ReadXplorer 2—detailed read mapping analysis and visualization from one single source

Hilker, Rolf; Stadermann, Kai Bernd; Schwengers, Oliver; Anisiforov, Evgeny; Jaenicke, Sebastian; Weißhaar, Bernd; Zimmermann, Tobias; Goesmann, Alexander

doi:10.1093/bioinformatics/btw541

Cited by 80 publications

(90 citation statements)

References 35 publications

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“…Reads aligned to the reference genome was converted to BAM format with samtools/1.9. The final analysis for identification and annotation of TSSs into pTSS and sTSS was done with ReadXplorer [31,67].…”

Section: Reads Mapping Of Tss Librarymentioning

confidence: 99%

“…To map dRNA-seq outputs, reads were split by replicon, converted to BAM format and sorted by position with samtools/1.9 [28]. These BAM files were used as input for ReadXplorer [31,67]…”

Section: Transcriptional Start Sites Annotation and Classificationmentioning

confidence: 99%

“…Transcriptional start sites determined in S. flexneri 5a M90T chromosome with ReadExplorer[31,67]. Transcriptional start sites determined in S. flexneri 5a M90T virulence plasmid (pWR100) with ReadExplorer[31,67].…”

mentioning

confidence: 99%

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Complete genome sequence and annotation of the laboratory reference strainShigella flexneriserotype 5a M90T and genome-wide transcriptional start site determination

Cervantes-Rivera

Tronnet

Puhar

2019

Preprint

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AbstractBackgroundShigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strain S. flexneri serotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches.ResultsWe have sequenced, assembled, annotated and manually curated the full genome of S. flexneri 5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new pipeline to prepare gapless, highly accurate genome sequences. Furthermore, we have performed genome-wide analysis of transcriptional start sites and determined the length of 5’ untranslated regions (5’-UTRs) at typical culture conditions for the inoculum of in vitro infection experiments. We identified 6,723 primary TSS (pTSS) and 7,328 secondary TSS (sTSS). The S. flexneri 5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) to use its analysis tools in S. flexneri 5a M90T genome.ConclusionsWe provide the first complete genome for S. flexneri serotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employing S. flexneri M90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation of S. flexneri 5a M90T. The hybrid pipeline that we report here combining genome sequencing with long-reads technology and polishing with RNAseq data defines a powerful strategy for genome assembly, polishing and annotation in any type of organism.

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Section: Reads Mapping Of Tss Librarymentioning

confidence: 99%

“…To map dRNA-seq outputs, reads were split by replicon, converted to BAM format and sorted by position with samtools/1.9 [28]. These BAM files were used as input for ReadXplorer [31,67]…”

Section: Transcriptional Start Sites Annotation and Classificationmentioning

confidence: 99%

See 1 more Smart Citation

Complete genome sequence and annotation of the laboratory reference strainShigella flexneriserotype 5a M90T and genome-wide transcriptional start site determination

Cervantes-Rivera

Tronnet

Puhar

2019

Preprint

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“…Lower case letters indicate the individual software tools. (a) ReadXplorer [136,152] provides tools for the visualization and analysis of read data originating from massive parallel sequencing. It is particularly useful for RNA-Seq experiments.…”

Section: Genomic Basicsmentioning

confidence: 99%

“…Such data clearly confirm that RNA-Seq has a potential to enhance genome annotation, thereby delivering a new foundation for consecutive functional experiments. ReadXplorer software [136,152] (Fig. 1, a) facilitates the visualization of mapped RNA-Seq reads [116], often an essential prerequisite to biologically construing such transcriptome data.…”

Section: Validation and Augmentation Of Genome Annotations Based On Tmentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development

Kuhl

Rückert

Gläser

et al. 2021

Biotech & Bioengineering

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Actinobacteria provide a rich spectrum of bioactive natural products and therefore display an invaluable source towards commercially valuable pharmaceuticals and agrochemicals. Here, we studied the use of inorganic talc microparticles (hydrous magnesium silicate, 3MgO•4SiO 2 •H 2 O, 10 µm) as a general supplement to enhance natural product formation in this important class of bacteria. Added to cultures of recombinant Streptomyces lividans, talc enhanced production of the macrocyclic peptide antibiotic bottromycin A2 and its methylated derivative Met-bottromycin A2 up to 109 mg L −1 , the highest titer reported so far. Hereby, the microparticles fundamentally affected metabolism. With 10 g L −1 talc, S. lividans grew to 40% smaller pellets and, using RNA sequencing, revealed accelerated morphogenesis and aging, indicated by early upregulation of developmental regulator genes such as ssgA, ssgB, wblA, sigN, and bldN. Furthermore, the microparticles re-balanced the expression of individual bottromycin cluster genes, resulting in a higher macrocyclization efficiency at the level of BotAH and correspondingly lower levels of noncyclized shunt by-products, driving the production of mature bottromycin. Testing a variety of Streptomyces species, talc addition resulted in up to 13-fold higher titers for the RiPPs bottromycin and cinnamycin, the alkaloid undecylprodigiosin, the polyketide pamamycin, the tetracycline-type oxytetracycline, and the anthramycinanalogs usabamycins. Moreover, talc addition boosted production in other actinobacteria, outside of the genus of Streptomyces: vancomycin (Amycolatopsis japonicum DSM 44213), teicoplanin (Actinoplanes teichomyceticus ATCC 31121), and the angucyclinone-type antibiotic simocyclinone (Kitasatospora sp.). For teicoplanin, the microparticles were even crucial to activate production. Taken together, the use of talc was beneficial in 75% of all tested cases and optimized natural and heterologous hosts forming the substance of interest with clusters under native and This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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ReadXplorer 2—detailed read mapping analysis and visualization from one single source

Cited by 80 publications

References 35 publications

Complete genome sequence and annotation of the laboratory reference strainShigella flexneriserotype 5a M90T and genome-wide transcriptional start site determination

Complete genome sequence and annotation of the laboratory reference strainShigella flexneriserotype 5a M90T and genome-wide transcriptional start site determination

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development

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