Vol 33 ◽  
pp. 106416
Author(s):  
Asset Daniyarov ◽  
Askhat Molkenov ◽  
Saule Rakhimova ◽  
Ainur Akhmetova ◽  
Zhannur Nurkina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lynsey K. Whitacre ◽  
Jesse L. Hoff ◽  
Robert D. Schnabel ◽  
Sara Albarella ◽  
Francesca Ciotola ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Birth Defect ◽  
Genetic Basis ◽  
Sequence Data ◽  
Model Organism ◽  
Bubalus Bubalis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data
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