scholarly journals Changes in Dimethylsulfoniopropionate Demethylase Gene Assemblages in Response to an Induced Phytoplankton Bloom

2010 ◽  
Vol 77 (2) ◽  
pp. 524-531 ◽  
Author(s):  
Erinn C. Howard ◽  
Shulei Sun ◽  
Christopher R. Reisch ◽  
Daniela A. del Valle ◽  
Helmut Bürgmann ◽  
...  
Keyword(s):  
Surface Waters ◽  
Nucleotide Sequence Identity ◽  
High Throughput Sequencing ◽  
Phytoplankton Bloom ◽  
Marine Bacterioplankton ◽  
Taxonomic Change ◽  
Sequence Identity ◽  
Sequencing Technologies ◽  
Ecological Implications ◽  
Clustering Criterion

ABSTRACTOver half of the bacterioplankton cells in ocean surface waters are capable of carrying out a demethylation of the phytoplankton metabolite dimethylsulfoniopropionate (DMSP) that routes the sulfur moiety away from the climatically active gas dimethylsulfide (DMS). In this study, we tracked changes indmdA, the gene responsible for DMSP demethylation, over the course of an induced phytoplankton bloom in Gulf of Mexico seawater microcosms. Analysis of >91,000 amplicon sequences indicated 578 differentdmdAsequence clusters at a conservative clustering criterion of ≥90% nucleotide sequence identity over the 6-day study. The representation of the major clades ofdmdA, several of which are linked to specific taxa through genomes of cultured marine bacterioplankton, remained fairly constant. However, the representation of clusters within these major clades shifted significantly in response to the bloom, including twoRoseobacter-like clusters and a SAR11-like cluster, and the best correlate with shifts of the dominantdmdAclades was chlorophyllaconcentration. Concurrent 16S rRNA amplification and sequencing indicated the presence ofRoseobacter, SAR11, OM60, and marineRhodospirillalespopulations, all of which are known to harbordmdAgenes, although the largest taxonomic change was an increase inFlavobacteriaceae, a group not yet demonstrated to have DMSP-demethylating capabilities. Sequence heterogeneity indmdAand other functional gene populations is becoming increasingly evident with the advent of high-throughput sequencing technologies, and understanding the ecological implications of this heterogeneity is a major challenge for marine microbial ecology.

scholarly journals Structure and Genome Organization of a Novel Fiji Strain of Sweet Potato Vein Clearing Virus Identified by High-Throughput Sequencing

2018 ◽  
Vol 6 (24) ◽  
Author(s):  
Liping Wu ◽  
Huawei Liu ◽  
Jorge Abad ◽  
Ronald D. French ◽  
Ruhui Li
Keyword(s):  
Sweet Potato ◽  
Genome Organization ◽  
Nucleotide Sequence Identity ◽  
Type Species ◽  
High Throughput Sequencing ◽  
Sequence Comparisons ◽  
Content Type ◽  
Vein Clearing ◽  
Sequence Identity ◽  
Nicotiana Bigelovii

ABSTRACT The complete genome of a Sweet potato vein clearing virus (SPVCV) isolate infecting a quarantined sweet potato accession from Fiji was determined. Sequence comparisons revealed the highest nucleotide sequence identity of 94.6% with that of the SPVCV type species, an isolate from the Dominican Republic. The virus was mechanically transmitted to Nicotiana bigelovii plants.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

scholarly journals Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

2021 ◽  
Author(s):  
Stella C. Yuan ◽  
Eric Malekos ◽  
Melissa T. R. Hawkins
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Museum Specimens ◽  
Museum Specimen ◽  
Genotyping Errors ◽  
Allelic Dropout ◽  
Parallel Sequencing ◽  
Sequencing Technologies

AbstractThe use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

scholarly journals Sequence identity in an early chorion multigene family is the result of localized gene conversion.

