scholarly journals A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

2020 ◽  
Vol 8 (10) ◽  
Author(s):  
Brian J. Sanderson ◽  
Stephen P. DiFazio ◽  
Quentin C. B. Cronk ◽  
Tao Ma ◽  
Matthew S. Olson
Keyword(s):  
Population Genomics ◽  
Sequence Capture ◽  
Targeted Sequence Capture

scholarly journals Targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

2020 ◽  
Author(s):  
Brian J. Sanderson ◽  
Stephen P. DiFazio ◽  
Quentin C. Cronk ◽  
Tao Ma ◽  
Matthew S. Olson
Keyword(s):  
Population Genomics ◽  
Sequence Data ◽  
Gene Trees ◽  
Base Pairs ◽  
Phylogenetic Information ◽  
Sequence Capture ◽  
Population Genomic ◽  
The Family ◽  
Genomic Studies ◽  
Targeted Sequence Capture

AbstractPremise of the studyThe family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.MethodsWe used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 base pairs of exonic regions of 972 genes.ResultsWe recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, as well as some population genomic summary statistics for these loci.ConclusionsOur sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.

scholarly journals New Compound Heterozygous CYP4V2 Mutations in Bietti Crystalline Corneoretinal Dystrophy

2020 ◽  
Author(s):  
Ting Wang ◽  
Qingshan Chen ◽  
Longhao Kuang ◽  
Jiantao Wang ◽  
Xiaohe Yan
Keyword(s):  
Autosomal Recessive ◽  
Frameshift Mutation ◽  
Retinal Dystrophy ◽  
Genetic Diagnosis ◽  
Compound Heterozygous ◽  
Retinal Diseases ◽  
Sequence Capture ◽  
Pathogenic Genes ◽  
Compound Heterozygous Mutations ◽  
Targeted Sequence Capture

Abstract Background: Bietti crystalline corneoretinal dystrophy (BCD) is an autosomal recessive retinal dystrophy which is caused by the mutations of CYP4V2.Here we identified new CYP4V2compound heterozygous mutations in BCD.Methods:381 pathogenic genes related to retinal diseases were screened by targeted sequence capture array techniques and confirmed by Sanger sequencing.Results:Two female siblings with BCD carry two compound heterozygous mutations in CYP4V2. One was missense mutation c.1198C>T (p.R400C) and the other was frameshift mutation c.802-8_810delinsGC (p.V268_E329del).Optical coherence tomography (OCT) showed that the ellipsoid zone was absent in the macular regions and electroretinogram (ERG) revealed poor cone and rod responses. Conclusions:Newcompound heterozygous mutations in CYP4V2 are related to the BCD.Our study expands our knowledge of heterogenic phenotypes and genotypes through genetic diagnosis of the BCD patients.

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 Evaluating the performance of targeted sequence capture, RNA‐Seq, and degenerate‐primer PCR cloning for sequencing the largest mammalian multigene family

2019 ◽  
Vol 20 (1) ◽  
pp. 140-153 ◽  
Author(s):  
Laurel R. Yohe ◽  
Kalina T. J. Davies ◽  
Nancy B. Simmons ◽  
Karen E. Sears ◽  
Elizabeth R. Dumont ◽  
...  
Keyword(s):  
Multigene Family ◽  
Degenerate Primer ◽  
Rna Seq ◽  
Pcr Cloning ◽  
Sequence Capture ◽  
Targeted Sequence Capture

scholarly journals Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1358
Author(s):  
Leonard Schuele ◽  
Hayley Cassidy ◽  
Erley Lizarazo ◽  
Katrin Strutzberg-Minder ◽  
Sabine Schuetze ◽  
...  
Keyword(s):  
Influenza A ◽  
Simultaneous Detection ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Genome Coverage ◽  
Sequence Capture ◽  
Shotgun Metagenomic Sequencing ◽  
Oxford Nanopore ◽  
The One ◽  
Targeted Sequence Capture

Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.

scholarly journals Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 973 ◽  
Author(s):  
Thibaud Dugat ◽  
Valentin Loux ◽  
Sylvain Marthey ◽  
Marco Moroldo ◽  
Anne-Claire Lagrée ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Anaplasma Phagocytophilum ◽  
Sequence Capture ◽  
Targeted Sequence Capture
Sign in / Sign up

Export Citation Format

Share Document