scholarly journals Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fathiya M. Khamis ◽  
Paul O. Mireji ◽  
Fidelis L. O. Ombura ◽  
Anna R. Malacrida ◽  
Erick O. Awuoche ◽  
...  
Keyword(s):  
Sibling Species ◽  
Gut Microbiome ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Fruit Fly ◽  
Sensu Stricto ◽  
Transcriptional Profiles ◽  
Species Specific ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractThe fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

scholarly journals The effect of variant interference on de novo assembly for viral deep sequencing

2019 ◽  
Author(s):  
Christina J. Castro ◽  
Rachel L. Marine ◽  
Edward Ramos ◽  
Terry Fei Fan Ng
Keyword(s):  
Deep Sequencing ◽  
De Novo ◽  
Gc Content ◽  
Read Length ◽  
Viral Genomes ◽  
Minor Variant ◽  
Main Driver ◽  
Next Generation Sequencing Ngs ◽  
Viral Sequences ◽  
Generation Sequencing

AbstractViruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approach has surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. Our results from >15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This “variant interference” (VI) is highly consistent and reproducible by ten most used de novo assemblers, and occurs independent of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the “rescue” of full viral genomes from fragmented contigs. These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.

scholarly journals Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3982 ◽  
Author(s):  
RuiJuan Feng ◽  
Xin Wang ◽  
Min Tao ◽  
Guanchao Du ◽  
Qishuo Wang
Keyword(s):  
Genome Size ◽  
Aquatic Plant ◽  
Nuclear Dna ◽  
De Novo ◽  
Repetitive Sequences ◽  
Nuclear Dna Content ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.

Zellfreie fetale DNA im mütterlichen Blut: neue Möglichkeiten in der pränatalen Diagnostik/Cell free fetal DNA in maternal blood: new possibilities in prenatal diagnosis

2012 ◽  
Vol 36 (5) ◽  
Author(s):  
Markus Stumm ◽  
Rolf-Dieter Wegner ◽  
Wera Hofmann
Keyword(s):  
Prenatal Diagnosis ◽  
Next Generation Sequencing ◽  
De Novo ◽  
Maternal Blood ◽  
Fetal Dna ◽  
Cell Free Fetal Dna ◽  
Next Generation Sequencing Ngs ◽  
Fetale Dna ◽  
Generation Sequencing ◽  
Zellfreie Fetale Dna

ZusammenfassungDie zellfreie fetale DNA (cff-DNA) im mütterlichen Blut bietet viele neue Möglichkeiten der pränatalen genetischen Diagnostik. Im Gegensatz zu den etablierten invasiven Techniken der Chorionzottenbiopsie (CVS) und der Amniozentese (AC), die beide mit einem spezifischen Risiko (0,5–1%) einer eingriffsbedingten Fehlgeburt einhergehen, ist die Grundlage für die Gewinnung der cff-DNA eine einfache venöse Blutentnahme der Mutter, die keinerlei Risiko für den Embryo oder Feten darstellt. Damit bietet die cff-DNA die Möglichkeit einer risikofreien genetischen Diagnostik von bestehenden Schwangerschaften. Molekulargenetische Techniken werden schon seit längerer Zeit zum qualitativen Nachweis von spezifischen fetalen Sequenzen, wie paternal vererbten oder neu entstandenen (de novo) Mutationen, eingesetzt. Durch den Einsatz digitaler PCR und Next-Generation-Sequencing (NGS) Technologien gelingt mittlerweile aber auch der sichere quantitative Nachweis von mutierten Allelen sowie von klinisch relevanten Aneuploidien (Trisomie 13, 18 und 21) aus fetaler DNA im mütterlichen Blut.

scholarly journals Detection of Respiratory Pathogens in Parapneumonic Effusions by Hypothesis-free, Next-Generation Sequencing (NGS)