Genetics ◽  
1991 ◽  
Vol 128 (3) ◽  
pp. 595-606
Author(s):  
B L Hibner ◽  
W D Burke ◽  
T H Eickbush
Keyword(s):  
Nucleotide Sequence ◽  
Gene Conversion ◽  
Nucleotide Sequence Identity ◽  
Early Period ◽  
Gene Families ◽  
Multigene Families ◽  
Coding Regions ◽  
Sequence Identity ◽  
Isolation And Characterization ◽  
Sequence Exchange

Abstract The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.

scholarly journals Multi-omics approach to precision medicine for immune-mediated diseases

2021 ◽  
Vol 41 (1) ◽  
Author(s):  
Mineto Ota ◽  
Keishi Fujio
Keyword(s):  
Treatment Response ◽  
High Throughput Sequencing ◽  
Disease Risk ◽  
Clinical Information ◽  
Clinical Settings ◽  
Social Significance ◽  
Sequencing Technologies ◽  
Immune Mediated ◽  
Recent Innovation ◽  
Future Direction

AbstractRecent innovation in high-throughput sequencing technologies has drastically empowered the scientific research. Consequently, now, it is possible to capture comprehensive profiles of samples at multiple levels including genome, epigenome, and transcriptome at a time. Applying these kinds of rich information to clinical settings is of great social significance. For some traits such as cardiovascular diseases, attempts to apply omics datasets in clinical practice for the prediction of the disease risk have already shown promising results, although still under way for immune-mediated diseases. Multiple studies have tried to predict treatment response in immune-mediated diseases using genomic, transcriptomic, or clinical information, showing various possible indicators. For better prediction of treatment response or disease outcome in immune-mediated diseases, combining multi-layer information together may increase the power. In addition, in order to efficiently pick up meaningful information from the massive data, high-quality annotation of genomic functions is also crucial. In this review, we discuss the achievement so far and the future direction of multi-omics approach to immune-mediated diseases.

scholarly journals Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 429 ◽  
Author(s):  
Daniela Barros-Silva ◽  
C. Marques ◽  
Rui Henrique ◽  
Carmen Jerónimo
Keyword(s):  
Dna Methylation ◽  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Epigenetic Modification ◽  
Response To Therapy ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Prognosis And Prediction ◽  
Novel Biomarkers ◽  
Generation Sequencing

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.

scholarly journals Trophic state of benthic deep-sea ecosystems from two different continental margins off Iberia

2013 ◽  
Vol 10 (5) ◽  
pp. 2945-2957 ◽  
Author(s):  
A. Dell'Anno ◽  
A. Pusceddu ◽  
C. Corinaldesi ◽  
M. Canals ◽  
S. Heussner ◽  
...  
Keyword(s):  
Organic Matter ◽  
Water Depth ◽  
Surface Waters ◽  
Deep Sea ◽  
Nutritional Value ◽  
Trophic State ◽  
Phytoplankton Bloom ◽  
Continental Margins ◽  
Organic C ◽  
Deep Sea Sediments

Abstract. The bioavailability of organic matter in benthic deep-sea ecosystems, commonly used to define their trophic state, can greatly influence key ecological processes such as biomass production and nutrient cycling. Here, we assess the trophic state of deep-sea sediments from open slopes and canyons of the Catalan (NW Mediterranean) and Portuguese (NE Atlantic) continental margins, offshore east and west Iberia, respectively, by using a biomimetic approach based on enzymatic digestion of protein and carbohydrate pools. Patterns of sediment trophic state were analyzed in relation to increasing water depth, including repeated samplings over a 3 yr period in the Catalan margin. Two out of the three sampling periods occurred a few months after dense shelf water cascading events. The benthic deep-sea ecosystems investigated in this study were characterized by high amounts of bioavailable organic matter when compared to other deep-sea sediments. Bioavailable organic matter and its nutritional value were significantly higher in the Portuguese margin than in the Catalan margin, thus reflecting differences in primary productivity of surface waters reported for the two regions. Similarly, sediments of the Catalan margin were characterized by significantly higher food quantity and quality in spring, when the phytoplankton bloom occurs in surface waters, than in summer and autumn. Differences in the benthic trophic state of canyons against open slopes were more evident in the Portuguese than in the Catalan margin. In both continental margins, bioavailable organic C concentrations did not vary or increase with increasing water depth. Overall, our findings suggest that the intensity of primary production processes along with the lateral transfer of organic particles, even amplified by episodic events, can have a role in controlling the quantity and distribution of bioavailable organic detritus and its nutritional value along these continental margin ecosystems.

