High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

Download Full-text

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Forests ◽

10.3390/f10080681 ◽

2019 ◽

Vol 10 (8) ◽

pp. 681 ◽

Cited By ~ 1

Author(s):

Huiquan Zheng ◽

Dehuo Hu ◽

Ruping Wei ◽

Shu Yan ◽

Runhui Wang

Keyword(s):

Population Structure ◽

Genetic Structure ◽

High Throughput ◽

High Throughput Sequencing ◽

Breeding Population ◽

Population Diversity ◽

Chinese Fir ◽

High Density ◽

Population Structure Analysis ◽

Snp Panel

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

Download Full-text

Lethal Outcome of Leptospirosis in Southern Russia: Characterization of Leptospira Interrogans Isolated from a Deceased Teenager

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17124238 ◽

2020 ◽

Vol 17 (12) ◽

pp. 4238

Author(s):

Andrei Samoilov ◽

Nataliya Stoyanova ◽

Nikolai Tokarevich ◽

Birgitta Evengard ◽

Elena Zueva ◽

...

Keyword(s):

Mass Spectrometry ◽

High Throughput ◽

High Throughput Sequencing ◽

Agglutination Test ◽

Leptospira Interrogans ◽

Whole Genome ◽

Highly Qualified ◽

Lethal Outcome ◽

Southern Russia

This article describes a lethal case of leptospirosis that occurred in Southern Russia. The Leptospira strain was isolated and characterized using a microscopic agglutination test, MALDI-TOF mass spectrometry, targeted PCR, and high-throughput sequencing. We show that molecular and mass-spectrometry methods can be an alternative to conventional methods of leptospirosis diagnostics and Leptospira study, which require highly qualified staff and can be performed only at specialized laboratories. We also report the first whole genome of L. interrogans isolated in Russia.

Download Full-text

Grafting-responsive miRNAs in cucumber and pumpkin seedlings identified by high-throughput sequencing at whole genome level

Physiologia Plantarum ◽

10.1111/ppl.12122 ◽

2013 ◽

Vol 151 (4) ◽

pp. 406-422 ◽

Cited By ~ 25

Author(s):

Chaohan Li ◽

Yansu Li ◽

Longqiang Bai ◽

Tieyao Zhang ◽

Chaoxing He ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Whole Genome ◽

Genome Level

Download Full-text

Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing

PLoS ONE ◽

10.1371/journal.pone.0048792 ◽

2012 ◽

Vol 7 (11) ◽

pp. e48792 ◽

Cited By ~ 11

Author(s):

Nikki le Roex ◽

Harry Noyes ◽

Andrew Brass ◽

Daniel G. Bradley ◽

Steven J. Kemp ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

African Buffalo ◽

Snp Discovery ◽

Syncerus Caffer ◽

Novel Snp

Download Full-text

An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing

PLoS ONE ◽

10.1371/journal.pone.0022213 ◽

2011 ◽

Vol 6 (7) ◽

pp. e22213 ◽

Cited By ~ 49

Author(s):

Sarah Auburn ◽

Susana Campino ◽

Taane G. Clark ◽

Abdoulaye A. Djimde ◽

Issaka Zongo ◽

...

Keyword(s):

Plasmodium Falciparum ◽

High Throughput ◽

High Throughput Sequencing ◽

Whole Genome ◽

Blood Samples

Download Full-text

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data

F1000Research ◽

10.12688/f1000research.2-217.v2 ◽

2014 ◽

Vol 2 ◽

pp. 217 ◽

Cited By ~ 8

Author(s):

Guillermo Barturen ◽

Antonio Rueda ◽

José L. Oliver ◽

Michael Hackenberg

Keyword(s):

High Throughput ◽

Sequence Variation ◽

High Throughput Sequencing ◽

Whole Genome ◽

Single Nucleotide Variants ◽

High Quality ◽

Single Nucleotide ◽

Error Sources ◽

Link Type ◽

Genome Methylation

Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants.We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP.MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.

Download Full-text

A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X

10.1101/142356 ◽

2017 ◽

Cited By ~ 1

Author(s):

Gregory L. Owens ◽

Marco Todesco ◽

Emily B. M. Drummond ◽

Sam Yeaman ◽

Loren H. Rieseberg

Keyword(s):

Allele Frequency ◽

High Throughput ◽

High Throughput Sequencing ◽

Sequence Data ◽

Molecular Ecology ◽

Whole Genome Shotgun ◽

Whole Genome ◽

Illumina Hiseq ◽

Illumina Hiseq Platform ◽

Post Hoc

AbstractHigh throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that ‘index switching’, where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may. We leverage unbalanced heterozygotes, which may be produced by index switching, and ask whether the under-sequenced allele is more likely to be found in other samples in the same lane than expected based on the allele frequency. Although we validate the sensitivity of this method using simulations, we find that neither the HiSeq 2500 nor the HiSeq X have evidence of index switching. This suggests that, thankfully, index switching may not be a ubiquitous problem in HiSeq X sequence data. Lastly, we provide scripts for applying our method so that index switching can be tested for in other datasets.

Download Full-text

Antigenic and genetic characterization of Streptococcus pneumoniae strains isolated from patients with invasive and non-invasive pneumococcal infections by using high-throughput sequencing

Journal of microbiology epidemiology immunobiology ◽

10.36233/0372-9311-144 ◽

2021 ◽

Vol 98 (5) ◽

pp. 512-518

Author(s):

K. O. Mironov ◽

I. I. Gaponova ◽

V. I. Korchagin ◽

Yu. V. Mikhailova ◽

A. A. Shelenkov ◽

...

Keyword(s):

Data Analysis ◽

Streptococcus Pneumoniae ◽

High Throughput ◽

High Throughput Sequencing ◽

Whole Genome ◽

Pneumococcal Infections ◽

Genome Sequences ◽

Illumina Platform ◽

Genetic Characteristics ◽

Non Invasive

The objective of this study was to characterize and compare antigenic and genetic characteristics of Streptococcus pneumoniae strains isolated from patients with invasive and non-invasive pneumococcal infections (PIs) by using the data of high-throughput sequencing.Materials and methods. A total of 158 S. pneumoniae strains were studied. All of them were isolated during different stages of the PEHASus multicenter study performed in 2015-2020. The data analysis was based on the information about whole-genome sequences of 46 strains isolated during the above study. Real-time PCR methods and high-throughput sequencing (the Illumina platform) were used for identification of serotypes. The SeroBA, PneumoCaT software and PubMLST.org website resources were used in the data processing.Results and discussion. The serotypes of all the studied strains were identified. A number of discrepancies among serotypes in serogroup 6 and one discordant result were revealed by the analysis of whole-genome sequences using 2 programs. The PCR methods were effectively used to characterize serotypes in 87% and 69% of the pathogens of invasive and non-invasive PIs, respectively. The serotypes contained in PCV13 accounted for 59% and 37%, while PPV23 serotypes accounted for 78% and 53% of the strains isolated from patients with invasive and non-invasive PIs, respectively. The data analysis was unable to identify either the dominant sequence type (a total of 81 sequence types have been identified) or clonal complexes, except for serotype 3 strains, thus demonstrating consistency with the data from previous studies suggesting the absence of a well-represented clonal structure of S. pneumoniae associated with pneumococcal meningitis in Russia.Conclusion. The obtained data made it possible to identify the distribution of the circulating serotypes and genetic characteristics of the strains isolated from PI patients, thus being instrumental for assessment of the effectiveness of the existing polyvalent vaccines and providing information for improvement of the PCR-based methods of serotyping.

Download Full-text