Comparative evaluation of full-length isoform quantification from RNA-Seq

Sarantopoulou, Dimitra; Brooks, Thomas G.; Nayak, Soumyashant; Mrčela, Antonijo; Lahens, Nicholas F.; Grant, Gregory R.

doi:10.1186/s12859-021-04198-1

Cited by 32 publications

(46 citation statements)

References 43 publications

(119 reference statements)

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“…Standard parameters (-b 100) were employed for PE mapping. As recently reported in an exhaustive benchmark evaluation [ 44 ], Kallisto is effective for large datasets, such as the one reported herein. In addition, since this software is accurate and fast during the mapping and quantification procedure, it will be useful for keeping BEB up-to-date as more RNA-Seq datasets become available in the future.…”

Section: Methodsmentioning

confidence: 71%

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The Botrytis cinerea Gene Expression Browser

Pérez-Lara

Moyano

Vega

et al. 2023

JoF

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For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.

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Section: Methodsmentioning

confidence: 71%

“…As more RNA-Seq datasets become available, this table (and associated metadata file) will be expanded in , as detailed herein and in the online information. We will rely on Kallisto software for accurate mapping and rapid quantification of RNA-Seq data, as described previously [ 44 ].…”

Section: Resultsmentioning

confidence: 99%

The Botrytis cinerea Gene Expression Browser

Pérez-Lara

Moyano

Vega

et al. 2023

JoF

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“…Salmon quantifies expression at the transcript level using an RNA-Seq pseudo-alignment approach. Our previous benchmarking study found that Salmon was a top transcript-level quantifier 20 , which is the motivation to evaluate its performance further.…”

Section: Resultsmentioning

confidence: 99%

BEERS2: RNA-Seq simulation through high fidelityin silicomodeling

Brooks

Lahens

Mrčela

et al. 2023

Preprint

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Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

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“…More specifically, we considered several available RNA‐Seq data from wheat plants that were either infected with major fungal pathogens, artificially treated with chitin and flagellin 22, or stressed with cold temperatures (Table S2). Because of the high accuracy of expression estimates for gene duplicates and isoforms (Sarantopoulou et al, 2021; Soneson et al, 2015), Salmon (Patro et al, 2017) was used for estimating the expression of wheat coding sequences (IWGSC RefSeq v1.0). It was run in mapping‐based mode with standard parameters and the estimated number of mapped reads (NumReads) were used for differential expression analysis as previously described by Praz et al (2018).…”

Section: Methodsmentioning

confidence: 99%

A survey of lineage‐specific genes in Triticeae reveals de novo gene evolution from genomic raw material

et al. 2023

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Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage‐specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage‐specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae‐specific genes (TSGs), of which 2337 were validated as protein‐coding genes in wheat. Differential gene expression analyses revealed that stress‐induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non‐host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non‐coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage‐specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non‐coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.

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Comparative evaluation of full-length isoform quantification from RNA-Seq

Cited by 32 publications

References 43 publications

The Botrytis cinerea Gene Expression Browser

The Botrytis cinerea Gene Expression Browser

BEERS2: RNA-Seq simulation through high fidelityin silicomodeling

A survey of lineage‐specific genes in Triticeae reveals de novo gene evolution from genomic raw material

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