STAR: ultrafast universal RNA-seq aligner

Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix; Drenkow, Jörg; Zaleski, Chris; Jha, Sonali; Batut, Philippe; Chaisson, Mark; Gingeras, T

doi:10.1093/bioinformatics/bts635

Cited by 40,241 publications

(31,305 citation statements)

References 22 publications

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“…High-throughput RNA-seq data were aligned to the T. muris reference genome models (WormBase WS255; http://parasite.wormbase.org; [31]) using the STAR transcriptome aligner [32]. Prior to downstream analysis, rRNA-like sequences were removed from the metatranscriptomic dataset using riboPicker-0.4.3 (http://ribopicker.sourceforge.net; [33]).…”

Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

112

145

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Whipworms are parasitic nematodes that live in the gut of more than 500 million people worldwide. Owing to the difficulty in obtaining parasite material, the mouse whipworm Trichuris muris has been extensively used as a model to study human whipworm infections. These nematodes secrete a multitude of compounds that interact with host tissues where they orchestrate a parasitic existence. Herein we provide the first comprehensive characterization of the excretory/secretory products of T. muris. We identify 148 proteins secreted by T. muris and show for the first time that the mouse whipworm secretes exosome-like extracellular vesicles (EVs) that can interact with host cells. We use an Optiprep® gradient to purify the EVs, highlighting the suitability of this method for purifying EVs secreted by a parasitic nematode. We also characterize the proteomic and genomic content of the EVs, identifying >350 proteins, 56 miRNAs (22 novel) and 475 full-length mRNA transcripts mapping to T. muris gene models. Many of the miRNAs putatively mapped to mouse genes are involved in regulation of inflammation, implying a role in parasite-driven immunomodulation. In addition, for the first time to our knowledge, colonic organoids have been used to demonstrate the internalization of parasite EVs by host cells. Understanding how parasites interact with their host is crucial to develop new control measures. This first characterization of the proteins and EVs secreted by T. muris provides important information on whipworm–host communication and forms the basis for future studies.

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Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

112

145

View full text Add to dashboard Cite

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“…FASTQ files were mapped onto the human reference genome (hg19) using the STAR aligner (v_2.3.0e_r291) (Dobin et al , 2013). To this end, we first generated a reference genome index with , , a splice junction overhang size of 99 () and GTF annotation files containing all transcripts and all MXE candidates.…”

Section: Methodsmentioning

confidence: 99%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

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Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.

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“…The mapping has been performed with the second‐pass approach (Engström et al., 2013) of star v2.4.1 d (Dobin et al., 2013), by lowering the maximum allowed ratio of mismatches to read length to 0.11. The best practices recommendations (DePristo et al., 2011; Van Auwera et al., 2013) for gatk version 3 (McKenna et al., 2010) have been followed, but with a hybrid approach between RNA and DNA sequencing as the analyses have been performed on a reference transcriptome, not a full genome.…”

Section: Methodsmentioning

confidence: 99%

“…For analyses of DE, the filtered RNAseq reads were mapped to the Dactylorhiza reference using star v.2.4.1 b (Dobin et al., 2013) with default settings allowing for up to 20 multiple mapping reads. A unigene‐level table of counts was obtained with corset v.1.04 (Davidson & Oshlack, 2014), by filtering out any transcripts with fewer than 18 reads aligning over the nine samples.…”

Section: Methodsmentioning

confidence: 99%

“…After demultiplexing and adapter removal, we selected for each accession the reads with lengths from 20 to 22 nucleotides (hereafter “mi/tasiRNA”) and, separately, of 24 nucleotides (hereafter “siRNA”) and analysed them as two classes. Length‐selected sRNA reads were mapped to the Dactylorhiza reference transcriptome using star v 2.5.1b (Dobin et al., 2013) not allowing for any mismatch (–outFilterMismatchNmax 0) and discarding any read mapping to more than one contig (–outFilterMultimapNmax 0). These settings for mapping on the Dactylorhiza reference transcriptome were chosen to include only unambiguous signals in further analyses.…”

Section: Methodsmentioning

confidence: 99%

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Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

et al. 2017

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The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage‐specific adaptive evolution of protein‐coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post‐transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA‐dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.

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STAR: ultrafast universal RNA-seq aligner

Abstract: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.

Cited by 40,241 publications

References 22 publications

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

The landscape of human mutually exclusive splicing

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

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