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S17-S17
Author(s):  
Krow Ampofo ◽  
Andrew Pavia ◽  
Anne J Blaschke ◽  
Robert Schlaberg
Keyword(s):  
Next Generation Sequencing ◽  
Pathogen Detection ◽  
Respiratory Pathogens ◽  
Bacterial Identification ◽  
Next Generation ◽  
University Of Utah ◽  
Species Specific ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Background Species-specific polymerase chain reaction (PCR) testing of pleural fluid (PF) from children with parapneumonic effusion (PPE) has increased pathogen identification in pediatric PPE. However, a pathogen is not detected in 25–35% of cases. Hypothesis-free, next-generation sequencing (NGS) provides a more comprehensive alternative and has led to pathogen detection in PCR-negative samples. However, the utility of NGS in the evaluation of PF from children with PPE is unknown. Methods Archived PF (n = 20) from children younger than 18 years with PPE and hospitalized at Primary Children’s Hospital, Utah, in 2015 and previously tested by PCR were evaluated. Ten PCR-negative and 10 PCR-positive PF specimens were tested using RNA-seq at an average depth of 7.7×106 sequencing reads per sample. NGS data were analyzed with Taxonomer. We compared pathogens detected by blood and PF culture, PCR, and NGS. Results Overall, compared with blood/PF culture, PF PCR and PF NGS testing of PF increased bacterial identification from 15% to 50% (P < 0.05) and 65% (P = 0.003), respectively. Pathogen detection in PF by PCR and NGS were comparable (50 vs. 65%, p = NS) (Table). However, compared with PF PCR, NGS significantly increased detection of S. pyogenes (20% vs. 55%; P < 0.05), with 100% concordance when detected by PCR and culture. Detection of Fusobacterium spp. (10 vs. 10%) by PF NGS and PF PCR were comparable. In contrast, there was no detection of S. pneumoniae (15 vs. 0%) by PF NGS compared with PF PCR. Conclusion PF NGS testing significantly improves bacterial identification and comparable to PF PCR testing, which can help inform antimicrobial selection. However there were differences in detection of S. pneumoniae and S. pyogenes. Further studies of NGS testing of PF of children with PPE are needed to assess its potential in the evaluation of PPE in children. Disclosures A. J. Blaschke, BioFire Diagnostics LLC: Collaborator, Have intellectual property in BioFire Diagnostics through the University of Utah and Investigator, Licensing agreement or royalty and Research support; R. Schlaberg, IDbyDNA: Co-founder, Consultant and Shareholder, Stock

scholarly journals HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intra-Host Viral Populations

2020 ◽  
Author(s):  
Matthew L Bendall ◽  
Keylie M Gibson ◽  
Margaret C Steiner ◽  
Uzma Rentia ◽  
Marcos Pérez-Losada ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
De Novo ◽  
Consensus Sequence ◽  
Haplotype Reconstruction ◽  
Consensus Sequences ◽  
Genome Wide ◽  
Genomic Regions ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Deep sequencing of viral populations using next generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observed sequences from a sample as a single consensus sequence, thus discarding valuable information about the intra-host viral molecular epidemiology. Furthermore, existing analytical pipelines may only analyze genomic regions involved in drug resistance, thus are not suited for full viral genome analysis. Here we present HAPHPIPE, a HAplotype and PHylodynamics PIPEline for genome-wide assembly of viral consensus sequences and haplotypes. The HAPHPIPE protocol includes modules for quality trimming, error correction, de novo assembly, alignment, and haplotype reconstruction. The resulting consensus sequences, haplotypes, and alignments can be further analyzed using a variety of phylogenetic and population genetic software. HAPHPIPE is designed to provide users with a single pipeline to rapidly analyze sequences from viral populations generated from NGS platforms and provide quality output properly formatted for downstream evolutionary analyses.

scholarly journals Elucidating biosynthetic pathway of piperine using comparative transcriptome analysis of leaves, root and spike in Piper longum L

2021 ◽  
Author(s):  
Prem Kumar Dantu ◽  
Mrinalini Prasad ◽  
Rajiv Ranjan
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Gene Families ◽  
Comparative Transcriptome ◽  
Illumina Platform ◽  
Piper Longum ◽  
Comparative Transcriptome Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractPiper longum (Pipli; Piperaceae) is an important spice valued for its pungent alkaloids, especially piperine. Albeit, its importance, the mechanism of piperine biosynthesis is still poorly understood. The Next Generation Sequencing (NGS) for P. longum leaves, root and spikes was performed using Illumina platform, which generated 16901456, 54993496 and 22900035, respectively of high quality reads. In de novo assembly P. longum 173381 numbers of transcripts were analyzed. Analysis of transcriptome data from leaf, root and spike showed gene families that were involved in the biosynthetic pathway of piperine and other secondary metabolites. To validate differential expression of the identified genes, 27 genes were randomly selected to confirm the expression level by quantitative real time PCR (qRT-PCR) based on the up regulation and down regulation of differentially expressed genes obtained through comparative transcriptome analysis of leaves and spike of P. longum. With the help of UniProt database the function of all characterized genes was generated.

scholarly journals Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation

2021 ◽  
Vol 12 ◽  
Author(s):  
Felipe Cabarcas ◽  
Ana Luz Galvan-Diaz ◽  
Laura M. Arias-Agudelo ◽  
Gisela María García-Montoya ◽  
Juan M. Daza ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Cryptosporidium Hominis ◽  
Stool Samples ◽  
Metagenomic Assembly ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Cryptosporidium is a leading cause of waterborne outbreaks globally, and Cryptosporidium hominis and C. parvum are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages.

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