scholarly journals Detection of novel allelic variations in soybean mutant population using Tilling by Sequencing

2019 ◽  
Author(s):  
Reneth Millas ◽  
Mary Espina ◽  
CM Sabbir Ahmed ◽  
Angelina Bernardini ◽  
Ekundayo Adeleke ◽  
...  
Keyword(s):  
Fatty Acid ◽  
High Throughput ◽  
Reverse Genetics ◽  
High Throughput Sequencing ◽  
Fatty Acid Biosynthesis ◽  
Induced Mutations ◽  
Mutant Population ◽  
Sequencing Technologies ◽  
Allelic Variations ◽  
Tilling By Sequencing

ABSTRACTOne of the most important tools in genetic improvement is mutagenesis, which is a useful tool to induce genetic and phenotypic variation for trait improvement and discovery of novel genes. JTN-5203 (MG V) mutant population was generated using an induced ethyl methane sulfonate (EMS) mutagenesis and was used for detection of induced mutations in FAD2-1A and FAD2-1B genes using reverse genetics approach. Optimum concentration of EMS was used to treat 15,000 bulk JTN-5203 seeds producing 1,820 M2 population. DNA was extracted, normalized, and pooled from these individuals. Specific primers were designed from FAD2-1A and FAD2-1B genes that are involved in the fatty acid biosynthesis pathway for further analysis using next-generation sequencing. High throughput mutation discovery through TILLING-by-Sequencing approach was used to detect novel allelic variations in this population. Several mutations and allelic variations with high impacts were detected for FAD2-1A and FAD2-1B. This includes GC to AT transition mutations in FAD2-1A (20%) and FAD2-1B (69%). Mutation density for this population is estimated to be about 1/136kb. Through mutagenesis and high-throughput sequencing technologies, novel alleles underlying the mutations observed in mutants with reduced polyunsaturated fatty acids will be identified, and these mutants can be further used in breeding soybean lines with improved fatty acid profile, thereby developing heart-healthy-soybeans.

scholarly journals A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

2020 ◽  
Author(s):  
Wenbin Zhou ◽  
John Soghigian ◽  
Qiu-yun (Jenny) Xiang
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Disjunct Distribution ◽  
Divergence Times ◽  
Target Enrichment ◽  
Sequencing Technologies ◽  
Duplication Events ◽  
The Witch ◽  
Phylogenomic Analyses

ABSTRACTTarget enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, and the choice between methods is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms, especially in plants, where extensive genome duplication events may complicate phylogenomic analyses. Unfortunately, currently widely used pipelines for target enrichment data analysis do not have a vigorous procedure for remove paralogs in Hyb-Seq data. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian-eastern North American disjunct distribution. We compared these two methods side by side and developed a new pipeline (PPD) with a more vigorous removal of putative paralogs from Hyb-Seq data. The new pipeline considers both sequence similarity and heterozygous sites at each locus in identification of paralogous. We used our pipeline to construct robust datasets for comparison between methods and downstream analyses on the two genera. Our results demonstrated that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed significant differences between data from HybPiper and data from our new PPD pipeline, likely due to the error signals from the paralogous genes undetected by HybPiper, but trimmed by PPD. We found that phylogenies and divergence times estimated from our RAD-seq and Hyb-Seq-PPD were largely congruent. We highlight the importance of removal paralogs in enrichment data, and discuss the merits of RAD-seq and Hyb-Seq. Finally, phylogenetic analyses of RAD-seq and Hyb-Seq resulted in well-resolved species relationships, and revealed ancient introgression in both genera. Biogeographic analyses including fossil data revealed a complicated history of each genus involving multiple intercontinental dispersals and local extinctions in areas outside of the taxa’s modern ranges in both the Paleogene and Neogene. Our study demonstrates the value of additional steps for filtering paralogous gene content from Angiosperm 353 data, such as our new PPD pipeline described in this study. [RAD-seq, Hyb-Seq, paralogs, Castanea, Hamamelis, eastern Asia-eastern North America disjunction, biogeography, ancient introgression]

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