fastp: an ultra-fast all-in-one FASTQ preprocessor

Chen, Shifu; Zhou, Yanqing; Chen, Yaru; Gu, Jia

doi:10.1093/bioinformatics/bty560

Cited by 14,014 publications

(10,062 citation statements)

References 13 publications

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“…was shotgun‐sequenced on the same platform by Novogene Co., Ltd. (Beijing, China) used for 150 bp paired‐end reads. Raw paired‐end reads were filtered using fastp v.0.13.2 (Chen et al , ) with the following parameters: ‐q 5 ‐u 50 ‐l 50 ‐n 15. Default values were used for the other settings.…”

Section: Methodsmentioning

confidence: 99%

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

Kusy

Motyka

Boček

et al. 2019

Systematic Entomology

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Net‐winged beetles (Coleoptera: Lycidae) are a diverse group of elateroids known for aposematism and neoteny. Phylogenetic analyses of morphological and molecular data have revealed different results with respect to within‐group relationships. In this study, we recovered a highly supported phylogenomic phylogeny and identified seven subfamilies: Dexorinae stat.n., Calochrominae stat.n., Erotinae, Ateliinae, Lycinae, Lyropaeinae stat.n. and Metriorrhynchinae stat.n. Our results suggest that female neoteny evolved multiple times. Therefore, the development of similar morphological modifications in neotenics may be linked and may have produced characteristics such as body miniaturization, structural simplification, i.e. reduction of mouthparts, fewer antennomeres and palpomeres, uniquely shaped terminal palpomeres, shortened elytra, the loss of coadaptation between the elytra and pronotum, and others. Additional traits evolved in parallel due to similarities in biology, function and sexual selection. These characteristics include mimetic similarities, the presence of the rostrum, pronotal carinae and elytral costae, and the structure of male genitalia. By comparing the phylogenomic topology with the evolution of morphological characters, we were able to identify evolutionary trends in lycids and compare them with analogues for other neotenic elateroids. These traits have not been accepted as homoplasies due to the ambiguous phylogenetic signal from Sanger sequencing markers.

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Section: Methodsmentioning

confidence: 99%

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

Kusy

Motyka

Boček

et al. 2019

Systematic Entomology

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“…Raw reads from mRNA-seq were first trimmed using fastp with default settings (v0.19.5; [129]). Remaining reads were locally aligned to the recently published long-read T. brucei Lister 427 2018 version 9.0 genome assembly (downloaded from [80]) and the Lister 427 BES sequences [82], using Bowtie2 version 2.3.4.1 [130].…”

Section: Rna-seq Analysismentioning

confidence: 99%

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

et al. 2020

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Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination in kinetoplastid protozoa. Little is understood regarding how specific thymine residues are targeted for J-modification or the mechanism of J regulated transcription termination. To identify proteins involved in J-synthesis, we expressed a tagged version of the J-glucosyltransferase (JGT) in Leishmania tarentolae, and identified four co-purified proteins by mass spectrometry: protein phosphatase (PP1), a homolog of Wdr82, a potential PP1 regulatory protein (PNUTS) and a protein containing a J-DNA binding domain (named JBP3). Gel shift studies indicate JBP3 is a J-DNA binding protein. Reciprocal tagging, co-IP and sucrose gradient analyses indicate PP1, JGT, JBP3, Wdr82 and PNUTS form a multimeric complex in kinetoplastids, similar to the mammalian PTW/PP1 complex involved in transcription termination via PP1 mediated dephosphorylation of Pol II. Using RNAi and analysis of Pol II termination by RNA-seq and RT-PCR, we demonstrate that ablation of PNUTS, JBP3 and Wdr82 lead to defects in Pol II termination at the 3'-end of polycistronic gene arrays in Trypanosoma brucei. Mutants also contain increased antisense RNA levels upstream of transcription start sites, suggesting an additional role of the complex in regulating termination of bi-directional transcription. In addition, PNUTS loss causes derepression of silent Variant Surface Glycoprotein genes involved in host immune evasion. Our results suggest a novel mechanistic link between base J and Pol II polycistronic transcription termination in kinetoplastids. Author summaryTrypanosoma brucei is a parasitic protozoan that causes African sleeping sickness in humans. The genome of T. brucei is organized into polycistronic gene clusters that contain multiple genes that are co-transcribed from a single promoter. We have recently described the presence of a modified DNA base J and variant of histone H3 (H3.V) at transcription termination sites within gene clusters where the loss of base J and H3.V leads to read-through transcription and the expression of downstream genes. We now PLOS Genetics | https://doi.identify a novel stable multimeric complex containing a J binding protein (JBP3), base J glucosyltransferase (JGT), PP1 phosphatase, PP1 interactive-regulatory protein (PNUTS) and Wdr82, which we refer to as PJW/PP1. A similar complex (PTW/PP1) has been shown to be involved in Pol II termination in humans and yeast. We demonstrate that PNUTS, JBP3 and Wdr82 mutants lead to read-through transcription in T. brucei. Our data suggest the PJW/PP1 complex regulates termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of specific proteins (including Pol II and termination factors) by PP1. These findings significantly expand our understanding of mechanisms underlying transcription termination in eukaryotes, including organisms that utilize polycistronic transcription and novel epigenetic marks...

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“…An Illumina MiSeq sequencing library was constructed and paired‐end sequenced at the West Virginia University Genomics Core Facility. Raw sequence reads were quality controlled and trimmed using fastp (Chen et al., ). A total of 18,020,464 sequence reads were queried by MSATCOMMANDER version 1.0.8 (Faircloth, ) with default settings, minimum primer size was set at 20 bp, maximum primer GC content was limited to 50%, and a PIG‐tail sequence (GTTT) (Brownstein et al., ) was added to one primer.…”

Section: Methods and Resultsmentioning

confidence: 99%

Development of 17 microsatellite markers in the federally endangered species Liatris helleri (Asteraceae)

2019

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Premise Microsatellite markers were developed in the federally endangered species Liatris helleri (Asteraceae) to evaluate species boundaries with closely related congeners within the genus. Methods and Results Using Illumina data, 17 primer pairs were developed in populations of L. helleri . The primers amplified motifs from tri‐ to hexanucleotide repeats with one to 17 alleles per locus. Primers were also tested for cross‐amplification in L. aspera , L. microcephala , and L. pycnostachya . Conclusions The developed primers for L. helleri serve as a novel genetic tool for future investigations in this genus, allowing for more explicit species delineation as well as population genetic analyses.

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fastp: an ultra-fast all-in-one FASTQ preprocessor

Cited by 14,014 publications

References 13 publications

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

Development of 17 microsatellite markers in the federally endangered species Liatris helleri (Asteraceae)

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